Starting phenix.real_space_refine on Sun Sep 13 01:33:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pzz_20541/09_2026/6pzz_20541.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzz_20541/09_2026/6pzz_20541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pzz_20541/09_2026/6pzz_20541.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pzz_20541/09_2026/6pzz_20541.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pzz_20541/09_2026/6pzz_20541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzz_20541/09_2026/6pzz_20541.map" model { file = "/net/cci-nas-00/data/ceres_data/6pzz_20541/09_2026/6pzz_20541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzz_20541/09_2026/6pzz_20541.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.090 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 12320 2.51 5 N 3348 2.21 5 O 3980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19772 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, G, J, F, I, K, O, Q, S, P, R, T Time building chain proxies: 3.95, per 1000 atoms: 0.20 Number of scatterers: 19772 At special positions: 0 Unit cell: (192.61, 192.61, 85.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 3980 8.00 N 3348 7.00 C 12320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.02 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.04 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.02 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.02 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA P 3 " - " MAN P 7 " " MAN P 7 " - " MAN P 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG A 501 " - " ASN A 86 " " NAG B 501 " - " ASN B 86 " " NAG C 501 " - " ASN C 86 " " NAG D 501 " - " ASN D 86 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 200 " " NAG O 1 " - " ASN B 146 " " NAG P 1 " - " ASN B 200 " " NAG Q 1 " - " ASN C 146 " " NAG R 1 " - " ASN C 200 " " NAG S 1 " - " ASN D 146 " " NAG T 1 " - " ASN D 200 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 783.5 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 52 sheets defined 6.3% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 60 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 356 through 359 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.962A pdb=" N GLY A 90 " --> pdb=" O TYR A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.660A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA A 420 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 125 removed outlier: 5.356A pdb=" N THR A 138 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ARG A 118 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN A 136 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 134 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL A 122 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR A 132 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS A 124 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 184 removed outlier: 5.709A pdb=" N TYR A 207 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 243 removed outlier: 3.561A pdb=" N LYS A 264 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 282 removed outlier: 5.471A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.186A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.809A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.626A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.962A pdb=" N GLY B 90 " --> pdb=" O TYR B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.661A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA B 420 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 115 through 125 removed outlier: 5.355A pdb=" N THR B 138 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ARG B 118 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN B 136 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU B 134 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 122 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR B 132 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS B 124 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG B 130 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 179 through 184 removed outlier: 5.709A pdb=" N TYR B 207 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 236 through 243 removed outlier: 3.564A pdb=" N LYS B 264 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 282 removed outlier: 5.472A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.186A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.683A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.683A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.809A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.626A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.962A pdb=" N GLY C 90 " --> pdb=" O TYR C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.661A pdb=" N SER C 445 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA C 420 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 115 through 125 removed outlier: 5.355A pdb=" N THR C 138 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ARG C 118 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLN C 136 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU C 134 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL C 122 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR C 132 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS C 124 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG C 130 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 179 through 184 removed outlier: 5.707A pdb=" N TYR C 207 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 236 through 243 removed outlier: 3.562A pdb=" N LYS C 264 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 276 through 282 removed outlier: 5.472A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.186A pdb=" N TYR C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 393 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.809A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.626A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.961A pdb=" N GLY D 90 " --> pdb=" O TYR D 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.661A pdb=" N SER D 445 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA D 420 " --> pdb=" O SER D 448 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 115 through 125 removed outlier: 5.355A pdb=" N THR D 138 