Starting phenix.real_space_refine on Sun Mar 24 19:23:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kw7_23050/03_2024/7kw7_23050_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kw7_23050/03_2024/7kw7_23050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kw7_23050/03_2024/7kw7_23050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kw7_23050/03_2024/7kw7_23050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kw7_23050/03_2024/7kw7_23050_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kw7_23050/03_2024/7kw7_23050_trim_updated.pdb" } resolution = 3.57 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= 0.002 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 Mg 2 5.21 5 S 101 5.16 5 C 13803 2.51 5 N 3723 2.21 5 O 4217 1.98 5 H 21928 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 699": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43780 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 10157 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 15, 'TRANS': 607} Chain breaks: 1 Chain: "B" Number of atoms: 10233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 10233 Classifications: {'peptide': 628} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 611} Chain breaks: 2 Chain: "C" Number of atoms: 7897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 7897 Classifications: {'peptide': 511} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 489} Chain breaks: 1 Chain: "D" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5882 Classifications: {'peptide': 379} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 365} Chain: "E" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5321 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "F" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4232 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 247} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 16.62, per 1000 atoms: 0.38 Number of scatterers: 43780 At special positions: 0 Unit cell: (145.083, 154.614, 130.257, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 2 19.00 S 101 16.00 P 4 15.00 Mg 2 11.99 O 4217 8.00 N 3723 7.00 C 13803 6.00 H 21928 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: 37.44 Conformation dependent library (CDL) restraints added in 4.1 seconds 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 25 sheets defined 49.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.31 Creating SS restraints... Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 41 through 65 removed outlier: 3.637A pdb=" N GLU A 47 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 128 through 134 removed outlier: 4.408A pdb=" N GLY A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 192 through 198 removed outlier: 5.199A pdb=" N GLU A 196 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 407 through 428 Processing helix chain 'A' and resid 431 through 451 removed outlier: 4.371A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 462 removed outlier: 5.292A pdb=" N LYS A 457 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.506A pdb=" N ARG A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 506 through 513 removed outlier: 5.232A pdb=" N ARG A 510 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 512 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 4.500A pdb=" N VAL A 530 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 569 through 578 Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 641 through 652 Processing helix chain 'A' and resid 657 through 673 Processing helix chain 'A' and resid 681 through 695 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 41 through 65 removed outlier: 3.624A pdb=" N GLU B 47 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 51 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 58 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 111 through 123 removed outlier: 5.277A pdb=" N LYS B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 134 removed outlier: 4.323A pdb=" N GLY B 132 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 192 through 198 removed outlier: 4.893A pdb=" N GLU B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 352 through 357 removed outlier: 4.761A pdb=" N LYS B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 407 through 429 Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.502A pdb=" N LYS B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 462 removed outlier: 3.780A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 513 removed outlier: 5.223A pdb=" N ARG B 510 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 4.515A pdb=" N VAL B 530 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 567 Processing helix chain 'B' and resid 569 through 578 Processing helix chain 'B' and resid 608 through 620 Processing helix chain 'B' and resid 641 through 652 Processing