Starting phenix.real_space_refine on Sat Mar 23 04:51:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mh1_23833/03_2024/7mh1_23833_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mh1_23833/03_2024/7mh1_23833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mh1_23833/03_2024/7mh1_23833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mh1_23833/03_2024/7mh1_23833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mh1_23833/03_2024/7mh1_23833_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mh1_23833/03_2024/7mh1_23833_trim_updated.pdb" } resolution = 2.8 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= 0.212 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 24 5.49 5 Mg 8 5.21 5 S 92 5.16 5 C 11308 2.51 5 N 3072 2.21 5 O 3332 1.98 5 H 17800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H ASP 246": "OD1" <-> "OD2" Residue "H GLU 259": "OE1" <-> "OE2" Residue "H GLU 268": "OE1" <-> "OE2" Residue "H PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 290": "OD1" <-> "OD2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 347": "OE1" <-> "OE2" Residue "H GLU 349": "OE1" <-> "OE2" Residue "H ASP 420": "OD1" <-> "OD2" Residue "H PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 435": "OD1" <-> "OD2" Residue "H GLU 460": "OE1" <-> "OE2" Residue "H PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 493": "OE1" <-> "OE2" Residue "H PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 503": "OD1" <-> "OD2" Residue "H ASP 505": "OD1" <-> "OD2" Residue "H ASP 507": "OD1" <-> "OD2" Residue "H GLU 510": "OE1" <-> "OE2" Residue "H GLU 513": "OE1" <-> "OE2" Residue "H PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 46": "OD1" <-> "OD2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J ASP 70": "OD1" <-> "OD2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 85": "OD1" <-> "OD2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J GLU 191": "OE1" <-> "OE2" Residue "J GLU 228": "OE1" <-> "OE2" Residue "J ASP 246": "OD1" <-> "OD2" Residue "J GLU 259": "OE1" <-> "OE2" Residue "J GLU 268": "OE1" <-> "OE2" Residue "J PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 290": "OD1" <-> "OD2" Residue "J GLU 293": "OE1" <-> "OE2" Residue "J GLU 347": "OE1" <-> "OE2" Residue "J GLU 349": "OE1" <-> "OE2" Residue "J ASP 420": "OD1" <-> "OD2" Residue "J PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 435": "OD1" <-> "OD2" Residue "J GLU 460": "OE1" <-> "OE2" Residue "J PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 493": "OE1" <-> "OE2" Residue "J PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 503": "OD1" <-> "OD2" Residue "J ASP 505": "OD1" <-> "OD2" Residue "J ASP 507": "OD1" <-> "OD2" Residue "J GLU 510": "OE1" <-> "OE2" Residue "J GLU 513": "OE1" <-> "OE2" Residue "J PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 46": "OD1" <-> "OD2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K ASP 70": "OD1" <-> "OD2" Residue "K PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 85": "OD1" <-> "OD2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 101": "OE1" <-> "OE2" Residue "K ASP 134": "OD1" <-> "OD2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K GLU 191": "OE1" <-> "OE2" Residue "K GLU 228": "OE1" <-> "OE2" Residue "K ASP 246": "OD1" <-> "OD2" Residue "K GLU 259": "OE1" <-> "OE2" Residue "K GLU 268": "OE1" <-> "OE2" Residue "K PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 290": "OD1" <-> "OD2" Residue "K GLU 293": "OE1" <-> "OE2" Residue "K GLU 347": "OE1" <-> "OE2" Residue "K GLU 349": "OE1" <-> "OE2" Residue "K ASP 420": "OD1" <-> "OD2" Residue "K PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 435": "OD1" <-> "OD2" Residue "K GLU 460": "OE1" <-> "OE2" Residue "K PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 493": "OE1" <-> "OE2" Residue "K PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 503": "OD1" <-> "OD2" Residue "K ASP 505": "OD1" <-> "OD2" Residue "K ASP 507": "OD1" <-> "OD2" Residue "K GLU 510": "OE1" <-> "OE2" Residue "K GLU 513": "OE1" <-> "OE2" Residue "K PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 46": "OD1" <-> "OD2" Residue "L GLU 66": "OE1" <-> "OE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L GLU 173": "OE1" <-> "OE2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "L GLU 228": "OE1" <-> "OE2" Residue "L ASP 246": "OD1" <-> "OD2" Residue "L GLU 259": "OE1" <-> "OE2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 290": "OD1" <-> "OD2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L GLU 347": "OE1" <-> "OE2" Residue "L GLU 349": "OE1" <-> "OE2" Residue "L ASP 420": "OD1" <-> "OD2" Residue "L PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 435": "OD1" <-> "OD2" Residue "L GLU 460": "OE1" <-> "OE2" Residue "L PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 493": "OE1" <-> "OE2" Residue "L PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 503": "OD1" <-> "OD2" Residue "L ASP 505": "OD1" <-> "OD2" Residue "L ASP 507": "OD1" <-> "OD2" Residue "L GLU 510": "OE1" <-> "OE2" Residue "L GLU 513": "OE1" <-> "OE2" Residue "L PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 554": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 35636 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 8849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8849 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "J" Number of atoms: 8849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8849 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "K" Number of atoms: 8849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8849 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "L" Number of atoms: 8849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8849 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU H 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU H 155 " occ=0.75 residue: pdb=" N CYS H 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS H 243 " occ=0.75 residue: pdb=" N GLU J 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU J 155 " occ=0.75 residue: pdb=" N CYS J 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS J 243 " occ=0.75 residue: pdb=" N GLU K 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU K 155 " occ=0.75 residue: pdb=" N CYS K 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS K 243 " occ=0.75 residue: pdb=" N GLU L 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU L 155 " occ=0.75 residue: pdb=" N CYS L 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS L 243 " occ=0.75 Time building chain proxies: 14.42, per 1000 atoms: 0.40 Number of scatterers: 35636 At special positions: 0 Unit cell: (122.85, 141.75, 91.35, 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 92 16.00 P 24 15.00 Mg 8 11.99 O 3332 8.00 N 3072 7.00 C 11308 6.00 H 17800 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.08 Conformation dependent library (CDL) restraints added in 3.5 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 16 sheets defined 38.8% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.59 Creating SS restraints... Processing helix chain 'H' and resid 16 through 29 Processing helix chain 'H' and resid 69 through 77 removed outlier: 3.573A pdb=" N TYR H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 90 through 103 Processing helix chain 'H' and resid 113 through 129 removed outlier: 7.164A pdb=" N THR H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 169 removed outlier: 4.628A pdb=" N PHE H 168 " --> pdb=" O ARG H 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS H 169 " --> pdb=" O GLN H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 207 Processing helix chain 'H' and resid 224 through 234 Processing helix chain 'H' and resid 238 through 240 No H-bonds generated for 'chain 'H' and resid 238 through 240' Processing helix chain 'H' and resid 250 through 259 Proline residue: H 254 - end of helix removed outlier: 3.585A pdb=" N GLU H 258 " --> pdb=" O VAL H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 269 Processing helix chain 'H' and resid 281 through 294 removed outlier: 3.511A pdb=" N ASN H 287 " --> pdb=" O LYS H 284 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA H 289 " --> pdb=" O ARG H 286 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU H 293 " --> pdb=" O ASP H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 339 through 342 Processing helix chain 'H' and resid 346 through 348 No H-bonds generated for 'chain 'H' and resid 346 through 348' Processing helix chain 'H' and resid 351 through 362 Processing helix chain 'H' and resid 378 through 390 Processing helix chain 'H' and resid 399 through 413 removed outlier: 4.117A pdb=" N LEU H 404 " --> pdb=" O GLY H 401 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU H 408 " --> pdb=" O ALA H 405 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN H 412 " --> pdb=" O PHE H 409 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS H 413 " --> pdb=" O ALA H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 467 Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 538 through 548 Processing helix chain 'H' and resid 551 through 556 removed outlier: 4.485A pdb=" N GLN H 556 " --> pdb=" O ASN H 552 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 Processing helix chain 'J' and resid 69 through 77 removed outlier: 3.574A pdb=" N TYR J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'J' and resid 90 through 103 Processing helix chain 'J' and resid 113 through 129 removed outlier: 7.164A pdb=" N THR J 118 " --> pdb=" O VAL J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 169 removed outlier: 4.628A pdb=" N PHE J 168 " --> pdb=" O ARG J 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS J 169 " --> pdb=" O GLN J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 207 Processing helix chain 'J' and resid 224 through 234 Processing helix chain 'J' and resid 238 through 240 No H-bonds generated for 'chain 'J' and resid 238 through 240' Processing helix chain 'J' and resid 250 through 259 Proline residue: J 254 - end of helix removed outlier: 3.584A pdb=" N GLU J 258 " --> pdb=" O VAL J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 269 Processing helix chain 'J' and resid 281 through 294 removed outlier: 3.511A pdb=" N ASN J 287 " --> pdb=" O LYS J 284 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 289 " --> pdb=" O ARG J 286 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU J 293 " --> pdb=" O ASP J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 327 Processing helix chain 'J' and resid 339 through 342 Processing helix chain 'J' and resid 346 through 348 No H-bonds generated for 'chain 'J' and resid 346 through 348' Processing helix chain 'J' and resid 351 through 362 Processing helix chain 'J' and resid 378 through 390 Processing helix chain 'J' and resid 399 through 413 removed outlier: 4.118A pdb=" N LEU J 404 " --> pdb=" O GLY J 401 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU J 408 " --> pdb=" O ALA J 405 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN J 412 " --> pdb=" O PHE J 409 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS J 413 " --> pdb=" O ALA J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 463 through 467 Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 538 through 548 Processing helix chain 'J' and resid 551 through 556 removed outlier: 4.485A pdb=" N GLN J 556 " --> pdb=" O ASN J 552 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 29 Processing helix chain 'K' and resid 69 through 77 removed outlier: 3.573A pdb=" N TYR K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing helix chain 'K' and resid 90 through 103 Processing helix chain 'K' and resid 113 through 129 removed outlier: 7.164A pdb=" N THR K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 169 removed outlier: 4.628A pdb=" N PHE K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS K 169 " --> pdb=" O GLN K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 207 Processing helix chain 'K' and resid 224 through 234 Processing helix chain 'K' and resid 238 through 240 No H-bonds generated for 'chain 'K' and resid 238 through 240' Processing helix chain 'K' and resid 250 through 259 Proline residue: K 254 - end of helix removed outlier: 3.584A pdb=" N GLU K 258 " --> pdb=" O VAL K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 269 Processing helix chain 'K' and resid 281 through 294 removed outlier: 3.511A pdb=" N ASN K 287 " --> pdb=" O LYS K 284 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA K 289 " --> pdb=" O ARG K 286 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU K 293 " --> pdb=" O ASP K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 327 Processing helix chain 'K' and resid 339 through 342 Processing helix chain 'K' and resid 346 through 348 No H-bonds generated for 'chain 'K' and resid 346 through 348' Processing helix chain 'K' and resid 351 through 362 Processing helix chain 'K' and resid 378 through 390 Processing helix chain 'K' and resid 399 through 413 removed outlier: 4.117A pdb=" N LEU K 404 " --> pdb=" O GLY K 401 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU K 408 " --> pdb=" O ALA K 405 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN K 412 " --> pdb=" O PHE K 409 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS K 413 " --> pdb=" O ALA K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 467 Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 538 through 548 Processing helix chain 'K' and resid 551 through 556 removed outlier: 4.486A pdb=" N GLN K 556 " --> pdb=" O ASN K 552 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 29 Processing helix chain 'L' and resid 69 through 77 removed outlier: 3.574A pdb=" N TYR L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 86 No H-bonds generated for 'chain 'L' and resid 84 through 86' Processing helix chain 'L' and resid 90 through 103 Processing helix chain 'L' and resid 113 through 129 removed outlier: 7.164A pdb=" N THR L 118 " --> pdb=" O VAL L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 169 removed outlier: 4.628A pdb=" N PHE L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS L 169 " --> pdb=" O GLN L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 224 through 234 Processing helix chain 'L' and resid 238 through 240 No H-bonds generated for 'chain 'L' and resid 238 through 240' Processing helix chain 'L' and resid 250 through 259 Proline residue: L 254 - end of helix removed outlier: 3.584A pdb=" N GLU L 258 " --> pdb=" O VAL L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 269 Processing helix chain 'L' and resid 281 through 294 removed outlier: 3.510A pdb=" N ASN L 287 " --> pdb=" O LYS L 284 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA L 289 " --> pdb=" O ARG L 286 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU L 293 " --> pdb=" O ASP L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 327 Processing helix chain 'L' and resid 339 through 342 Processing helix chain 'L' and resid 346 through 348 No H-bonds generated for 'chain 'L' and resid 346 through 348' Processing helix chain 'L' and resid 351 through 362 Processing helix chain 'L' and resid 378 through 390 Processing helix chain 'L' and resid 399 through 413 removed outlier: 4.117A pdb=" N LEU L 404 " --> pdb=" O GLY L 401 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU L 408 " --> pdb=" O ALA L 405 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN L 412 " --> pdb=" O PHE L 409 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS L 413 " --> pdb=" O ALA L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 467 Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 538 through 548 Processing helix chain 'L' and resid 551 through 556 removed outlier: 4.486A pdb=" N GLN L 556 " --> pdb=" O ASN L 552 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 241 through 245 removed outlier: 6.293A pdb=" N ILE H 214 " --> pdb=" O ILE H 242 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE H 244 " --> pdb=" O ILE H 214 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS H 216 " --> pdb=" O ILE H 244 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR H 3 " --> pdb=" O CYS H 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE H 178 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU H 5 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL H 180 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR H 7 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU H 182 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY H 8 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 58 through 60 Processing sheet with id= C, first strand: chain 'H' and resid 331 through 338 removed outlier: 6.868A pdb=" N GLY H 366 " --> pdb=" O ALA H 302 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL H 304 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU H 368 " --> pdb=" O VAL H 304 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL H 369 " --> pdb=" O PRO H 394 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU H 396 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE H 520 " --> pdb=" O LEU H 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU H 513 " --> pdb=" O PHE H 499 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE H 499 " --> pdb=" O GLU H 513 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 433 through 435 Processing sheet with id= E, first strand: chain 'J' and resid 241 through 245 removed outlier: 6.293A pdb=" N ILE J 214 " --> pdb=" O ILE J 242 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE J 244 " --> pdb=" O ILE J 214 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS J 216 " --> pdb=" O ILE J 244 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR J 3 " --> pdb=" O CYS J 176 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE J 178 " --> pdb=" O TYR J 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU J 5 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL J 180 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR J 7 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LEU J 182 " --> pdb=" O THR J 7 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY J 8 " --> pdb=" O LEU J 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 58 through 60 Processing sheet with id= G, first strand: chain 'J' and resid 331 through 338 removed outlier: 6.868A pdb=" N GLY J 366 " --> pdb=" O ALA J 302 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL J 304 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU J 368 " --> pdb=" O VAL J 304 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL J 369 " --> pdb=" O PRO J 394 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU J 396 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE J 520 " --> pdb=" O LEU J 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU J 513 " --> pdb=" O PHE J 499 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE J 499 " --> pdb=" O GLU J 513 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 433 through 435 Processing sheet with id= I, first strand: chain 'K' and resid 241 through 245 removed outlier: 6.293A pdb=" N ILE K 214 " --> pdb=" O ILE K 242 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE K 244 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS K 216 " --> pdb=" O ILE K 244 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR K 3 " --> pdb=" O CYS K 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE K 178 " --> pdb=" O TYR K 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU K 5 " --> pdb=" O ILE K 178 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL K 180 " --> pdb=" O LEU K 5 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR K 7 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LEU K 182 " --> pdb=" O THR K 7 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY K 8 " --> pdb=" O LEU K 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 58 through 60 Processing sheet with id= K, first strand: chain 'K' and resid 331 through 338 removed outlier: 6.868A pdb=" N GLY K 366 " --> pdb=" O ALA K 302 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL K 304 " --> pdb=" O GLY K 366 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU K 368 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL K 369 " --> pdb=" O PRO K 394 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU K 396 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE K 520 " --> pdb=" O LEU K 514 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU K 513 " --> pdb=" O PHE K 499 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE K 499 " --> pdb=" O GLU K 513 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 433 through 435 Processing sheet with id= M, first strand: chain 'L' and resid 241 through 245 removed outlier: 6.294A pdb=" N ILE L 214 " --> pdb=" O ILE L 242 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE L 244 " --> pdb=" O ILE L 214 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS L 216 " --> pdb=" O ILE L 244 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR L 3 " --> pdb=" O CYS L 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE L 178 " --> pdb=" O TYR L 3 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 5 " --> pdb=" O ILE L 178 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL L 180 " --> pdb=" O LEU L 5 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR L 7 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU L 182 " --> pdb=" O THR L 7 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY L 8 " --> pdb=" O LEU L 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 58 through 60 Processing sheet with id= O, first strand: chain 'L' and resid 331 through 338 removed outlier: 6.868A pdb=" N GLY L 366 " --> pdb=" O ALA L 302 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL L 304 " --> pdb=" O GLY L 366 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU L 368 " --> pdb=" O VAL L 304 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL L 369 " --> pdb=" O PRO L 394 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU L 396 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE L 520 " --> pdb=" O LEU L 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU L 513 " --> pdb=" O PHE L 499 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE L 499 " --> pdb=" O GLU L 513 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 433 through 435 664 hydrogen bonds defined for protein. 1692 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: 13.16 Time building geometry restraints manager: 30.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 1731 1.01 - 1.21: 16033 1.21 - 1.41: 7498 1.41 - 1.61: 10602 1.61 - 1.81: 144 Bond restraints: 36008 Sorted by residual: bond pdb=" N VAL K 97 " pdb=" H VAL K 97 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N ASN J 412 " pdb=" H ASN J 412 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N TYR K 106 " pdb=" H TYR K 106 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" NE ARG K 508 " pdb=" HE ARG K 508 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" CD2 HIS J 96 " pdb=" HD2 HIS J 96 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 ... (remaining 36003 not shown) Histogram of bond angle deviations from ideal: 95.76 - 103.54: 256 103.54 - 111.33: 37233 111.33 - 119.11: 14379 119.11 - 126.89: 13086 126.89 - 134.67: 318 Bond angle restraints: 65272 Sorted by residual: angle pdb=" N PRO K 538 " pdb=" CA PRO K 538 " pdb=" C PRO K 538 " ideal model delta sigma weight residual 110.70 118.62 -7.92 1.22e+00 6.72e-01 4.21e+01 angle pdb=" N PRO H 538 " pdb=" CA PRO H 538 " pdb=" C PRO H 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" N PRO J 538 " pdb=" CA PRO J 538 " pdb=" C PRO J 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" N PRO L 538 " pdb=" CA PRO L 538 " pdb=" C PRO L 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" CA ASN K 443 " pdb=" CB ASN K 443 " pdb=" CG ASN K 443 " ideal model delta sigma weight residual 112.60 119.02 -6.42 1.00e+00 1.00e+00 4.12e+01 ... (remaining 65267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 16052 35.09 - 70.19: 724 70.19 - 105.28: 46 105.28 - 140.37: 8 140.37 - 175.46: 10 Dihedral angle restraints: 16840 sinusoidal: 9388 harmonic: 7452 Sorted by residual: dihedral pdb=" O1G CTP J 604 " pdb=" O3B CTP J 604 " pdb=" PG CTP J 604 " pdb=" PB CTP J 604 " ideal model delta sinusoidal sigma weight residual 82.72 -101.82 -175.46 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1G CTP K 603 " pdb=" O3B CTP K 603 " pdb=" PG CTP K 603 " pdb=" PB