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ARG D 118 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN D 136 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU D 134 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL D 122 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR D 132 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS D 124 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG D 130 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 179 through 184 removed outlier: 5.708A pdb=" N TYR D 207 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 236 through 243 removed outlier: 3.562A pdb=" N LYS D 264 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 276 through 282 removed outlier: 5.472A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 353 through 354 removed outlier: 6.186A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.684A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.684A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.809A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.626A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1536 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: 3.78 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3542 1.31 - 1.44: 6109 1.44 - 1.57: 10419 1.57 - 1.70: 38 1.70 - 1.83: 152 Bond restraints: 20260 Sorted by residual: bond pdb=" NE1 TRP D 161 " pdb=" CE2 TRP D 161 " ideal model delta sigma weight residual 1.370 1.289 0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" NE1 TRP B 161 " pdb=" CE2 TRP B 161 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.34e+01 bond pdb=" NE1 TRP A 161 " pdb=" CE2 TRP A 161 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.23e+01 bond pdb=" NE1 TRP C 161 " pdb=" CE2 TRP C 161 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.22e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.70e+01 ... (remaining 20255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 21543 2.03 - 4.07: 4791 4.07 - 6.10: 986 6.10 - 8.13: 200 8.13 - 10.16: 64 Bond angle restraints: 27584 Sorted by residual: angle pdb=" C GLY B 196 " pdb=" N PRO B 197 " pdb=" CA PRO B 197 " ideal model delta sigma weight residual 120.21 129.48 -9.27 9.60e-01 1.09e+00 9.32e+01 angle pdb=" C GLY C 196 " pdb=" N PRO C 197 " pdb=" CA PRO C 197 " ideal model delta sigma weight residual 120.21 129.48 -9.27 9.60e-01 1.09e+00 9.32e+01 angle pdb=" C GLY A 196 " pdb=" N PRO A 197 " pdb=" CA PRO A 197 " ideal model delta sigma weight residual 120.21 129.45 -9.24 9.60e-01 1.09e+00 9.26e+01 angle pdb=" C GLY D 196 " pdb=" N PRO D 197 " pdb=" CA PRO D 197 " ideal model delta sigma weight residual 120.21 129.42 -9.21 9.60e-01 1.09e+00 9.20e+01 angle pdb=" C ASP D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta sigma weight residual 120.98 130.85 -9.87 1.07e+00 8.73e-01 8.50e+01 ... (remaining 27579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 11154 16.59 - 33.18: 402 33.18 - 49.78: 88 49.78 - 66.37: 36 66.37 - 82.96: 20 Dihedral angle restraints: 11700 sinusoidal: 4588 harmonic: 7112 Sorted by residual: dihedral pdb=" CB CYS C 318 " pdb=" SG CYS C 318 " pdb=" SG CYS C 337 " pdb=" CB CYS C 337 " ideal model delta sinusoidal sigma weight residual 93.00 132.99 -39.99 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 132.98 -39.98 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS B 337 " pdb=" CB CYS B 337 " ideal model delta sinusoidal sigma weight residual 93.00 132.98 -39.98 1 1.00e+01 1.00e-02 2.24e+01 ... (remaining 11697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2127 0.102 - 0.203: 821 0.203 - 0.305: 133 0.305 - 0.407: 31 0.407 - 0.508: 4 Chirality restraints: 3116 Sorted by residual: chirality pdb=" C1 MAN N 5 " pdb=" O2 MAN N 4 " pdb=" C2 MAN N 5 " pdb=" O5 MAN N 5 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.52e+01 chirality pdb=" C1 MAN P 5 " pdb=" O2 MAN P 4 " pdb=" C2 MAN P 5 " pdb=" O5 MAN P 5 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.43e+01 chirality pdb=" C1 MAN R 5 " pdb=" O2 MAN R 4 " pdb=" C2 MAN R 5 " pdb=" O5 MAN R 5 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-02 2.50e+03 5.10e+01 ... (remaining 3113 not shown) Planarity restraints: 3496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 155 " -0.071 2.00e-02 2.50e+03 3.82e-02 2.91e+01 pdb=" CG TYR B 155 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 155 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR B 155 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 155 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 155 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 155 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 155 " 0.071 2.00e-02 2.50e+03 3.81e-02 2.90e+01 pdb=" CG TYR D 155 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR D 155 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR D 155 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR D 155 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR D 155 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 155 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 155 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 155 " -0.071 2.00e-02 2.50e+03 3.81e-02 2.90e+01 pdb=" CG TYR C 155 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR C 155 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR C 155 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR C 155 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 155 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 155 " -0.057 2.00e-02 2.50e+03 ... (remaining 3493 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6213 2.81 - 3.33: 17785 3.33 - 3.86: 35678 3.86 - 4.38: 42645 4.38 - 4.90: 70420 Nonbonded interactions: 172741 Sorted by model distance: nonbonded pdb=" O ASN H 56 " pdb=" OG1 THR H 57 " model vdw 2.292 3.040 nonbonded pdb=" O ASN I 56 " pdb=" OG1 THR I 57 " model vdw 2.292 3.040 nonbonded pdb=" O ASN K 56 " pdb=" OG1 THR K 57 " model vdw 2.292 3.040 nonbonded pdb=" O ASN F 56 " pdb=" OG1 THR F 57 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR A 354 " pdb=" O CYS A 421 " model vdw 2.363 3.040 ... (remaining 172736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'L' selection = chain 'E' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'F' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } 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: 1.650 