helix chain 'B' and resid 657 through 673 Processing helix chain 'B' and resid 681 through 696 Processing helix chain 'C' and resid 52 through 58 removed outlier: 4.008A pdb=" N ASN C 57 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.539A pdb=" N LYS C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 135 Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 230 through 249 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.954A pdb=" N SER C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 307 through 323 removed outlier: 3.923A pdb=" N THR C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 368 through 380 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'D' and resid 53 through 58 removed outlier: 3.901A pdb=" N GLN D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 70 through 73 No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.384A pdb=" N LYS D 88 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 135 Processing helix chain 'D' and resid 152 through 165 Processing helix chain 'D' and resid 175 through 182 Processing helix chain 'D' and resid 231 through 249 Processing helix chain 'D' and resid 257 through 275 Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 307 through 323 removed outlier: 3.637A pdb=" N THR D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU D 314 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 339 through 342 Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 368 through 380 Processing helix chain 'E' and resid 220 through 237 Processing helix chain 'E' and resid 241 through 254 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 296 through 312 Processing helix chain 'E' and resid 316 through 329 Processing helix chain 'E' and resid 333 through 354 Processing helix chain 'E' and resid 357 through 373 removed outlier: 3.714A pdb=" N LYS E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 389 Processing helix chain 'E' and resid 394 through 406 Processing helix chain 'E' and resid 410 through 423 Processing helix chain 'E' and resid 428 through 440 Processing helix chain 'E' and resid 444 through 457 Processing helix chain 'E' and resid 462 through 477 removed outlier: 3.798A pdb=" N MET E 473 " --> pdb=" O GLN E 469 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TYR E 476 " --> pdb=" O MET E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 491 removed outlier: 3.741A pdb=" N ALA E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 500 Processing helix chain 'E' and resid 502 through 513 Processing helix chain 'E' and resid 515 through 523 removed outlier: 4.223A pdb=" N LYS E 523 " --> pdb=" O SER E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 536 removed outlier: 4.210A pdb=" N LYS E 530 " --> pdb=" O VAL E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 538 Processing helix chain 'F' and resid 557 through 579 removed outlier: 5.159A pdb=" N LEU F 563 " --> pdb=" O MET F 560 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 566 " --> pdb=" O LEU F 563 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP F 577 " --> pdb=" O ALA F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 586 No H-bonds generated for 'chain 'F' and resid 584 through 586' Processing helix chain 'F' and resid 589 through 615 removed outlier: 5.872A pdb=" N MET F 601 " --> pdb=" O GLN F 597 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER F 602 " --> pdb=" O TYR F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 634 No H-bonds generated for 'chain 'F' and resid 631 through 634' Processing helix chain 'F' and resid 637 through 656 removed outlier: 5.686A pdb=" N GLN F 642 " --> pdb=" O CYS F 638 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS F 645 " --> pdb=" O ASP F 641 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET F 646 " --> pdb=" O GLN F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 672 removed outlier: 4.058A pdb=" N LEU F 672 " --> pdb=" O THR F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 705 removed outlier: 3.824A pdb=" N ARG F 704 " --> pdb=" O ALA F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 741 removed outlier: 4.265A pdb=" N HIS F 726 " --> pdb=" O LEU F 722 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU F 727 " --> pdb=" O ASP F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 745 No H-bonds generated for 'chain 'F' and resid 743 through 745' Processing helix chain 'F' and resid 751 through 764 Proline residue: F 762 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 17 through 21 removed outlier: 7.108A pdb=" N HIS A 189 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 148 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 187 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 150 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LYS A 185 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 