CTP K 603 " ideal model delta sinusoidal sigma weight residual 82.72 -101.87 -175.41 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3A CTP K 601 " pdb=" O3B CTP K 601 " pdb=" PB CTP K 601 " pdb=" PG CTP K 601 " ideal model delta sinusoidal sigma weight residual 204.50 46.10 158.40 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 16837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1568 0.080 - 0.161: 756 0.161 - 0.241: 348 0.241 - 0.321: 60 0.321 - 0.402: 16 Chirality restraints: 2748 Sorted by residual: chirality pdb=" CA PRO K 538 " pdb=" N PRO K 538 " pdb=" C PRO K 538 " pdb=" CB PRO K 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA PRO H 538 " pdb=" N PRO H 538 " pdb=" C PRO H 538 " pdb=" CB PRO H 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA PRO J 538 " pdb=" N PRO J 538 " pdb=" C PRO J 538 " pdb=" CB PRO J 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 2745 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 269 " 0.523 9.50e-02 1.11e+02 1.90e-01 1.57e+02 pdb=" NE ARG J 269 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG J 269 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG J 269 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG J 269 " -0.109 2.00e-02 2.50e+03 pdb="HH11 ARG J 269 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG J 269 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG J 269 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG J 269 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 269 " -0.523 9.50e-02 1.11e+02 1.90e-01 1.57e+02 pdb=" NE ARG L 269 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG L 269 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG L 269 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG L 269 " 0.109 2.00e-02 2.50e+03 pdb="HH11 ARG L 269 " -0.010 2.00e-02 2.50e+03 pdb="HH12 ARG L 269 " 0.050 2.00e-02 2.50e+03 pdb="HH21 ARG L 269 " 0.044 2.00e-02 2.50e+03 pdb="HH22 ARG L 269 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 269 " 0.522 9.50e-02 1.11e+02 1.90e-01 1.56e+02 pdb=" NE ARG H 269 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG H 269 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG H 269 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG H 269 " -0.109 2.00e-02 2.50e+03 pdb="HH11 ARG H 269 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG H 269 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG H 269 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG H 269 " 0.173 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 1207 2.06 - 2.70: 49538 2.70 - 3.33: 111428 3.33 - 3.97: 147957 3.97 - 4.60: 217852 Nonbonded interactions: 527982 Sorted by model distance: nonbonded pdb="HD21 ASN K 44 " pdb=" HE1 PHE K 50 " model vdw 1.426 2.100 nonbonded pdb="HD21 ASN J 44 " pdb=" HE1 PHE J 50 " model vdw 1.427 2.100 nonbonded pdb="HD21 ASN H 44 " pdb=" HE1 PHE H 50 " model vdw 1.427 2.100 nonbonded pdb="HD21 ASN L 44 " pdb=" HE1 PHE L 50 " model vdw 1.427 2.100 nonbonded pdb=" HG1 THR H 49 " pdb=" OE2 GLU K 101 " model vdw 1.579 1.850 ... (remaining 527977 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 'H' and resid 1 through 557) selection = (chain 'J' and resid 1 through 557) selection = (chain 'K' and resid 1 through 557) selection = (chain 'L' and resid 1 through 557) } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.480 Extract box with map and model: 7.210 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 107.010 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.120 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:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.053 18208 Z= 0.799 Angle : 2.030 12.894 24688 Z= 1.339 Chirality : 0.110 0.402 2748 Planarity : 0.016 0.155 3172 Dihedral : 16.816 175.465 6884 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.44 % Allowed : 7.22 % Favored : 91.34 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2220 helix: -0.97 (0.15), residues: 880 sheet: -0.74 (0.24), residues: 372 loop : -0.34 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.023 TRP K 285 HIS 0.011 0.004 HIS L 235 PHE 0.085 0.013 PHE K 163 TYR 0.135 0.021 TYR L 307 ARG 0.011 0.002 ARG K 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 465 time to evaluate : 2.690 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: H 68 ASP cc_start: 0.6846 (t0) cc_final: 0.6467 (t0) REVERT: H 75 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7723 (mt-10) REVERT: H 78 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8150 (mp) REVERT: H 123 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6704 (mt-10) REVERT: H 134 ASP cc_start: 0.7293 (t0) cc_final: 0.7092 (t70) REVERT: H 172 ARG cc_start: 0.7537 (tpt170) cc_final: 0.7293 (tpt90) REVERT: H 224 MET cc_start: 0.6998 (tpt) cc_final: 0.6680 (tpp) REVERT: H 322 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6995 (mt-10) REVERT: H 402 MET cc_start: 0.8501 (tmt) cc_final: 0.7810 (tmt) REVERT: H 513 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6404 (tm-30) REVERT: H 514 LEU cc_start: 0.7909 (tp) cc_final: 0.7348 (tp) REVERT: J 68 ASP cc_start: 0.6847 (t0) cc_final: 0.6438 (t0) REVERT: J 78 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8156 (mp) REVERT: J 123 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6764 (mt-10) REVERT: J 224 MET cc_start: 0.6945 (tpt) cc_final: 0.6654 (tpp) REVERT: J 322 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6982 (mt-10) REVERT: J 402 MET cc_start: 0.8497 (tmt) cc_final: 0.7844 (tmt) REVERT: J 507 ASP cc_start: 0.6878 (m-30) cc_final: 0.6617 (m-30) REVERT: J 513 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6338 (tt0) REVERT: K 68 ASP cc_start: 0.6827 (t0) cc_final: 0.6447 (t0) REVERT: K 75 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7685 (mt-10) REVERT: K 78 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8143 (mp) REVERT: K 123 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6773 (mt-10) REVERT: K 134 ASP cc_start: 0.7361 (t0) cc_final: 0.7128 (t70) REVERT: K 224 MET cc_start: 0.6975 (tpt) cc_final: 0.6648 (tpp) REVERT: K 322 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7041 (mt-10) REVERT: K 402 MET cc_start: 0.8510 (tmt) cc_final: 0.7857 (tmt) REVERT: K 408 GLU cc_start: 0.7468 (pp20) cc_final: 0.7177 (pp20) REVERT: K 513 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6412 (tm-30) REVERT: K 514 LEU cc_start: 0.7903 (tp) cc_final: 0.7367 (tp) REVERT: L 68 ASP cc_start: 0.6825 (t0) cc_final: 0.6454 (t0) REVERT: L 75 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7671 (mt-10) REVERT: L 78 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8139 (mp) REVERT: L 123 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6785 (mt-10) REVERT: L 224 MET cc_start: 0.6965 (tpt) cc_final: 0.6653 (tpp) REVERT: L 322 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7074 (mt-10) REVERT: L 408 GLU cc_start: 0.7476 (pp20) cc_final: 0.7273 (pp20) REVERT: L 476 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7087 (mm-30) REVERT: L 509 MET cc_start: 0.6612 (mmt) cc_final: 0.6408 (mmm) REVERT: L 513 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6402 (tm-30) REVERT: L 514 LEU cc_start: 0.7923 (tp) cc_final: 0.7382 (tp) outliers start: 28 outliers final: 4 residues processed: 485 average time/residue: 2.4097 time to fit residues: 1340.2668 Evaluate side-chains 369 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 361 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 ASN H 165 GLN H 185 GLN H 287 ASN H 440 ASN H 443 ASN J 86 ASN J 165 GLN J 185 GLN J 287 ASN J 440 ASN J 443 ASN K 86 ASN K 165 GLN K 287 ASN K 440 ASN K 443 ASN L 86 ASN L 165 GLN L 185 GLN L 440 ASN L 443 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18208 Z= 0.220 Angle : 0.677 6.904 24688 Z= 0.338 Chirality : 0.046 0.143 2748 Planarity : 0.005 0.058 3172 Dihedral : 14.047 178.469 2532 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.35 % Allowed : 13.81 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2220 helix: 0.13 (0.17), residues: 900 sheet: -0.25 (0.25), residues: 392 loop : -0.09 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 358 HIS 0.006 0.001 HIS H 96 PHE 0.020 0.002 PHE J 424 