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 0.024 0.159 20352 Z= 1.297 Angle : 1.908 10.162 27816 Z= 1.235 Chirality : 0.108 0.508 3116 Planarity : 0.009 0.042 3484 Dihedral : 10.246 82.960 7040 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2440 helix: -0.45 (0.81), residues: 24 sheet: 0.79 (0.17), residues: 920 loop : 0.21 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 156 TYR 0.071 0.009 TYR B 155 PHE 0.029 0.008 PHE B 352 TRP 0.046 0.009 TRP L 35 HIS 0.018 0.003 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.02406 / 1.30 (20260) covalent geometry : angle 1.88540 / 1.23 (27584) SS BOND : bond 0.00815 / 0.56 ( 44) SS BOND : angle 3.01812 / 2.19 ( 88) hydrogen bonds : bond 0.16540 / 11.16 ( 628) hydrogen bonds : angle 8.20706 / 5.79 ( 1536) link_ALPHA1-2 : bond 0.04887 / 2.64 ( 8) link_ALPHA1-2 : angle 5.41699 / 3.42 ( 24) link_ALPHA1-3 : bond 0.03571 / 1.92 ( 8) link_ALPHA1-3 : angle 3.87202 / 2.49 ( 24) link_ALPHA1-6 : bond 0.03408 / 1.81 ( 8) link_ALPHA1-6 : angle 4.66752 / 3.16 ( 24) link_BETA1-4 : bond 0.03048 / 1.88 ( 12) link_BETA1-4 : angle 3.38444 / 2.20 ( 36) link_NAG-ASN : bond 0.03350 / 2.18 ( 12) link_NAG-ASN : angle 3.47394 / 2.45 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8263 (p) cc_final: 0.8037 (p) REVERT: B 168 THR cc_start: 0.8354 (p) cc_final: 0.8109 (p) REVERT: F 102 TYR cc_start: 0.8394 (m-80) cc_final: 0.7829 (m-80) REVERT: C 168 THR cc_start: 0.8339 (p) cc_final: 0.8100 (p) REVERT: D 168 THR cc_start: 0.8262 (p) cc_final: 0.8038 (p) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1665 time to fit residues: 102.5885 Evaluate side-chains 187 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 235 optimal weight: 5.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS A 226 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS B 226 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 226 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS D 226 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.058843 restraints weight = 58695.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.061055 restraints weight = 23962.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062428 restraints weight = 13106.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063308 restraints weight = 8601.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063818 restraints weight = 6451.147| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.004 0.032 20352 Z= 0.168 Angle : 0.793 9.176 27816 Z= 0.400 Chirality : 0.047 0.315 3116 Planarity : 0.005 0.059 3484 Dihedral : 5.401 21.294 2720 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.34 % Favored : 97.50 % Rotamer: Outliers : 1.75 % Allowed : 7.26 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.16), residues: 2440 helix: 1.02 (1.09), residues: 24 sheet: 0.39 (0.16), residues: 964 loop : -0.23 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 66 TYR 0.026 0.002 TYR G 36 PHE 0.021 0.002 PHE L 96 TRP 0.026 0.002 TRP A 206 HIS 0.003 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (20260) covalent geometry : angle 0.76710 / 0.40 (27584) SS BOND : bond 0.00180 / 0.12 ( 44) SS BOND : angle 0.85277 / 0.62 ( 88) hydrogen bonds : bond 0.04939 / 3.23 ( 628) hydrogen bonds : angle 6.64976 / 4.70 ( 1536) link_ALPHA1-2 : bond 0.01446 / 0.80 ( 8) link_ALPHA1-2 : angle 4.50022 / 2.97 ( 24) link_ALPHA1-3 : bond 0.00908 / 0.50 ( 8) link_ALPHA1-3 : angle 1.98544 / 1.35 ( 24) link_ALPHA1-6 : bond 0.01871 / 1.01 ( 8) link_ALPHA1-6 : angle 2.33933 / 1.64 ( 24) link_BETA1-4 : bond 0.00926 / 0.62 ( 12) link_BETA1-4 : angle 2.55062 / 1.69 ( 36) link_NAG-ASN : bond 0.00195 / 0.11 ( 12) link_NAG-ASN : angle 2.54316 / 1.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.9497 (mt) cc_final: 0.9249 (mm) REVERT: A 180 SER cc_start: 0.9281 (p) cc_final: 0.9045 (t) REVERT: A 310 MET cc_start: 0.8705 (ttm) cc_final: 0.8468 (mmm) REVERT: A 376 MET cc_start: 0.8699 (mmm) cc_final: 0.8484 (mmm) REVERT: A 446 MET cc_start: 0.9022 (mmm) cc_final: 0.8069 (mmm) REVERT: L 39 LYS cc_start: 0.9022 (mttt) cc_final: 0.8736 (mttp) REVERT: L 42 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8583 (mmmm) REVERT: L 55 GLN cc_start: 0.8103 (tp40) cc_final: 0.7681 (tp40) REVERT: L 89 GLN cc_start: 0.8682 (tt0) cc_final: 0.8385 (tm-30) REVERT: H 48 MET cc_start: 0.8563 (mmm) cc_final: 0.8362 (mmm) REVERT: H 69 MET cc_start: 0.8385 (mtt) cc_final: 0.7754 (mtt) REVERT: H 72 ASP cc_start: 0.8493 (t0) cc_final: 0.8244 (p0) REVERT: H 102 TYR cc_start: 0.8278 (m-80) cc_final: 0.7877 (m-80) REVERT: B 180 SER cc_start: 0.9259 (p) cc_final: 0.9022 (t) REVERT: B 310 MET cc_start: 0.8706 (ttm) cc_final: 0.8469 (mmm) REVERT: B 376 MET cc_start: 0.8711 (mmm) cc_final: 0.8490 (mmm) REVERT: B 446 MET cc_start: 0.9014 (mmm) cc_final: 0.8108 (mmm) REVERT: E 39 LYS cc_start: 0.9050 (mttt) cc_final: 0.8776 (mttp) REVERT: E 42 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8548 (mmmm) REVERT: E 55 GLN cc_start: 0.7986 (tp40) cc_final: 0.7666 (tp40) REVERT: E 89 GLN cc_start: 0.8655 (tt0) cc_final: 0.8331 (tm-30) REVERT: F 48 MET cc_start: 0.8569 (mmm) cc_final: 0.8363 (mmm) REVERT: F 69 MET cc_start: 0.8366 (mtt) cc_final: 0.7837 (mtt) REVERT: F 72 ASP cc_start: 0.8510 (t0) cc_final: 0.8263 (p0) REVERT: F 102 TYR cc_start: 0.8236 (m-80) cc_final: 0.7283 (m-80) REVERT: C 94 ILE cc_start: 0.9504 (mt) cc_final: 0.9261 (mm) REVERT: C 180 SER cc_start: 0.9279 (p) cc_final: 0.9052 (t) REVERT: C 310 MET cc_start: 0.8702 (ttm) cc_final: 0.8469 (mmm) REVERT: C 376 MET cc_start: 0.8720 (mmm) cc_final: 0.8506 (mmm) REVERT: C 446 MET cc_start: 0.9002 (mmm) cc_final: 0.8073 (mmm) REVERT: G 39 LYS cc_start: 0.9053 (mttt) cc_final: 0.8780 (mttp) REVERT: G 42 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8616 (mmmm) REVERT: G 55 GLN cc_start: 0.7953 (tp40) cc_final: 0.7713 (tp40) REVERT: G 89 GLN cc_start: 0.8662 (tt0) cc_final: 0.8340 (tm-30) REVERT: I 48 MET cc_start: 0.8561 (mmm) cc_final: 0.8358 (mmm) REVERT: I 69 MET cc_start: 0.8359 (mtt) cc_final: 0.7833 (mtt) REVERT: I 72 ASP cc_start: 0.8450 (t0) cc_final: 0.8186 (p0) REVERT: I 102 TYR cc_start: 0.8256 (m-80) cc_final: 0.7884 (m-80) REVERT: D 94 ILE cc_start: 0.9502 (mt) cc_final: 0.9258 (mm) REVERT: D 180 SER cc_start: 0.9290 (p) cc_final: 0.9057 (t) REVERT: D 310 MET cc_start: 0.8700 (ttm) cc_final: 0.8467 (mmm) REVERT: D 376 MET cc_start: 0.8727 (mmm) cc_final: 0.8509 (mmm) REVERT: D 446 MET cc_start: 0.9015 (mmm) cc_final: 0.8063 (mmm) REVERT: J 39 LYS cc_start: 0.9024 (mttt) cc_final: 0.8739 (mttp) REVERT: J 42 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8596 (mmmm) REVERT: J 55 GLN cc_start: 0.8064 (tp40) cc_final: 0.7721 (tp40) REVERT: J 89 GLN cc_start: 0.8685 (tt0) cc_final: 0.8393 (tm-30) REVERT: K 69 MET cc_start: 0.8359 (mtt) cc_final: 0.7832 (mtt) REVERT: K 72 ASP cc_start: 0.8446 (t0) cc_final: 0.8177 (p0) REVERT: K 102 TYR cc_start: 0.8252 (m-80) cc_final: 0.7841 (m-80) outliers start: 37 outliers final: 16 residues processed: 336 average time/residue: 0.1369 time to fit residues: 74.4709 Evaluate side-chains 252 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 142 optimal weight: 0.0050 chunk 54 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN L 37 GLN B 333 ASN B 441 ASN E 37 GLN C 333 ASN G 37 GLN D 333 ASN J 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.068349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054722 restraints weight = 60098.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056791 restraints weight = 24964.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058106 restraints weight = 13891.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058942 restraints weight = 9236.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.059428 restraints weight = 7008.107| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 20352 Z= 0.248 Angle : 0.737 9.733 27816 Z= 0.368 Chirality : 0.046 0.255 3116 Planarity : 0.005 0.045 3484 Dihedral : 5.131 22.546 2720 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 1.42 % Allowed : 9.91 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2440 helix: 0.26 (0.87), residues: 24 sheet: 0.29 (0.16), residues: 952 loop : -0.29 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 253 TYR 0.024 0.002 TYR E 36 PHE 0.025 0.002 PHE L 96 TRP 0.022 0.002 TRP C 206 HIS 0.005 0.002 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (20260) covalent geometry : angle 0.71492 / 0.36 (27584) SS BOND : bond 0.00754 / 0.59 ( 44) SS BOND : angle 0.87937 / 0.60 ( 88) hydrogen bonds : bond 0.04193 / 2.76 ( 628) hydrogen bonds : angle 6.26095 / 4.44 ( 1536) link_ALPHA1-2 : bond 0.01186 / 0.66 ( 8) link_ALPHA1-2 : angle 3.68903 / 2.44 ( 24) link_ALPHA1-3 : bond 0.00822 / 0.44 ( 8) link_ALPHA1-3 : angle 2.26744 / 1.55 ( 24) link_ALPHA1-6 : bond 0.01326 / 0.72 ( 8) link_ALPHA1-6 : angle 2.47116 / 1.76 ( 24) link_BETA1-4 : bond 0.00521 / 0.35 ( 12) link_BETA1-4 : angle 1.85063 / 1.28 ( 36) link_NAG-ASN : bond 0.00269 / 0.17 ( 12) link_NAG-ASN : angle 2.41438 / 1.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.776 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: L 70 ASP cc_start: 0.8509 (m-30) cc_final: 0.8118 (p0) REVERT: H 48 MET cc_start: 0.8502 (mmm) cc_final: 0.8283 (mmm) REVERT: H 69 MET cc_start: 0.8485 (mtt) cc_final: 0.7941 (mtt) REVERT: H 80 MET cc_start: 0.8472 (tmm) cc_final: 0.7780 (ppp) REVERT: H 102 TYR cc_start: 0.8598 (m-80) cc_final: 0.8250 (m-80) REVERT: E 70 ASP cc_start: 0.8476 (m-30) cc_final: 0.8094 (p0) REVERT: F 48 MET cc_start: 0.8506 (mmm) cc_final: 0.8291 (mmm) REVERT: F 69 MET cc_start: 0.8509 (mtt) cc_final: 0.7993 (mtt) REVERT: F 102 TYR cc_start: 0.8490 (m-80) cc_final: 0.8233 (m-80) REVERT: G 70 ASP cc_start: 0.8480 (m-30) cc_final: 0.8095 (p0) REVERT: I 48 MET cc_start: 0.8498 (mmm) cc_final: 0.8281 (mmm) REVERT: I 69 MET cc_start: 0.8492 (mtt) cc_final: 0.7951 (mtt) REVERT: I 80 MET cc_start: 0.8446 (tmm) cc_final: 0.7738 (ppp) REVERT: I 102 TYR cc_start: 0.8582 (m-80) cc_final: 0.8260 (m-80) REVERT: J 55 GLN cc_start: 0.8174 (tp40) cc_final: 0.7961 (tp40) REVERT: J 70 ASP cc_start: 0.8515 (m-30) cc_final: 0.8117 (p0) REVERT: K 69 MET cc_start: 0.8481 (mtt) cc_final: 0.7944 (mtt) REVERT: K 80 MET cc_start: 0.8460 (tmm) cc_final: 0.7777 (ppp) REVERT: K 102 TYR cc_start: 0.8597 (m-80) cc_final: 0.8248 (m-80) outliers start: 30 outliers final: 24 residues processed: 267 average time/residue: 0.1463 time to fit residues: 61.4321 Evaluate side-chains 204 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 163 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN F 61 GLN G 37 GLN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055962 restraints weight = 59212.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.058061 restraints weight = 24452.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059365 restraints weight = 13576.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060195 restraints weight = 9069.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.060689 restraints weight = 6917.712| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20352 Z= 0.160 Angle : 0.665 8.779 27816 Z= 0.331 Chirality : 0.045 0.184 3116 Planarity : 0.004 0.049 3484 Dihedral : 4.901 20.237 2720 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 1.93 % Allowed : 10.52 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2440 helix: -0.14 (0.77), residues: 24 sheet: 0.43 (0.17), residues: 916 loop : -0.41 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 284 TYR 0.018 0.002 TYR K 100C PHE 0.016 0.002 PHE G 96 TRP 0.026 0.002 TRP C 456 HIS 0.003 0.001 HIS D 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (20260) covalent geometry : angle 0.64243 / 0.33 (27584) SS BOND : bond 0.00192 / 0.13 ( 44) SS BOND : angle 0.90664 / 0.61 ( 88) hydrogen bonds : bond 0.03638 / 2.40 ( 628) hydrogen bonds : angle 6.05576 / 4.31 ( 1536) link_ALPHA1-2 : bond 0.01134 / 0.63 ( 8) link_ALPHA1-2 : angle 3.67417 / 2.37 ( 24) link_ALPHA1-3 : bond 0.00846 / 0.46 ( 8) link_ALPHA1-3 : angle 2.16198 / 1.45 ( 24) link_ALPHA1-6 : bond 0.01003 / 0.55 ( 8) link_ALPHA1-6 : angle 2.49980 / 1.85 ( 24) link_BETA1-4 : bond 0.00607 / 0.41 ( 12) link_BETA1-4 : angle 1.58368 / 1.07 ( 36) link_NAG-ASN : bond 0.00084 / 0.05 ( 12) link_NAG-ASN : angle 2.09548 / 1.38 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.837 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: L 37 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: L 42 LYS cc_start: 0.8749 (mmmm) cc_final: 0.7935 (mmmm) REVERT: L 70 ASP cc_start: 0.8481 (m-30) cc_final: 0.8120 (p0) REVERT: H 48 MET cc_start: 0.8548 (mmm) cc_final: 0.8336 (mmm) REVERT: H 69 MET cc_start: 0.8476 (mtt) cc_final: 0.7956 (mtt) REVERT: H 80 MET cc_start: 0.8397 (tmm) cc_final: 0.7625 (ppp) REVERT: H 102 TYR cc_start: 0.8492 (m-80) cc_final: 0.8173 (m-80) REVERT: B 411 MET cc_start: 0.8762 (mtm) cc_final: 0.8516 (mtp) REVERT: E 37 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: E 42 LYS cc_start: 0.8781 (mmmm) cc_final: 0.7958 (mmmm) REVERT: E 70 ASP cc_start: 0.8457 (m-30) cc_final: 0.8099 (p0) REVERT: E 74 THR cc_start: 0.9028 (t) cc_final: 0.8811 (m) REVERT: F 48 MET cc_start: 0.8573 (mmm) cc_final: 0.8361 (mmm) REVERT: F 69 MET cc_start: 0.8430 (mtt) cc_final: 0.7920 (mtt) REVERT: F 80 MET cc_start: 0.8367 (tmm) cc_final: 0.7840 (ppp) REVERT: F 102 TYR cc_start: 0.8616 (m-80) cc_final: 0.8382 (m-80) REVERT: C 411 MET cc_start: 0.8761 (mtm) cc_final: 0.8532 (mtp) REVERT: G 37 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: G 42 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8558 (mmmm) REVERT: G 70 ASP cc_start: 0.8460 (m-30) cc_final: 0.8099 (p0) REVERT: I 3 GLN cc_start: 0.8271 (mt0) cc_final: 0.8018 (mm110) REVERT: I 69 MET cc_start: 0.8451 (mtt) cc_final: 0.7939 (mtt) REVERT: I 80 MET cc_start: 0.8381 (tmm) cc_final: 0.7855 (ppp) REVERT: I 102 TYR cc_start: 0.8493 (m-80) cc_final: 0.8198 (m-80) REVERT: D 411 MET cc_start: 0.8763 (mtm) cc_final: 0.8555 (mtp) REVERT: J 37 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: J 42 LYS cc_start: 0.8752 (mmmm) cc_final: 0.7925 (mmmm) REVERT: J 70 ASP cc_start: 0.8461 (m-30) cc_final: 0.8099 (p0) REVERT: J 79 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6752 (pt0) REVERT: K 48 MET cc_start: 0.8586 (mmm) cc_final: 0.8333 (mmm) REVERT: K 69 MET cc_start: 0.8424 (mtt) cc_final: 0.7910 (mtt) REVERT: K 80 MET cc_start: 0.8405 (tmm) cc_final: 0.7658 (ppp) REVERT: K 102 TYR cc_start: 0.8495 (m-80) cc_final: 0.8186 (m-80) outliers start: 41 outliers final: 29 residues processed: 253 average time/residue: 0.1384 time to fit residues: 56.5472 Evaluate side-chains 223 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 138 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 221 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN L 79 GLN E 37 GLN E 79 GLN G 37 GLN G 79 GLN J 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056232 restraints weight = 58704.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058325 restraints weight = 24320.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059644 restraints weight = 13438.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060464 restraints weight = 8936.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.061006 restraints weight = 6789.240| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20352 Z= 0.133 Angle : 0.624 6.852 27816 Z= 0.314 Chirality : 0.044 0.155 3116 Planarity : 0.004 0.048 3484 Dihedral : 4.754 20.305 2720 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 2.31 % Allowed : 10.90 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2440 helix: -0.63 (0.70), residues: 24 sheet: 0.46 (0.17), residues: 920 loop : -0.41 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 284 TYR 0.020 0.002 TYR J 92 PHE 0.013 0.001 PHE J 96 TRP 0.027 0.001 TRP B 456 HIS 0.003 0.001 HIS D 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (20260) covalent geometry : angle 0.60316 / 0.31 (27584) SS BOND : bond 0.00165 / 0.11 ( 44) SS BOND : angle 0.79608 / 0.54 ( 88) hydrogen bonds : bond 0.03407 / 2.25 ( 628) hydrogen bonds : angle 5.84683 / 4.16 ( 1536) link_ALPHA1-2 : bond 0.01111 / 0.62 ( 8) link_ALPHA1-2 : angle 3.50913 / 2.26 ( 24) link_ALPHA1-3 : bond 0.00780 / 0.43 ( 8) link_ALPHA1-3 : angle 2.20642 / 1.48 ( 24) link_ALPHA1-6 : bond 0.00734 / 0.40 ( 8) link_ALPHA1-6 : angle 2.06637 / 1.48 ( 24) link_BETA1-4 : bond 0.00575 / 0.38 ( 12) link_BETA1-4 : angle 1.52229 / 1.03 ( 36) link_NAG-ASN : bond 0.00034 / 0.03 ( 12) link_NAG-ASN : angle 1.95893 / 1.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.730 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: L 6 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: L 70 ASP cc_start: 0.8463 (m-30) cc_final: 0.8103 (p0) REVERT: L 74 THR cc_start: 0.9070 (t) cc_final: 0.8822 (m) REVERT: L 79 GLN cc_start: 0.7631 (pt0) cc_final: 0.7391 (pt0) REVERT: H 69 MET cc_start: 0.8473 (mtt) cc_final: 0.8064 (mmt) REVERT: H 80 MET cc_start: 0.8364 (tmm) cc_final: 0.7731 (ppp) REVERT: H 102 TYR cc_start: 0.8567 (m-80) cc_final: 0.8278 (m-80) REVERT: E 6 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7286 (mt0) REVERT: E 70 ASP cc_start: 0.8458 (m-30) cc_final: 0.8020 (p0) REVERT: E 74 THR cc_start: 0.9060 (t) cc_final: 0.8829 (m) REVERT: E 79 GLN cc_start: 0.7725 (pt0) cc_final: 0.7380 (pt0) REVERT: F 69 MET cc_start: 0.8432 (mtt) cc_final: 0.8009 (mmt) REVERT: F 80 MET cc_start: 0.8312 (tmm) cc_final: 0.7874 (ppp) REVERT: F 102 TYR cc_start: 0.8568 (m-80) cc_final: 0.8364 (m-80) REVERT: G 6 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: G 38 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8474 (tm-30) REVERT: G 70 ASP cc_start: 0.8404 (m-30) cc_final: 0.8029 (p0) REVERT: G 74 THR cc_start: 0.9036 (t) cc_final: 0.8798 (m) REVERT: G 79 GLN cc_start: 0.7512 (pt0) cc_final: 0.7236 (pt0) REVERT: I 3 GLN cc_start: 0.8380 (mt0) cc_final: 0.8093 (mm110) REVERT: I 48 MET cc_start: 0.8610 (mmm) cc_final: 0.8379 (mmm) REVERT: I 69 MET cc_start: 0.8417 (mtt) cc_final: 0.8052 (mmt) REVERT: I 80 MET cc_start: 0.8322 (tmm) cc_final: 0.7871 (ppp) REVERT: I 102 TYR cc_start: 0.8583 (m-80) cc_final: 0.8304 (m-80) REVERT: J 6 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: J 55 GLN cc_start: 0.8247 (tp40) cc_final: 0.7963 (tp40) REVERT: J 70 ASP cc_start: 0.8396 (m-30) cc_final: 0.8033 (p0) REVERT: K 48 MET cc_start: 0.8710 (mmm) cc_final: 0.8474 (mmm) REVERT: K 69 MET cc_start: 0.8392 (mtt) cc_final: 0.8045 (mmt) REVERT: K 80 MET cc_start: 0.8342 (tmm) cc_final: 0.7709 (ppp) REVERT: K 102 TYR cc_start: 0.8562 (m-80) cc_final: 0.8276 (m-80) outliers start: 49 outliers final: 38 residues processed: 266 average time/residue: 0.1443 time to fit residues: 61.2117 Evaluate side-chains 245 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN E 37 GLN G 37 GLN J 37 GLN ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.070045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.056495 restraints weight = 58437.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058594 restraints weight = 24296.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059928 restraints weight = 13416.