152 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY A 183 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 368 through 371 removed outlier: 6.953A pdb=" N LEU A 363 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LYS A 362 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY A 387 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TYR A 364 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 389 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 540 through 543 Processing sheet with id= D, first strand: chain 'A' and resid 585 through 588 removed outlier: 3.671A pdb=" N LYS A 585 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 174 removed outlier: 7.021A pdb=" N HIS B 189 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL B 148 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 187 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 150 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS B 185 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 152 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY B 183 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B 80 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR B 219 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE B 221 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 368 through 371 removed outlier: 6.778A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LYS B 362 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY B 387 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR B 364 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B 389 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 464 through 466 Processing sheet with id= H, first strand: chain 'B' and resid 540 through 543 Processing sheet with id= I, first strand: chain 'B' and resid 585 through 588 removed outlier: 4.322A pdb=" N LYS B 585 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 168 through 174 removed outlier: 7.665A pdb=" N ILE C 144 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE C 172 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 146 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN C 174 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 7 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR C 145 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE C 9 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 19 through 22 Processing sheet with id= L, first strand: chain 'C' and resid 66 through 68 Processing sheet with id= M, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= N, first strand: chain 'C' and resid 333 through 337 removed outlier: 6.554A pdb=" N THR C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL C 219 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP C 213 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 279 through 284 Processing sheet with id= P, first strand: chain 'C' and resid 409 through 414 removed outlier: 6.790A pdb=" N LEU C 401 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN C 441 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU C 444 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU C 455 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 422 through 428 removed outlier: 3.909A pdb=" N LYS C 497 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 168 through 174 removed outlier: 7.522A pdb=" N ILE D 144 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE D 172 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL D 146 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN D 174 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 7 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N THR D 145 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE D 9 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 19 through 22 Processing sheet with id= T, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= U, first strand: chain 'D' and resid 93 through 96 removed outlier: 3.517A pdb=" N GLN D 93 " --> pdb=" O GLN D 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 333 through 337 removed outlier: 6.646A pdb=" N THR D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL D 219 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASP D 213 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 279 through 284 Processing sheet with id= X, first strand: chain 'F' and resid 674 through 676 Processing sheet with id= Y, first strand: chain 'F' and resid 621 through 624 removed outlier: 4.373A pdb=" N LEU F 621 " --> pdb=" O ILE F 629 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU F 627 " --> pdb=" O PHE F 623 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 2841 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: 19.05 Time building geometry restraints manager: 38.