TYR 0.011 0.002 TYR H 265 ARG 0.007 0.001 ARG H 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 398 time to evaluate : 2.828 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: H 28 LYS cc_start: 0.7749 (tptp) cc_final: 0.7548 (tttp) REVERT: H 49 THR cc_start: 0.8841 (m) cc_final: 0.8490 (p) REVERT: H 123 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6791 (mt-10) REVERT: H 157 MET cc_start: 0.8158 (mmt) cc_final: 0.7874 (mmt) REVERT: H 224 MET cc_start: 0.6980 (tpt) cc_final: 0.6715 (tpp) REVERT: H 228 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6995 (mt-10) REVERT: H 286 ARG cc_start: 0.6903 (ttt90) cc_final: 0.6678 (ttp-110) REVERT: H 402 MET cc_start: 0.8456 (tmt) cc_final: 0.7520 (tmt) REVERT: H 500 VAL cc_start: 0.9026 (m) cc_final: 0.8640 (p) REVERT: H 513 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6423 (tt0) REVERT: H 543 LEU cc_start: 0.8224 (tm) cc_final: 0.7935 (tt) REVERT: J 49 THR cc_start: 0.8881 (m) cc_final: 0.8543 (p) REVERT: J 78 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7553 (mp) REVERT: J 172 ARG cc_start: 0.7721 (tpt90) cc_final: 0.7313 (tpt170) REVERT: J 224 MET cc_start: 0.6909 (tpt) cc_final: 0.6659 (tpp) REVERT: J 228 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: J 252 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7830 (ttm-80) REVERT: J 402 MET cc_start: 0.8450 (tmt) cc_final: 0.7623 (tmt) REVERT: J 500 VAL cc_start: 0.9034 (m) cc_final: 0.8636 (p) REVERT: J 513 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6503 (tt0) REVERT: J 543 LEU cc_start: 0.8238 (tm) cc_final: 0.7936 (tt) REVERT: K 49 THR cc_start: 0.8870 (m) cc_final: 0.8549 (p) REVERT: K 78 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7537 (mp) REVERT: K 123 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6879 (mt-10) REVERT: K 157 MET cc_start: 0.8171 (mmt) cc_final: 0.7872 (mmt) REVERT: K 224 MET cc_start: 0.6964 (tpt) cc_final: 0.6470 (tpp) REVERT: K 228 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7009 (mm-30) REVERT: K 252 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7816 (ttm-80) REVERT: K 284 LYS cc_start: 0.7412 (mtpp) cc_final: 0.7194 (ttmm) REVERT: K 329 ASN cc_start: 0.6953 (OUTLIER) cc_final: 0.6613 (t0) REVERT: K 402 MET cc_start: 0.8443 (tmt) cc_final: 0.7566 (tmt) REVERT: K 500 VAL cc_start: 0.9042 (m) cc_final: 0.8628 (p) REVERT: K 513 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6474 (tt0) REVERT: K 543 LEU cc_start: 0.8234 (tm) cc_final: 0.7935 (tt) REVERT: L 49 THR cc_start: 0.8869 (m) cc_final: 0.8520 (p) REVERT: L 54 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6629 (mt-10) REVERT: L 123 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6851 (mt-10) REVERT: L 146 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: L 224 MET cc_start: 0.6966 (tpt) cc_final: 0.6724 (tpp) REVERT: L 228 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: L 284 LYS cc_start: 0.7442 (mtpp) cc_final: 0.7192 (ttmm) REVERT: L 329 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6607 (t0) REVERT: L 402 MET cc_start: 0.8433 (tmt) cc_final: 0.7561 (tmt) REVERT: L 509 MET cc_start: 0.6619 (mmt) cc_final: 0.6372 (mmm) REVERT: L 513 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6481 (tt0) REVERT: L 543 LEU cc_start: 0.8233 (tm) cc_final: 0.7950 (tt) outliers start: 65 outliers final: 11 residues processed: 433 average time/residue: 2.4568 time to fit residues: 1211.3252 Evaluate side-chains 375 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 355 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 240 GLN Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 329 ASN Chi-restraints excluded: chain L residue 424 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN H 323 HIS J 287 ASN J 323 HIS K 287 ASN K 323 HIS K 333 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18208 Z= 0.311 Angle : 0.661 7.248 24688 Z= 0.330 Chirality : 0.047 0.149 2748 Planarity : 0.005 0.051 3172 Dihedral : 12.801 172.236 2528 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.04 % Allowed : 16.39 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2220 helix: 0.40 (0.17), residues: 900 sheet: -0.25 (0.24), residues: 392 loop : 0.09 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 358 HIS 0.006 0.001 HIS H 116 PHE 0.014 0.001 PHE L 163 TYR 0.013 0.002 TYR H 42 ARG 0.010 0.001 ARG J 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 367 time to evaluate : 2.562 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: H 49 THR cc_start: 0.9024 (m) cc_final: 0.8703 (p) REVERT: H 109 LYS cc_start: 0.8565 (mttm) cc_final: 0.8318 (mttm) REVERT: H 224 MET cc_start: 0.6990 (tpt) cc_final: 0.6713 (tpp) REVERT: H 228 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: H 286 ARG cc_start: 0.7049 (ttt90) cc_final: 0.6716 (ttp-110) REVERT: H 402 MET cc_start: 0.8389 (tmt) cc_final: 0.7574 (tmt) REVERT: H 500 VAL cc_start: 0.9048 (m) cc_final: 0.8677 (p) REVERT: H 513 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6611 (tt0) REVERT: H 543 LEU cc_start: 0.8166 (tm) cc_final: 0.7875 (tt) REVERT: J 49 THR cc_start: 0.9028 (m) cc_final: 0.8709 (p) REVERT: J 78 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7400 (mp) REVERT: J 224 MET cc_start: 0.6934 (tpt) cc_final: 0.6645 (tpp) REVERT: J 228 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: J 252 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.8034 (ttm-80) REVERT: J 402 MET cc_start: 0.8382 (tmt) cc_final: 0.7606 (tmt) REVERT: J 500 VAL cc_start: 0.9031 (m) cc_final: 0.8638 (p) REVERT: J 513 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6594 (tt0) REVERT: J 543 LEU cc_start: 0.8184 (tm) cc_final: 0.7866 (tt) REVERT: K 49 THR cc_start: 0.9029 (m) cc_final: 0.8713 (p) REVERT: K 78 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7435 (mp) REVERT: K 123 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6993 (mt-10) REVERT: K 224 MET cc_start: 0.6973 (tpt) cc_final: 0.6552 (tpp) REVERT: K 252 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8168 (ttm-80) REVERT: K 402 MET cc_start: 0.8393 (tmt) cc_final: 0.7547 (tmt) REVERT: K 481 ARG cc_start: 0.6957 (mtp85) cc_final: 0.6681 (mtp85) REVERT: K 500 VAL cc_start: 0.9039 (m) cc_final: 0.8638 (p) REVERT: K 513 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6634 (tt0) REVERT: K 543 LEU cc_start: 0.8182 (tm) cc_final: 0.7886 (tt) REVERT: L 49 THR cc_start: 0.9030 (m) cc_final: 0.8709 (p) REVERT: L 78 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7331 (mp) REVERT: L 224 MET cc_start: 0.6969 (tpt) cc_final: 0.6682 (tpp) REVERT: L 227 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7767 (mtpt) REVERT: L 228 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: L 252 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8128 (ttm-80) REVERT: L 258 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: L 261 SER cc_start: 0.8707 (t) cc_final: 0.8499 (m) REVERT: L 284 LYS cc_start: 0.7578 (mtpp) cc_final: 0.7277 (ttmm) REVERT: L 329 ASN cc_start: 0.7156 (t0) cc_final: 0.6704 (t0) REVERT: L 402 MET cc_start: 0.8388 (tmt) cc_final: 0.7564 (tmt) REVERT: L 481 ARG cc_start: 0.6929 (mtp85) cc_final: 0.6648 (mtp85) REVERT: L 500 VAL cc_start: 0.9066 (m) cc_final: 0.8687 (p) REVERT: L 509 MET cc_start: 0.6779 (mmt) cc_final: 0.6531 (mmm) REVERT: L 513 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6656 (tt0) REVERT: L 543 LEU cc_start: 0.8179 (tm) cc_final: 0.7893 (tt) outliers start: 59 outliers final: 30 residues processed: 409 average time/residue: 2.6449 time to fit residues: 1226.5031 Evaluate side-chains 382 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 345 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 367 ILE Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 530 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 530 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 367 ILE Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 530 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 424 PHE Chi-restraints excluded: chain L residue 530 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 GLN H 296 GLN H 333 ASN J 333 ASN K 136 ASN L 333 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18208 