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060768 restraints weight = 8867.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.061276 restraints weight = 6683.777| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20352 Z= 0.133 Angle : 0.618 6.898 27816 Z= 0.309 Chirality : 0.044 0.154 3116 Planarity : 0.004 0.046 3484 Dihedral : 4.659 20.124 2720 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.94 % Rotamer: Outliers : 2.03 % Allowed : 11.65 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2440 helix: -0.88 (0.71), residues: 24 sheet: 0.36 (0.17), residues: 928 loop : -0.46 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 61 TYR 0.018 0.001 TYR D 423 PHE 0.011 0.001 PHE E 96 TRP 0.023 0.001 TRP B 456 HIS 0.002 0.001 HIS D 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (20260) covalent geometry : angle 0.59911 / 0.30 (27584) SS BOND : bond 0.00217 / 0.15 ( 44) SS BOND : angle 0.75696 / 0.51 ( 88) hydrogen bonds : bond 0.03269 / 2.17 ( 628) hydrogen bonds : angle 5.74479 / 4.09 ( 1536) link_ALPHA1-2 : bond 0.01043 / 0.58 ( 8) link_ALPHA1-2 : angle 3.37847 / 2.17 ( 24) link_ALPHA1-3 : bond 0.00704 / 0.39 ( 8) link_ALPHA1-3 : angle 2.26737 / 1.54 ( 24) link_ALPHA1-6 : bond 0.00721 / 0.39 ( 8) link_ALPHA1-6 : angle 1.75540 / 1.23 ( 24) link_BETA1-4 : bond 0.00579 / 0.39 ( 12) link_BETA1-4 : angle 1.49833 / 1.01 ( 36) link_NAG-ASN : bond 0.00032 / 0.02 ( 12) link_NAG-ASN : angle 1.83565 / 1.23 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.741 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: L 70 ASP cc_start: 0.8464 (m-30) cc_final: 0.7978 (p0) REVERT: H 48 MET cc_start: 0.8634 (mmm) cc_final: 0.8415 (mmm) REVERT: H 69 MET cc_start: 0.8457 (mtt) cc_final: 0.8026 (mmt) REVERT: H 80 MET cc_start: 0.8352 (tmm) cc_final: 0.7873 (ppp) REVERT: H 102 TYR cc_start: 0.8630 (m-80) cc_final: 0.8345 (m-80) REVERT: E 70 ASP cc_start: 0.8456 (m-30) cc_final: 0.7976 (p0) REVERT: F 48 MET cc_start: 0.8613 (mmm) cc_final: 0.8393 (mmm) REVERT: F 69 MET cc_start: 0.8424 (mtt) cc_final: 0.7995 (mmt) REVERT: F 80 MET cc_start: 0.8322 (tmm) cc_final: 0.7835 (ppp) REVERT: F 102 TYR cc_start: 0.8584 (m-80) cc_final: 0.8362 (m-80) REVERT: G 6 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: G 42 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8381 (mppt) REVERT: G 70 ASP cc_start: 0.8407 (m-30) cc_final: 0.7984 (p0) REVERT: I 3 GLN cc_start: 0.8408 (mt0) cc_final: 0.8139 (mm110) REVERT: I 48 MET cc_start: 0.8660 (mmm) cc_final: 0.8421 (mmm) REVERT: I 69 MET cc_start: 0.8419 (mtt) cc_final: 0.8055 (mmt) REVERT: I 80 MET cc_start: 0.8333 (tmm) cc_final: 0.7818 (ppp) REVERT: I 102 TYR cc_start: 0.8624 (m-80) cc_final: 0.8339 (m-80) REVERT: J 37 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: J 70 ASP cc_start: 0.8457 (m-30) cc_final: 0.7971 (p0) REVERT: K 48 MET cc_start: 0.8692 (mmm) cc_final: 0.8464 (mmm) REVERT: K 69 MET cc_start: 0.8413 (mtt) cc_final: 0.8052 (mmt) REVERT: K 80 MET cc_start: 0.8359 (tmm) cc_final: 0.7872 (ppp) REVERT: K 102 TYR cc_start: 0.8630 (m-80) cc_final: 0.8350 (m-80) outliers start: 43 outliers final: 28 residues processed: 262 average time/residue: 0.1375 time to fit residues: 56.7053 Evaluate side-chains 221 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 218 optimal weight: 0.0170 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 220 optimal weight: 0.5980 chunk 165 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN J 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056354 restraints weight = 58898.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058435 restraints weight = 24440.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059761 restraints weight = 13501.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060589 restraints weight = 8936.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.061094 restraints weight = 6756.969| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20352 Z= 0.139 Angle : 0.621 6.914 27816 Z= 0.311 Chirality : 0.044 0.210 3116 Planarity : 0.004 0.049 3484 Dihedral : 4.613 20.508 2720 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.81 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 12.78 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2440 helix: -1.03 (0.68), residues: 24 sheet: 0.35 (0.17), residues: 932 loop : -0.48 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.030 0.002 TYR F 27 PHE 0.033 0.002 PHE L 62 TRP 0.021 0.001 TRP B 456 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (20260) covalent geometry : angle 0.60232 / 0.31 (27584) SS BOND : bond 0.00248 / 0.18 ( 44) SS BOND : angle 0.91693 / 0.61 ( 88) hydrogen bonds : bond 0.03256 / 2.16 ( 628) hydrogen bonds : angle 5.60512 / 4.00 ( 1536) link_ALPHA1-2 : bond 0.00987 / 0.55 ( 8) link_ALPHA1-2 : angle 3.28172 / 2.10 ( 24) link_ALPHA1-3 : bond 0.00661 / 0.36 ( 8) link_ALPHA1-3 : angle 2.24619 / 1.53 ( 24) link_ALPHA1-6 : bond 0.00684 / 0.37 ( 8) link_ALPHA1-6 : angle 1.74275 / 1.22 ( 24) link_BETA1-4 : bond 0.00516 / 0.35 ( 12) link_BETA1-4 : angle 1.47907 / 1.00 ( 36) link_NAG-ASN : bond 0.00044 / 0.03 ( 12) link_NAG-ASN : angle 1.83159 / 1.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.794 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: L 55 GLN cc_start: 0.8185 (tp40) cc_final: 0.7876 (tp40) REVERT: L 70 ASP cc_start: 0.8406 (m-30) cc_final: 0.7978 (p0) REVERT: H 48 MET cc_start: 0.8611 (mmm) cc_final: 0.8382 (mmm) REVERT: H 69 MET cc_start: 0.8447 (mtt) cc_final: 0.8005 (mmt) REVERT: H 100 TYR cc_start: 0.6350 (t80) cc_final: 0.5913 (t80) REVERT: H 102 TYR cc_start: 0.8659 (m-80) cc_final: 0.8363 (m-80) REVERT: E 17 ASP cc_start: 0.8019 (m-30) cc_final: 0.7743 (m-30) REVERT: E 70 ASP cc_start: 0.8410 (m-30) cc_final: 0.7985 (p0) REVERT: F 48 MET cc_start: 0.8629 (mmm) cc_final: 0.8397 (mmm) REVERT: F 69 MET cc_start: 0.8418 (mtt) cc_final: 0.7982 (mmt) REVERT: F 102 TYR cc_start: 0.8623 (m-80) cc_final: 0.8375 (m-80) REVERT: G 38 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8485 (tm-30) REVERT: G 70 ASP cc_start: 0.8460 (m-30) cc_final: 0.7960 (p0) REVERT: I 48 MET cc_start: 0.8705 (mmm) cc_final: 0.8467 (mmm) REVERT: I 69 MET cc_start: 0.8422 (mtt) cc_final: 0.7987 (mmt) REVERT: I 102 TYR cc_start: 0.8667 (m-80) cc_final: 0.8372 (m-80) REVERT: J 70 ASP cc_start: 0.8411 (m-30) cc_final: 0.7984 (p0) REVERT: J 74 THR cc_start: 0.9373 (m) cc_final: 0.9090 (p) REVERT: K 48 MET cc_start: 0.8693 (mmm) cc_final: 0.8468 (mmm) REVERT: K 69 MET cc_start: 0.8419 (mtt) cc_final: 0.8049 (mmt) REVERT: K 102 TYR cc_start: 0.8647 (m-80) cc_final: 0.8351 (m-80) outliers start: 44 outliers final: 36 residues processed: 247 average time/residue: 0.1315 time to fit residues: 53.3116 Evaluate side-chains 227 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055913 restraints weight = 59356.