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 21900 1.13 - 1.31: 4215 1.31 - 1.49: 9486 1.49 - 1.68: 8373 1.68 - 1.86: 167 Bond restraints: 44141 Sorted by residual: bond pdb=" CD GLU D 175 " pdb=" OE1 GLU D 175 " ideal model delta sigma weight residual 1.249 1.059 0.190 1.90e-02 2.77e+03 9.96e+01 bond pdb=" NE2 HIS D 240 " pdb=" HE2 HIS D 240 " ideal model delta sigma weight residual 0.860 1.059 -0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" NE1 TRP B 297 " pdb=" HE1 TRP B 297 " ideal model delta sigma weight residual 0.860 1.054 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" NE2 HIS C 240 " pdb=" HE2 HIS C 240 " ideal model delta sigma weight residual 0.860 1.053 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" CD GLU C 175 " pdb=" OE2 GLU C 175 " ideal model delta sigma weight residual 1.249 1.066 0.183 1.90e-02 2.77e+03 9.25e+01 ... (remaining 44136 not shown) Histogram of bond angle deviations from ideal: 94.10 - 102.34: 166 102.34 - 110.57: 44790 110.57 - 118.81: 16261 118.81 - 127.05: 18530 127.05 - 135.29: 224 Bond angle restraints: 79971 Sorted by residual: angle pdb=" C ASN E 390 " pdb=" N PRO E 391 " pdb=" CA PRO E 391 " ideal model delta sigma weight residual 119.56 129.56 -10.00 1.02e+00 9.61e-01 9.62e+01 angle pdb=" C GLU E 424 " pdb=" N PRO E 425 " pdb=" CA PRO E 425 " ideal model delta sigma weight residual 119.56 127.52 -7.96 1.02e+00 9.61e-01 6.09e+01 angle pdb=" C VAL B 343 " pdb=" N PRO B 344 " pdb=" CA PRO B 344 " ideal model delta sigma weight residual 120.03 127.70 -7.67 9.90e-01 1.02e+00 6.00e+01 angle pdb=" C ILE A 59 " pdb=" CA ILE A 59 " pdb=" CB ILE A 59 " ideal model delta sigma weight residual 112.02 101.99 10.03 1.31e+00 5.83e-01 5.86e+01 angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 108.17 118.75 -10.58 1.40e+00 5.10e-01 5.71e+01 ... (remaining 79966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 20243 34.74 - 69.48: 307 69.48 - 104.22: 16 104.22 - 138.96: 3 138.96 - 173.70: 2 Dihedral angle restraints: 20571 sinusoidal: 11412 harmonic: 9159 Sorted by residual: dihedral pdb=" C5' ADP C 701 " pdb=" O5' ADP C 701 " pdb=" PA ADP C 701 " pdb=" O2A ADP C 701 " ideal model delta sinusoidal sigma weight residual 300.00 126.30 173.70 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PA ADP D 701 " pdb=" PB ADP D 701 " ideal model delta sinusoidal sigma weight residual 300.00 156.14 143.86 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O1B ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PB ADP D 701 " pdb=" PA ADP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 78.19 -138.20 1 2.00e+01 2.50e-03 4.19e+01 ... (remaining 20568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1930 0.075 - 0.150: 1004 0.150 - 0.225: 342 0.225 - 0.300: 67 0.300 - 0.375: 16 Chirality restraints: 3359 Sorted by residual: chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.02 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB VAL E 268 " pdb=" CA VAL E 268 " pdb=" CG1 VAL E 268 " pdb=" CG2 VAL E 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 3356 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 732 " -0.029 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C ASP B 732 " 0.102 2.00e-02 2.50e+03 pdb=" O ASP B 732 " -0.037 2.00e-02 2.50e+03 pdb=" OXT ASP B 732 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 548 " 0.075 2.00e-02 2.50e+03 3.06e-02 2.80e+01 pdb=" CG TYR F 548 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 548 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR F 548 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR F 548 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 548 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR F 548 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR F 548 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TYR F 548 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR F 548 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR F 548 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR F 548 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 162 " 0.072 2.00e-02 2.50e+03 2.43e-02 2.35e+01 pdb=" CG TRP A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 162 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 162 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 162 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 162 " -0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP A 162 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 162 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 162 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 162 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP A 162 " 0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP A 162 " -0.010 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 162 " 0.018 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 162 " -0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 