Z= 0.222 Angle : 0.592 6.753 24688 Z= 0.293 Chirality : 0.045 0.137 2748 Planarity : 0.005 0.055 3172 Dihedral : 11.860 160.701 2528 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.35 % Allowed : 16.29 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2220 helix: 0.65 (0.18), residues: 900 sheet: -0.17 (0.25), residues: 392 loop : 0.22 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 358 HIS 0.004 0.001 HIS H 116 PHE 0.013 0.001 PHE L 424 TYR 0.012 0.001 TYR H 42 ARG 0.008 0.001 ARG L 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 363 time to evaluate : 2.980 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: H 109 LYS cc_start: 0.8538 (mttm) cc_final: 0.8284 (mttm) REVERT: H 224 MET cc_start: 0.6964 (tpt) cc_final: 0.6724 (tpp) REVERT: H 228 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: H 286 ARG cc_start: 0.6939 (ttt90) cc_final: 0.6587 (ttp-110) REVERT: H 402 MET cc_start: 0.8313 (tmt) cc_final: 0.7548 (tmt) REVERT: H 500 VAL cc_start: 0.9045 (m) cc_final: 0.8669 (p) REVERT: H 513 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6609 (tt0) REVERT: H 521 VAL cc_start: 0.8551 (p) cc_final: 0.8264 (t) REVERT: H 543 LEU cc_start: 0.8213 (tm) cc_final: 0.7872 (tt) REVERT: J 172 ARG cc_start: 0.7753 (tpt90) cc_final: 0.7372 (tpt170) REVERT: J 224 MET cc_start: 0.6967 (tpt) cc_final: 0.6767 (tpp) REVERT: J 228 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: J 475 GLU cc_start: 0.7305 (tt0) cc_final: 0.7045 (mt-10) REVERT: J 500 VAL cc_start: 0.9027 (m) cc_final: 0.8630 (p) REVERT: J 513 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6602 (tt0) REVERT: J 521 VAL cc_start: 0.8550 (p) cc_final: 0.8248 (t) REVERT: J 535 LYS cc_start: 0.7989 (pptt) cc_final: 0.7774 (pttp) REVERT: J 543 LEU cc_start: 0.8167 (tm) cc_final: 0.7861 (tt) REVERT: K 454 ARG cc_start: 0.8030 (ttm170) cc_final: 0.7788 (ttt180) REVERT: K 473 PHE cc_start: 0.8140 (p90) cc_final: 0.7881 (p90) REVERT: K 481 ARG cc_start: 0.6987 (mtp85) cc_final: 0.6705 (mtp85) REVERT: K 500 VAL cc_start: 0.9049 (m) cc_final: 0.8647 (p) REVERT: K 513 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6632 (tt0) REVERT: K 521 VAL cc_start: 0.8535 (p) cc_final: 0.8230 (t) REVERT: K 543 LEU cc_start: 0.8211 (tm) cc_final: 0.7871 (tt) REVERT: L 224 MET cc_start: 0.7008 (tpt) cc_final: 0.6752 (tpp) REVERT: L 227 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7774 (mtpt) REVERT: L 228 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: L 286 ARG cc_start: 0.7200 (ttp-110) cc_final: 0.6963 (ttp-110) REVERT: L 329 ASN cc_start: 0.7242 (t0) cc_final: 0.6773 (t0) REVERT: L 365 ASP cc_start: 0.7517 (m-30) cc_final: 0.7218 (t0) REVERT: L 481 ARG cc_start: 0.6950 (mtp85) cc_final: 0.6614 (mtp85) REVERT: L 500 VAL cc_start: 0.9058 (m) cc_final: 0.8679 (p) REVERT: L 509 MET cc_start: 0.6706 (mmt) cc_final: 0.6455 (mmm) REVERT: L 513 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6668 (tt0) REVERT: L 521 VAL cc_start: 0.8555 (p) cc_final: 0.8244 (t) REVERT: L 543 LEU cc_start: 0.8209 (tm) cc_final: 0.7875 (tt) outliers start: 65 outliers final: 36 residues processed: 406 average time/residue: 2.6227 time to fit residues: 1203.2650 Evaluate side-chains 390 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 351 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 367 ILE Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 367 ILE Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 424 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 0.0270 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 190 optimal weight: 0.0870 chunk 53 optimal weight: 0.7980 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN J 333 ASN L 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18208 Z= 0.177 Angle : 0.567 7.245 24688 Z= 0.277 Chirality : 0.044 0.137 2748 Planarity : 0.005 0.065 3172 Dihedral : 11.132 150.328 2524 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.04 % Allowed : 16.86 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2220 helix: 0.86 (0.18), residues: 900 sheet: -0.11 (0.25), residues: 392 loop : 0.36 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 358 HIS 0.003 0.001 HIS H 96 PHE 0.010 0.001 PHE L 424 TYR 0.011 0.001 TYR L 42 ARG 0.007 0.001 ARG K 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 361 time to evaluate : 2.779 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: H 109 LYS cc_start: 0.8532 (mttm) cc_final: 0.8270 (mttm) REVERT: H 228 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: H 286 ARG cc_start: 0.6921 (ttt90) cc_final: 0.6560 (ttp-110) REVERT: H 500 VAL cc_start: 0.9041 (m) cc_final: 0.8672 (p) REVERT: H 513 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6646 (tt0) REVERT: H 543 LEU cc_start: 0.8185 (tm) cc_final: 0.7871 (tt) REVERT: J 172 ARG cc_start: 0.7699 (tpt90) cc_final: 0.7299 (tpt170) REVERT: J 228 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: J 475 GLU cc_start: 0.7204 (tt0) cc_final: 0.6960 (mt-10) REVERT: J 500 VAL cc_start: 0.9046 (m) cc_final: 0.8656 (p) REVERT: J 513 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6636 (tt0) REVERT: J 535 LYS cc_start: 0.8018 (pptt) cc_final: 0.7806 (pttp) REVERT: J 543 LEU cc_start: 0.8171 (tm) cc_final: 0.7857 (tt) REVERT: K 261 SER cc_start: 0.8612 (m) cc_final: 0.8183 (p) REVERT: K 481 ARG cc_start: 0.6997 (mtp180) cc_final: 0.6702 (mtp85) REVERT: K 500 VAL cc_start: 0.9051 (m) cc_final: 0.8644 (p) REVERT: K 513 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6799 (tt0) REVERT: K 543 LEU cc_start: 0.8215 (tm) cc_final: 0.7907 (tt) REVERT: L 227 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7943 (mtpp) REVERT: L 228 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: L 261 SER cc_start: 0.8624 (m) cc_final: 0.8177 (p) REVERT: L 329 ASN cc_start: 0.7259 (t0) cc_final: 0.6800 (t0) REVERT: L 365 ASP cc_start: 0.7496 (m-30) cc_final: 0.7191 (t0) REVERT: L 481 ARG cc_start: 0.6927 (mtp85) cc_final: 0.6514 (mtp85) REVERT: L 513 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6699 (tt0) REVERT: L 543 LEU cc_start: 0.8209 (tm) cc_final: 0.7898 (tt) outliers start: 59 outliers final: 42 residues processed: 393 average time/residue: 2.5518 time to fit residues: 1137.5501 Evaluate side-chains 394 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 349 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 313 CYS Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 367 ILE Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 313 CYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 365 ASP Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 367 ILE Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 313 CYS Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 424 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 176 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN H 296 GLN J 287 ASN K 287 ASN L 287 ASN L 296 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18208 Z= 0.194 Angle : 0.562 7.508 24688 Z= 0.273 Chirality : 0.044 0.137 2748 Planarity : 0.005 0.051 3172 Dihedral : 10.511 142.990 2524 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.81 % Allowed : 15.88 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2220 helix: 0.96 (0.18), residues: 900 sheet: -0.08 (0.25), residues: 392 loop : 0.41 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 358 HIS 0.004 0.001 HIS J 96 PHE 0.010 0.001 PHE H 163 TYR 0.011 0.001 TYR K 42 ARG 0.011 0.001 ARG K 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 353 time to evaluate : 2.892 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: H 228 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: H 500 VAL cc_start: 0.9051 (m) cc_final: 0.8674 (p) REVERT: H 513 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6690 (tt0) REVERT: H 521 VAL cc_start: 0.8542 (p) cc_final: 0.8246 (t) REVERT: H 543 LEU cc_start: 0.8237 (tm) cc_final: 0.7921 (tt) REVERT: J 172 ARG cc_start: 0.7747 (tpt90) cc_final: 0.7324 (tpt170) REVERT: J 475 GLU cc_start: 0.7214 (tt0) cc_final: 0.6954 (mt-10) REVERT: J 500 VAL cc_start: 0.9048 (m) cc_final: 0.8654 (p) REVERT: J 513 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6648 (tt0) REVERT: J 535 LYS cc_start: 0.8029 (pptt) cc_final: 0.7799 (pttp) REVERT: J 543 LEU cc_start: 0.8235 (tm) cc_final: 0.7946 (tt) REVERT: K 481 ARG cc_start: 0.7038 (mtp180) cc_final: 0.6650 (mtp85) REVERT: K 500 VAL cc_start: 0.9049 (m) cc_final: 0.8638 (p) REVERT: K 513 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6802 (tt0) REVERT: K 543 LEU cc_start: 0.8243 (tm) cc_final: 0.7957 (tt) REVERT: L 227 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7952 (mtpp) REVERT: L 228 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: L 329 ASN cc_start: 0.7282 (t0) cc_final: 0.6807 (t0) REVERT: L 481 ARG cc_start: 0.6983 (mtp180) cc_final: 0.6540 (mtp85) REVERT: L 513 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6744 (tt0) REVERT: L 543 LEU cc_start: 0.8237 (tm) cc_final: 0.7927 (tt) outliers start: 74 outliers final: 45 residues processed: 401 average time/residue: 2.4688 time to fit residues: 1126.3646 Evaluate side-chains 393 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 346 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 313 CYS Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 530 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 313 CYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 365 ASP Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 530 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 367 ILE Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 530 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 313 CYS Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 424 PHE Chi-restraints excluded: chain L residue 530 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 GLN H 287 ASN J 287 ASN K 287 ASN L 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18208 Z= 0.290 Angle : 0.611 7.453 24688 Z= 0.297 Chirality : 0.046 0.139 2748 Planarity : 0.005 0.061 3172 Dihedral : 10.676 148.033 2524 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.35 % Allowed : 16.49 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2220 helix: 0.85 (0.18), residues: 904 sheet: 0.21 (0.27), residues: 352 loop : 0.17 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 124 HIS 0.005 0.001 HIS H 96 PHE 0.013 0.001 PHE J 163 TYR 0.012 0.002 TYR L 42 ARG 0.016 0.001 ARG H 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 350 time to evaluate : 2.931 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: H 109 LYS cc_start: 0.8598 (mttm) cc_final: 0.8355 (mttm) REVERT: H 228 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: H 500 VAL cc_start: 0.9063 (m) cc_final: 0.8669 (p) REVERT: H 513 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6832 (tt0) REVERT: H 535 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7770 (pptt) REVERT: H 543 LEU cc_start: 0.8248 (tm) cc_final: 0.7981 (tt) REVERT: J 172 ARG cc_start: 0.7786 (tpt90) cc_final: 0.7361 (tpt170) REVERT: J 258 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6775 (mm-30) REVERT: J 475 GLU cc_start: 0.7233 (tt0) cc_final: 0.7006 (mt-10) REVERT: J 481 ARG cc_start: 0.6883 (mmm-85) cc_final: 0.6494 (mtm110) REVERT: J 500 VAL cc_start: 0.9059 (m) cc_final: 0.8651 (p) REVERT: J 513 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6792 (tt0) REVERT: J 535 LYS cc_start: 0.8030 (pptt) cc_final: 0.7790 (pttp) REVERT: J 543 LEU cc_start: 0.8237 (tm) cc_final: 0.7967 (tt) REVERT: K 481 ARG cc_start: 0.7086 (mtp180) cc_final: 0.6696 (mtp85) REVERT: K 500 VAL cc_start: 0.9059 (m) cc_final: 0.8635 (p) REVERT: K 513 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6874 (tt0) REVERT: K 543 LEU cc_start: 0.8253 (tm) cc_final: 0.7992 (tt) REVERT: L 227 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7977 (mtpp) REVERT: L 228 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: L 258 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6637 (tp30) REVERT: L 329 ASN cc_start: 0.7227 (t0) cc_final: 0.6745 (t0) REVERT: L 365 ASP cc_start: 0.7446 (m-30) cc_final: 0.7208 (t0) REVERT: L 402 MET cc_start: 0.8280 (tmt) cc_final: 0.7582 (tmt) REVERT: L 481 ARG cc_start: 0.7064 (mtp180) cc_final: 0.6637 (mtp85) REVERT: L 500 VAL cc_start: 0.9085 (m) cc_final: 0.8695 (p) REVERT: L 513 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6893 (tt0) REVERT: L 543 LEU cc_start: 0.8254 (tm) cc_final: 0.7988 (tt) outliers start: 65 outliers final: 44 residues processed: 393 average time/residue: 2.5057 time to fit residues: 1119.9439 Evaluate side-chains 394 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 345 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 313 CYS Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 530 SER Chi-restraints excluded: chain H residue 535 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 313 CYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 365 ASP Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 530 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 530 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 313 CYS Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 424 PHE Chi-restraints excluded: chain L residue 530 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 19 optimal weight: 0.0870 chunk 166 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 167 GLN H 287 ASN J 287 ASN K 287 ASN K 323 HIS L 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18208 Z= 0.203 Angle : 0.569 7.149 24688 Z= 0.277 Chirality : 0.044 0.134 2748 Planarity : 0.005 0.079 3172 Dihedral : 10.035 141.480 2524 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.09 % Allowed : 16.86 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2220 helix: 1.00 (0.18), residues: 900 sheet: 0.22 (0.27), residues: 352 loop : 0.24 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 387 HIS 0.004 0.001 HIS H 96 PHE 0.011 0.001 PHE J 163 TYR 0.011 0.001 TYR J 42 ARG 0.015 0.001 ARG H 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 345 time to evaluate : 3.077 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: H 228 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: H 365 ASP cc_start: 0.7412 (m-30) cc_final: 0.7189 (t0) REVERT: H 500 VAL cc_start: 0.9054 (m) cc_final: 0.8672 (p) REVERT: H 513 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6834 (tt0) REVERT: H 543 LEU cc_start: 0.8228 (tm) cc_final: 0.7955 (tt) REVERT: J 172 ARG cc_start: 0.7762 (tpt90) cc_final: 0.7320 (tpt170) REVERT: J 365 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7220 (t0) REVERT: J 475 GLU cc_start: 0.7226 (tt0) cc_final: 0.6987 (mt-10) REVERT: J 500 VAL cc_start: 0.9054 (m) cc_final: 0.8651 (p) REVERT: J 513 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6864 (tt0) REVERT: J 535 LYS cc_start: 0.7992 (pptt) cc_final: 0.7757 (pttp) REVERT: J 543 LEU cc_start: 0.8203 (tm) cc_final: 0.7932 (tt) REVERT: K 18 ILE cc_start: 0.9369 (tp) cc_final: 0.9166 (tp) REVERT: K 258 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6800 (mm-30) REVERT: K 481 ARG cc_start: 0.7096 (mtp180) cc_final: 0.6687 (mtp85) REVERT: K 500 VAL cc_start: 0.9054 (m) cc_final: 0.8635 (p) REVERT: K 508 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7511 (mtt-85) REVERT: K 513 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6880 (tt0) REVERT: K 543 LEU cc_start: 0.8230 (tm) cc_final: 0.7989 (tt) REVERT: L 49 THR cc_start: 0.9077 (m) cc_final: 0.8815 (p) REVERT: L 227 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7962 (mtpp) REVERT: L 228 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: L 258 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6615 (tp30) REVERT: L 329 ASN cc_start: 0.7211 (t0) cc_final: 0.6735 (t0) REVERT: L 365 ASP cc_start: 0.7398 (m-30) cc_final: 0.7185 (t0) REVERT: L 481 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6575 (mtp85) REVERT: L 500 VAL cc_start: 0.9078 (m) cc_final: 0.8699 (p) REVERT: L 513 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6842 (tt0) REVERT: L 521 VAL cc_start: 0.8567 (p) cc_final: 0.8265 (t) REVERT: L 543 LEU cc_start: 0.8214 (tm) cc_final: 0.7944 (tt) outliers start: 60 outliers final: 39 residues processed: 387 average time/residue: 2.5193 time to fit residues: 1107.6288 Evaluate side-chains 382 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 338 