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057983 restraints weight = 24582.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.059298 restraints weight = 13579.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060126 restraints weight = 9024.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060616 restraints weight = 6825.719| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20352 Z= 0.153 Angle : 0.629 6.749 27816 Z= 0.314 Chirality : 0.044 0.163 3116 Planarity : 0.004 0.049 3484 Dihedral : 4.616 20.427 2720 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.73 % Favored : 96.11 % Rotamer: Outliers : 2.22 % Allowed : 12.88 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2440 helix: -1.20 (0.63), residues: 24 sheet: 0.49 (0.17), residues: 888 loop : -0.58 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 18 TYR 0.030 0.002 TYR I 27 PHE 0.023 0.002 PHE G 62 TRP 0.021 0.002 TRP C 456 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (20260) covalent geometry : angle 0.61134 / 0.31 (27584) SS BOND : bond 0.00198 / 0.13 ( 44) SS BOND : angle 0.89947 / 0.60 ( 88) hydrogen bonds : bond 0.03220 / 2.15 ( 628) hydrogen bonds : angle 5.58654 / 3.99 ( 1536) link_ALPHA1-2 : bond 0.00952 / 0.53 ( 8) link_ALPHA1-2 : angle 3.19460 / 2.02 ( 24) link_ALPHA1-3 : bond 0.00638 / 0.35 ( 8) link_ALPHA1-3 : angle 2.24402 / 1.53 ( 24) link_ALPHA1-6 : bond 0.00669 / 0.37 ( 8) link_ALPHA1-6 : angle 1.75836 / 1.23 ( 24) link_BETA1-4 : bond 0.00507 / 0.34 ( 12) link_BETA1-4 : angle 1.46879 / 1.00 ( 36) link_NAG-ASN : bond 0.00084 / 0.05 ( 12) link_NAG-ASN : angle 1.83507 / 1.25 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9157 (mmm) cc_final: 0.8225 (mmm) REVERT: L 17 ASP cc_start: 0.8124 (m-30) cc_final: 0.7847 (m-30) REVERT: L 70 ASP cc_start: 0.8399 (m-30) cc_final: 0.7961 (p0) REVERT: H 48 MET cc_start: 0.8693 (mmm) cc_final: 0.8475 (mmm) REVERT: H 69 MET cc_start: 0.8442 (mtt) cc_final: 0.8007 (mmt) REVERT: H 100 TYR cc_start: 0.6372 (t80) cc_final: 0.6140 (t80) REVERT: H 102 TYR cc_start: 0.8689 (m-80) cc_final: 0.8381 (m-80) REVERT: B 446 MET cc_start: 0.9146 (mmm) cc_final: 0.8226 (mmm) REVERT: E 17 ASP cc_start: 0.8024 (m-30) cc_final: 0.7744 (m-30) REVERT: E 70 ASP cc_start: 0.8405 (m-30) cc_final: 0.7959 (p0) REVERT: E 103 LYS cc_start: 0.9042 (tttt) cc_final: 0.8781 (ttpp) REVERT: F 48 MET cc_start: 0.8690 (mmm) cc_final: 0.8473 (mmm) REVERT: F 69 MET cc_start: 0.8395 (mtt) cc_final: 0.7939 (mmt) REVERT: F 102 TYR cc_start: 0.8659 (m-80) cc_final: 0.8407 (m-80) REVERT: C 446 MET cc_start: 0.9153 (mmm) cc_final: 0.8217 (mmm) REVERT: G 17 ASP cc_start: 0.8091 (m-30) cc_final: 0.7854 (m-30) REVERT: G 38 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8378 (tm-30) REVERT: G 70 ASP cc_start: 0.8400 (m-30) cc_final: 0.7959 (p0) REVERT: I 48 MET cc_start: 0.8733 (mmm) cc_final: 0.8503 (mmm) REVERT: I 69 MET cc_start: 0.8400 (mtt) cc_final: 0.7956 (mmt) REVERT: I 80 MET cc_start: 0.8255 (tmm) cc_final: 0.7461 (ppp) REVERT: I 102 TYR cc_start: 0.8670 (m-80) cc_final: 0.8352 (m-80) REVERT: D 446 MET cc_start: 0.9153 (mmm) cc_final: 0.8218 (mmm) REVERT: J 17 ASP cc_start: 0.8216 (m-30) cc_final: 0.7966 (m-30) REVERT: J 70 ASP cc_start: 0.8403 (m-30) cc_final: 0.7956 (p0) REVERT: J 74 THR cc_start: 0.9389 (m) cc_final: 0.9099 (p) REVERT: K 48 MET cc_start: 0.8692 (mmm) cc_final: 0.8482 (mmm) REVERT: K 69 MET cc_start: 0.8405 (mtt) cc_final: 0.7978 (mmt) REVERT: K 102 TYR cc_start: 0.8650 (m-80) cc_final: 0.8359 (m-80) outliers start: 47 outliers final: 37 residues processed: 248 average time/residue: 0.1323 time to fit residues: 52.9285 Evaluate side-chains 221 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 176 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.055290 restraints weight = 59352.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.057302 restraints weight = 24993.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.058586 restraints weight = 13953.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.059400 restraints weight = 9305.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.059922 restraints weight = 7079.892| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20352 Z= 0.182 Angle : 0.657 7.061 27816 Z= 0.328 Chirality : 0.045 0.168 3116 Planarity : 0.004 0.050 3484 Dihedral : 4.673 20.189 2720 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 2.22 % Allowed : 12.74 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2440 helix: -1.31 (0.59), residues: 24 sheet: 0.25 (0.17), residues: 972 loop : -0.46 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 284 TYR 0.021 0.002 TYR B 155 PHE 0.020 0.002 PHE J 62 TRP 0.023 0.002 TRP A 456 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (20260) covalent geometry : angle 0.64012 / 0.32 (27584) SS BOND : bond 0.00301 / 0.22 ( 44) SS BOND : angle 0.89457 / 0.60 ( 88) hydrogen bonds : bond 0.03323 / 2.22 ( 628) hydrogen bonds : angle 5.59811 / 4.00 ( 1536) link_ALPHA1-2 : bond 0.01004 / 0.56 ( 8) link_ALPHA1-2 : angle 3.09700 / 1.95 ( 24) link_ALPHA1-3 : bond 0.00598 / 0.33 ( 8) link_ALPHA1-3 : angle 2.28268 / 1.56 ( 24) link_ALPHA1-6 : bond 0.00636 / 0.34 ( 8) link_ALPHA1-6 : angle 1.84368 / 1.27 ( 24) link_BETA1-4 : bond 0.00470 / 0.32 ( 12) link_BETA1-4 : angle 1.46945 / 1.00 ( 36) link_NAG-ASN : bond 0.00178 / 0.11 ( 12) link_NAG-ASN : angle 1.90712 / 1.32 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7725 (ttm-80) REVERT: A 446 MET cc_start: 0.9174 (mmm) cc_final: 0.8234 (mmm) REVERT: L 17 ASP cc_start: 0.7996 (m-30) cc_final: 0.7714 (m-30) REVERT: L 70 ASP cc_start: 0.8407 (m-30) cc_final: 0.7940 (p0) REVERT: H 48 MET cc_start: 0.8728 (mmm) cc_final: 0.8505 (mmm) REVERT: H 69 MET cc_start: 0.8444 (mtt) cc_final: 0.7970 (mtt) REVERT: H 80 MET cc_start: 0.8300 (tmm) cc_final: 0.7418 (ppp) REVERT: H 102 TYR cc_start: 0.8728 (m-80) cc_final: 0.8401 (m-80) REVERT: B 446 MET cc_start: 0.9164 (mmm) cc_final: 