162 " 0.025 2.00e-02 2.50e+03 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.95: 968 1.95 - 2.75: 82940 2.75 - 3.55: 176330 3.55 - 4.34: 272231 4.34 - 5.14: 438918 Nonbonded interactions: 971387 Sorted by model distance: nonbonded pdb=" H PHE A 384 " pdb=" H ILE A 385 " model vdw 1.156 2.100 nonbonded pdb=" H PHE B 384 " pdb=" H ILE B 385 " model vdw 1.163 2.100 nonbonded pdb=" H VAL C 388 " pdb=" H GLN C 389 " model vdw 1.234 2.100 nonbonded pdb=" H THR C 278 " pdb=" H GLN C 279 " model vdw 1.314 2.100 nonbonded pdb=" OD1 ASP C 10 " pdb=" K K C 703 " model vdw 1.517 2.730 ... (remaining 971382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 16 through 699) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.650 Extract box with map and model: 9.330 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 142.950 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.021 0.194 22213 Z= 1.365 Angle : 1.733 13.555 29945 Z= 1.168 Chirality : 0.098 0.375 3359 Planarity : 0.009 0.059 3858 Dihedral : 11.040 173.701 8497 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.26 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.61 (0.15), residues: 2707 helix: -0.13 (0.12), residues: 1335 sheet: 1.32 (0.26), residues: 378 loop : 1.16 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.011 TRP A 162 HIS 0.010 0.002 HIS C 240 PHE 0.041 0.007 PHE D 150 TYR 0.069 0.009 TYR F 548 ARG 0.009 0.001 ARG F 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7273 (mtm) cc_final: 0.6962 (mtt) REVERT: A 614 MET cc_start: 0.8270 (mmm) cc_final: 0.8031 (mmm) REVERT: B 38 TYR cc_start: 0.5922 (t80) cc_final: 0.5659 (t80) REVERT: C 381 MET cc_start: 0.8236 (ptt) cc_final: 0.7758 (ppp) REVERT: E 224 GLN cc_start: 0.9210 (mt0) cc_final: 0.8908 (mm110) REVERT: E 303 TYR cc_start: 0.8742 (m-80) cc_final: 0.8434 (m-80) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.8704 time to fit residues: 428.4250 Evaluate side-chains 221 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN B 79 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN B 415 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN E 452 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22213 Z= 0.329 Angle : 0.701 7.239 29945 Z= 0.398 Chirality : 0.043 0.183 3359 Planarity : 0.005 0.041 3858 Dihedral : 7.104 145.621 2975 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.66 % Favored : 98.30 % Rotamer: Outliers : 0.79 % Allowed : 4.89 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.94 (0.15), residues: 2707 helix: 0.79 (0.13), residues: 1340 sheet: 0.80 (0.25), residues: 408 loop : 0.56 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 162 HIS 0.008 0.001 HIS C 240 PHE 0.019 0.002 PHE F 606 TYR 0.018 0.002 TYR A 434 ARG 0.005 0.001 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7120 (mtm) cc_final: 0.6881 (mtt) REVERT: C 381 MET cc_start: 0.8054 (ptt) cc_final: 0.7721 (ppp) REVERT: C 383 ASP cc_start: 0.7024 (p0) cc_final: 0.6670 (p0) REVERT: D 354 PHE cc_start: 0.8049 (m-80) cc_final: 0.7834 (m-10) outliers start: 19 outliers final: 16 residues processed: 250 average time/residue: 0.8953 time to fit residues: 332.8481 Evaluate side-chains 211 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain F residue 745 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 166 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 264 optimal weight: 50.0000 chunk 217 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 196 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22213 Z= 0.259 Angle : 0.600 6.832 29945 Z= 0.333 Chirality : 0.041 0.159 3359 Planarity : 0.004 0.035 3858 Dihedral : 6.613 149.149 2975 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.75 % Rotamer: Outliers : 0.88 % Allowed : 5.81 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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 (0.16), residues: 2707 helix: 0.86 (0.13), residues: 1346 sheet: 0.49 (0.26), residues: 394 loop : 0.40 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 600 HIS 0.009 0.001 HIS B 154 PHE 0.022 0.002 PHE F 606 TYR 0.019 0.002 TYR E 468 ARG 0.003 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 381 MET cc_start: 0.8029 (ptt) cc_final: 0.7742 (ppp) REVERT: C 383 ASP cc_start: 0.6821 (p0) cc_final: 0.6365 (p0) REVERT: F 634 MET cc_start: -0.2635 (tpp) cc_final: -0.3244 (ttm) outliers start: 21 outliers final: 18 residues processed: 214 average time/residue: 0.8831 time to fit residues: 286.4388 Evaluate side-chains 204 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain F residue 646 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 241 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 164 optimal weight: 40.0000 chunk 245 optimal weight: 2.9990 chunk 260 optimal weight: 30.0000 chunk 128 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22213 