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 313 CYS Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 530 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 313 CYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 365 ASP Chi-restraints excluded: chain J residue 530 SER Chi-restraints excluded: chain J residue 550 ASN Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 530 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 313 CYS Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 530 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 0.3980 chunk 197 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 128 GLN H 287 ASN J 287 ASN K 287 ASN L 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18208 Z= 0.209 Angle : 0.576 7.068 24688 Z= 0.279 Chirality : 0.044 0.139 2748 Planarity : 0.005 0.061 3172 Dihedral : 9.680 137.273 2524 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.94 % Allowed : 17.27 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2220 helix: 1.01 (0.18), residues: 904 sheet: 0.21 (0.27), residues: 352 loop : 0.24 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 387 HIS 0.004 0.001 HIS H 96 PHE 0.015 0.001 PHE L 424 TYR 0.011 0.001 TYR H 42 ARG 0.019 0.001 ARG K 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 336 time to evaluate : 2.565 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: H 185 GLN cc_start: 0.8431 (pt0) cc_final: 0.8218 (pt0) REVERT: H 228 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7097 (mt-10) REVERT: H 500 VAL cc_start: 0.9051 (m) cc_final: 0.8675 (p) REVERT: H 513 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6837 (tt0) REVERT: H 535 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7718 (pptt) REVERT: H 543 LEU cc_start: 0.8217 (tm) cc_final: 0.7972 (tt) REVERT: J 172 ARG cc_start: 0.7774 (tpt90) cc_final: 0.7325 (tpt170) REVERT: J 258 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6837 (mm-30) REVERT: J 365 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7212 (t0) REVERT: J 475 GLU cc_start: 0.7203 (tt0) cc_final: 0.6971 (mt-10) REVERT: J 500 VAL cc_start: 0.9053 (m) cc_final: 0.8651 (p) REVERT: J 513 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6873 (tt0) REVERT: J 535 LYS cc_start: 0.8014 (pptt) cc_final: 0.7774 (pttp) REVERT: J 543 LEU cc_start: 0.8204 (tm) cc_final: 0.7934 (tt) REVERT: K 49 THR cc_start: 0.9079 (m) cc_final: 0.8838 (p) REVERT: K 481 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6704 (mtp85) REVERT: K 500 VAL cc_start: 0.9079 (m) cc_final: 0.8655 (p) REVERT: K 513 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6862 (tt0) REVERT: K 543 LEU cc_start: 0.8222 (tm) cc_final: 0.7973 (tt) REVERT: L 227 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7958 (mtpp) REVERT: L 228 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: L 258 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6594 (tp30) REVERT: L 329 ASN cc_start: 0.7263 (t0) cc_final: 0.6786 (t0) REVERT: L 481 ARG cc_start: 0.7036 (mtp180) cc_final: 0.6558 (mtp85) REVERT: L 500 VAL cc_start: 0.9079 (m) cc_final: 0.8700 (p) REVERT: L 513 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6895 (tt0) REVERT: L 543 LEU cc_start: 0.8215 (tm) cc_final: 0.7959 (tt) outliers start: 57 outliers final: 38 residues processed: 375 average time/residue: 2.5074 time to fit residues: 1069.0190 Evaluate side-chains 378 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 334 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 313 CYS Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 530 SER Chi-restraints excluded: chain H residue 535 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 313 CYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 365 ASP Chi-restraints excluded: chain J residue 530 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 530 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 313 CYS Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 530 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 134 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN H 323 HIS J 167 GLN J 287 ASN J 323 HIS K 167 GLN K 287 ASN K 323 HIS L 128 GLN L 287 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18208 Z= 0.185 Angle : 0.565 6.977 24688 Z= 0.273 Chirality : 0.044 0.144 2748 Planarity : 0.005 0.095 3172 Dihedral : 9.221 129.951 2524 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.53 % Allowed : 17.78 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2220 helix: 1.08 (0.18), residues: 904 sheet: 0.22 (0.27), residues: 352 loop : 0.25 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 387 HIS 0.004 0.001 HIS K 96 PHE 0.012 0.001 PHE L 424 TYR 0.011 0.001 TYR H 42 ARG 0.020 0.001 ARG K 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 338 time to evaluate : 2.739 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: H 500 VAL cc_start: 0.9050 (m) cc_final: 0.8680 (p) REVERT: H 513 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6829 (tt0) REVERT: H 535 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7811 (pptt) REVERT: H 543 LEU cc_start: 0.8187 (tm) cc_final: 0.7945 (tt) REVERT: J 18 ILE cc_start: 0.9365 (tp) cc_final: 0.9145 (tp) REVERT: J 172 ARG cc_start: 0.7761 (tpt90) cc_final: 0.7305 (tpt170) REVERT: J 365 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7227 (t0) REVERT: J 475 GLU cc_start: 0.7201 (tt0) cc_final: 0.6969 (mt-10) REVERT: J 500 VAL cc_start: 0.9050 (m) cc_final: 0.8659 (p) REVERT: J 513 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6840 (tt0) REVERT: J 535 LYS cc_start: 0.8009 (pptt) cc_final: 0.7767 (pttp) REVERT: J 543 LEU cc_start: 0.8198 (tm) cc_final: 0.7930 (tt) REVERT: K 18 ILE cc_start: 0.9368 (tp) cc_final: 0.9143 (tp) REVERT: K 481 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6875 (mtm110) REVERT: K 500 VAL cc_start: 0.9068 (m) cc_final: 0.8650 (p) REVERT: K 508 ARG cc_start: 0.7794 (mtt-85) cc_final: 0.7430 (mtt-85) REVERT: K 513 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6867 (tt0) REVERT: K 543 LEU cc_start: 0.8197 (tm) cc_final: 0.7953 (tt) REVERT: L 228 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: L 329 ASN cc_start: 0.7270 (t0) cc_final: 0.6794 (t0) REVERT: L 481 ARG cc_start: 0.7029 (mtp180) cc_final: 0.6553 (mtp85) REVERT: L 500 VAL cc_start: 0.9084 (m) cc_final: 0.8715 (p) REVERT: L 513 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6878 (tt0) REVERT: L 543 LEU cc_start: 0.8192 (tm) cc_final: 0.7951 (tt) outliers start: 49 outliers final: 32 residues processed: 372 average time/residue: 2.5471 time to fit residues: 1084.6535 Evaluate side-chains 371 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 336 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 313 CYS Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 535 LYS Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 313 CYS Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 365 ASP Chi-restraints excluded: chain J residue 530 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 530 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 313 CYS Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 530 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.3980 chunk 53 optimal weight: 0.1980 chunk 160 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 128 GLN J 287 ASN K 128 GLN K 323 HIS L 167 GLN L 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122707 restraints weight = 54762.465| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.91 r_work: 0.3210 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18208 Z= 0.166 Angle : 0.552 6.805 24688 Z= 0.267 Chirality : 0.044 0.134 2748 Planarity : 0.005 0.081 3172 Dihedral : 8.607 117.573 2524 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.22 % Allowed : 18.09 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2220 helix: 1.14 (0.18), residues: 904 sheet: 0.24 (0.26), residues: 352 loop : 0.29 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 387 HIS 0.003 0.001 HIS J 96 PHE 0.011 0.001 PHE L 424 TYR 0.011 0.001 TYR H 42 ARG 0.019 0.001 ARG H 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16643.35 seconds wall clock time: 289 minutes 21.50 seconds (17361.50 seconds total)