Z= 0.209 Angle : 0.548 6.411 29945 Z= 0.297 Chirality : 0.040 0.154 3359 Planarity : 0.004 0.035 3858 Dihedral : 6.361 142.570 2975 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 0.96 % Allowed : 6.85 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.87 (0.16), residues: 2707 helix: 0.99 (0.14), residues: 1341 sheet: 0.25 (0.26), residues: 400 loop : 0.36 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 600 HIS 0.005 0.001 HIS B 154 PHE 0.017 0.001 PHE F 606 TYR 0.013 0.001 TYR E 468 ARG 0.004 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 381 MET cc_start: 0.8128 (ptt) cc_final: 0.7875 (ppp) REVERT: C 383 ASP cc_start: 0.6872 (p0) cc_final: 0.6461 (p0) REVERT: F 634 MET cc_start: -0.2674 (tpp) cc_final: -0.3322 (ttm) outliers start: 23 outliers final: 19 residues processed: 207 average time/residue: 0.8551 time to fit residues: 268.5199 Evaluate side-chains 201 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 314 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22213 Z= 0.377 Angle : 0.646 7.372 29945 Z= 0.357 Chirality : 0.041 0.151 3359 Planarity : 0.005 0.101 3858 Dihedral : 6.599 146.657 2975 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 1.21 % Allowed : 7.06 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: -0.05 (0.16), residues: 2707 helix: 0.31 (0.13), residues: 1330 sheet: -0.17 (0.26), residues: 398 loop : -0.21 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 162 HIS 0.007 0.002 HIS E 479 PHE 0.020 0.002 PHE A 37 TYR 0.019 0.002 TYR E 468 ARG 0.017 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 TYR cc_start: 0.6403 (t80) cc_final: 0.6182 (t80) REVERT: C 383 ASP cc_start: 0.6708 (p0) cc_final: 0.6218 (p0) REVERT: D 87 MET cc_start: 0.7831 (ppp) cc_final: 0.7619 (ppp) REVERT: F 634 MET cc_start: -0.2440 (tpp) cc_final: -0.3045 (ttm) REVERT: F 691 MET cc_start: 0.2586 (mmp) cc_final: 0.2350 (mmp) outliers start: 29 outliers final: 25 residues processed: 190 average time/residue: 0.8410 time to fit residues: 244.7652 Evaluate side-chains 187 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 537 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 0.1980 chunk 234 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22213 Z= 0.182 Angle : 0.524 6.271 29945 Z= 0.281 Chirality : 0.040 0.148 3359 Planarity : 0.004 0.041 3858 Dihedral : 6.310 142.126 2975 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % Rotamer: Outliers : 0.88 % Allowed : 7.86 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.44 (0.16), residues: 2707 helix: 0.83 (0.14), residues: 1329 sheet: -0.14 (0.27), residues: 371 loop : -0.07 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.004 0.001 HIS E 247 PHE 0.018 0.001 PHE D 198 TYR 0.015 0.001 TYR E 468 ARG 0.002 0.000 ARG A 591 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 3.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 383 ASP cc_start: 0.6754 (p0) cc_final: 0.5919 (t0) REVERT: D 87 MET cc_start: 0.7758 (ppp) cc_final: 0.7554 (ppp) REVERT: F 634 MET cc_start: -0.2436 (tpp) cc_final: -0.3039 (ttm) REVERT: F 691 MET cc_start: 0.2767 (mmp) cc_final: 0.2545 (mmp) outliers start: 21 outliers final: 17 residues processed: 190 average time/residue: 0.8260 time to fit residues: 243.3589 Evaluate side-chains 180 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain E residue 314 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 259 optimal weight: 50.0000 chunk 162 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 255 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22213 Z= 0.317 Angle : 0.587 6.444 29945 Z= 0.322 Chirality : 0.041 0.151 3359 Planarity : 0.004 0.044 3858 Dihedral : 6.460 144.266 2975 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 1.04 % Allowed : 8.36 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: -0.01 (0.16), residues: 2707 helix: 0.50 (0.14), residues: 1325 sheet: -0.47 (0.26), residues: 393 loop : -0.30 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 162 HIS 0.004 0.001 HIS E 247 PHE 0.015 0.002 PHE D 198 TYR 0.020 0.002 TYR B 38 ARG 0.006 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 3.908 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: C 383 ASP cc_start: 0.6842 (p0) cc_final: 0.5962 (t0) REVERT: F 634 MET cc_start: -0.2481 (tpp) cc_final: -0.3109 (ttm) REVERT: F 691 MET cc_start: 0.2487 (mmp) cc_final: 0.2251 (mmp) outliers start: 25 outliers final: 21 residues processed: 173 average time/residue: 0.8415 time to fit residues: 225.4258 Evaluate side-chains 175 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 314 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 160 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 164 optimal weight: 40.0000 chunk 176 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22213 Z= 0.196 Angle : 0.531 7.246 29945 Z= 0.284 Chirality : 0.040 0.176 3359 Planarity : 0.004 0.045 3858 Dihedral : 6.293 138.991 2975 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 0.79 % Allowed : 8.78 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.30 (0.16), residues: 2707 helix: 0.81 (0.14), residues: 1319 sheet: -0.42 (0.26), residues: 387 loop : -0.19 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.004 0.001 HIS C 240 PHE 0.013 0.001 PHE E 371 TYR 0.014 0.001 TYR E 468 ARG 0.004 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 3.776 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: C 383 ASP cc_start: 0.6638 (p0) cc_final: 0.5782 (t0) REVERT: F 634 MET cc_start: -0.2389 (tpp) cc_final: -0.3031 (ttm) REVERT: F 691 MET cc_start: 0.2588 (mmp) cc_final: 0.2356 (mmp) outliers start: 19 outliers final: 17 residues processed: 173 average time/residue: 0.8451 time to fit residues: 226.8563 Evaluate side-chains 169 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain E residue 314 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 248 optimal weight: 20.0000 chunk 226 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22213 Z= 0.193 Angle : 0.524 8.037 29945 Z= 0.279 Chirality : 0.040 0.142 3359 Planarity : 0.004 0.062 3858 Dihedral : 6.180 135.288 2975 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 0.79 % Allowed : 9.11 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.43 (0.16), residues: 2707 helix: 0.93 (0.14), residues: 1322 sheet: -0.42 (0.26), residues: 385 loop : -0.11 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 162 HIS 0.006 0.001 HIS A 684 PHE 0.020 0.001 PHE F 606 TYR 0.013 0.001 TYR E 468 ARG 0.010 0.000 ARG B 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 3.347 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: C 127 MET cc_start: 0.8381 (mmm) cc_final: 0.8173 (mmp) REVERT: C 383 ASP cc_start: 0.6471 (p0) cc_final: 0.5544 (t0) REVERT: D 152 ASP cc_start: 0.7103 (p0) cc_final: 0.6866 (p0) REVERT: F 634 MET cc_start: -0.2403 (tpp) cc_final: -0.3432 (ttm) REVERT: F 639 MET cc_start: 0.1250 (tpt) cc_final: -0.0270 (ttt) REVERT: F 691 MET cc_start: 0.2445 (mmp) cc_final: 0.2204 (mmp) outliers start: 19 outliers final: 16 residues processed: 172 average time/residue: 0.8235 time to fit residues: 216.4202 Evaluate side-chains 170 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain E residue 314 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 255 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 0.0010 chunk 130 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22213 Z= 0.213 Angle : 0.524 7.443 29945 Z= 0.280 Chirality : 0.040 0.142 3359 Planarity : 0.004 0.057 3858 Dihedral : 6.118 130.346 2975 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 0.67 % Allowed : 9.19 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.44 (0.16), residues: 2707 helix: 0.96 (0.14), residues: 1319 sheet: -0.47 (0.26), residues: 385 loop : -0.12 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 162 HIS 0.007 0.001 HIS A 684 PHE 0.027 0.001 PHE F 606 TYR 0.012 0.001 TYR E 468 ARG 0.009 0.000 ARG B 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 3.673 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: C 127 MET cc_start: 0.8404 (mmm) cc_final: 0.8178 (mmp) REVERT: C 383 ASP cc_start: 0.6257 (p0) cc_final: 0.5280 (t0) REVERT: D 152 ASP cc_start: 0.7106 (p0) cc_final: 0.6879 (p0) REVERT: F 634 MET cc_start: -0.2302 (tpp) cc_final: -0.3286 (ttm) REVERT: F 639 MET cc_start: 0.1166 (tpt) cc_final: -0.0287 (ttt) REVERT: F 691 MET cc_start: 0.2326 (mmp) cc_final: 0.2083 (mmp) outliers start: 16 outliers final: 15 residues processed: 167 average time/residue: 0.8536 time to fit residues: 218.4772 Evaluate side-chains 169 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 232 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.080573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.057665 restraints weight = 388010.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.059183 restraints weight = 169332.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.060523 restraints weight = 112074.415| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22213 Z= 0.368 Angle : 0.619 6.530 29945 Z= 0.341 Chirality : 0.042 0.147 3359 Planarity : 0.004 0.065 3858 Dihedral : 6.448 127.433 2975 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.64 % Rotamer: Outliers : 0.96 % Allowed : 8.90 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: -0.23 (0.16), residues: 2707 helix: 0.40 (0.14), residues: 1311 sheet: -0.72 (0.26), residues: 398 loop : -0.46 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 162 HIS 0.010 0.001 HIS A 684 PHE 0.021 0.002 PHE F 606 TYR 0.017 0.002 TYR E 468 ARG 0.008 0.001 ARG B 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7803.24 seconds wall clock time: 139 minutes 40.95 seconds (8380.95 seconds total)