0.8235 (mmm) REVERT: E 17 ASP cc_start: 0.8048 (m-30) cc_final: 0.7750 (m-30) REVERT: E 70 ASP cc_start: 0.8417 (m-30) cc_final: 0.7940 (p0) REVERT: F 48 MET cc_start: 0.8743 (mmm) cc_final: 0.8527 (mmm) REVERT: F 69 MET cc_start: 0.8390 (mtt) cc_final: 0.7941 (mtt) REVERT: F 102 TYR cc_start: 0.8679 (m-80) cc_final: 0.8420 (m-80) REVERT: C 156 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7691 (ttm-80) REVERT: C 446 MET cc_start: 0.9167 (mmm) cc_final: 0.8227 (mmm) REVERT: G 17 ASP cc_start: 0.8037 (m-30) cc_final: 0.7775 (m-30) REVERT: G 38 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8462 (tm-30) REVERT: G 70 ASP cc_start: 0.8420 (m-30) cc_final: 0.7940 (p0) REVERT: I 48 MET cc_start: 0.8735 (mmm) cc_final: 0.8517 (mmm) REVERT: I 69 MET cc_start: 0.8395 (mtt) cc_final: 0.7941 (mmt) REVERT: I 102 TYR cc_start: 0.8727 (m-80) cc_final: 0.8377 (m-80) REVERT: D 446 MET cc_start: 0.9169 (mmm) cc_final: 0.8230 (mmm) REVERT: J 17 ASP cc_start: 0.8036 (m-30) cc_final: 0.7768 (m-30) REVERT: J 37 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: J 70 ASP cc_start: 0.8420 (m-30) cc_final: 0.7952 (p0) REVERT: J 74 THR cc_start: 0.9386 (m) cc_final: 0.9044 (p) REVERT: K 69 MET cc_start: 0.8390 (mtt) cc_final: 0.7955 (mmt) REVERT: K 80 MET cc_start: 0.8243 (tmm) cc_final: 0.7447 (ppp) REVERT: K 102 TYR cc_start: 0.8727 (m-80) cc_final: 0.8396 (m-80) outliers start: 47 outliers final: 39 residues processed: 231 average time/residue: 0.1385 time to fit residues: 51.4674 Evaluate side-chains 221 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS G 37 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.066216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052825 restraints weight = 61283.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054757 restraints weight = 25482.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055998 restraints weight = 14230.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.056789 restraints weight = 9517.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.057300 restraints weight = 7260.941| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 20352 Z= 0.369 Angle : 0.807 10.143 27816 Z= 0.401 Chirality : 0.049 0.203 3116 Planarity : 0.005 0.058 3484 Dihedral : 5.217 24.532 2720 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.23 % Favored : 93.61 % Rotamer: Outliers : 2.12 % Allowed : 13.21 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2440 helix: -1.15 (0.72), residues: 24 sheet: -0.03 (0.16), residues: 964 loop : -0.72 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 253 TYR 0.023 0.002 TYR B 155 PHE 0.017 0.002 PHE J 62 TRP 0.035 0.003 TRP A 456 HIS 0.008 0.002 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.37 (20260) covalent geometry : angle 0.78938 / 0.40 (27584) SS BOND : bond 0.00419 / 0.29 ( 44) SS BOND : angle 0.93035 / 0.62 ( 88) hydrogen bonds : bond 0.04194 / 2.82 ( 628) hydrogen bonds : angle 5.90282 / 4.22 ( 1536) link_ALPHA1-2 : bond 0.01201 / 0.67 ( 8) link_ALPHA1-2 : angle 3.11783 / 1.96 ( 24) link_ALPHA1-3 : bond 0.00474 / 0.25 ( 8) link_ALPHA1-3 : angle 2.70166 / 1.85 ( 24) link_ALPHA1-6 : bond 0.00413 / 0.23 ( 8) link_ALPHA1-6 : angle 2.34818 / 1.57 ( 24) link_BETA1-4 : bond 0.00411 / 0.27 ( 12) link_BETA1-4 : angle 1.65399 / 1.15 ( 36) link_NAG-ASN : bond 0.00702 / 0.45 ( 12) link_NAG-ASN : angle 2.49070 / 1.75 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9199 (mmm) cc_final: 0.8876 (mmm) REVERT: L 17 ASP cc_start: 0.7979 (m-30) cc_final: 0.7728 (m-30) REVERT: H 69 MET cc_start: 0.8493 (mtt) cc_final: 0.8022 (mtt) REVERT: H 102 TYR cc_start: 0.8783 (m-80) cc_final: 0.8428 (m-80) REVERT: B 446 MET cc_start: 0.9192 (mmm) cc_final: 0.8873 (mmm) REVERT: E 17 ASP cc_start: 0.8029 (m-30) cc_final: 0.7780 (m-30) REVERT: E 103 LYS cc_start: 0.9119 (tttt) cc_final: 0.8832 (tttm) REVERT: F 69 MET cc_start: 0.8462 (mtt) cc_final: 0.7998 (mtt) REVERT: F 102 TYR cc_start: 0.8721 (m-80) cc_final: 0.8415 (m-80) REVERT: C 446 MET cc_start: 0.9192 (mmm) cc_final: 0.8853 (mmm) REVERT: G 17 ASP cc_start: 0.8112 (m-30) cc_final: 0.7862 (m-30) REVERT: I 69 MET cc_start: 0.8402 (mtt) cc_final: 0.7941 (mtt) REVERT: I 102 TYR cc_start: 0.8781 (m-80) cc_final: 0.8412 (m-80) REVERT: D 446 MET cc_start: 0.9198 (mmm) cc_final: 0.8863 (mmm) REVERT: J 17 ASP cc_start: 0.8071 (m-30) cc_final: 0.7816 (m-30) REVERT: J 37 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: J 74 THR cc_start: 0.9371 (m) cc_final: 0.9024 (p) REVERT: K 69 MET cc_start: 0.8435 (mtt) cc_final: 0.7970 (mtt) REVERT: K 80 MET cc_start: 0.8168 (tmm) cc_final: 0.7226 (ppp) REVERT: K 102 TYR cc_start: 0.8768 (m-80) cc_final: 0.8405 (m-80) outliers start: 45 outliers final: 44 residues processed: 210 average time/residue: 0.1466 time to fit residues: 49.2100 Evaluate side-chains 207 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 48 optimal weight: 5.9990 chunk 128 optimal weight: 0.0060 chunk 187 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 79 GLN E 6 GLN G 37 GLN J 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.068996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055580 restraints weight = 59699.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057630 restraints weight = 24474.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058930 restraints weight = 13313.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.059757 restraints weight = 8755.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060245 restraints weight = 6588.455| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20352 Z= 0.140 Angle : 0.675 12.849 27816 Z= 0.334 Chirality : 0.045 0.164 3116 Planarity : 0.004 0.052 3484 Dihedral : 4.882 23.824 2720 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 1.84 % Allowed : 13.68 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2440 helix: -1.28 (0.55), residues: 24 sheet: 0.42 (0.17), residues: 904 loop : -0.81 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.018 0.002 TYR E 36 PHE 0.022 0.002 PHE L 62 TRP 0.021 0.002 TRP A 456 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (20260) covalent geometry : angle 0.65984 / 0.33 (27584) SS BOND : bond 0.00219 / 0.15 ( 44) SS BOND : angle 0.77904 / 0.53 ( 88) hydrogen bonds : bond 0.03319 / 2.21 ( 628) hydrogen bonds : angle 5.78061 / 4.14 ( 1536) link_ALPHA1-2 : bond 0.01082 / 0.60 ( 8) link_ALPHA1-2 : angle 3.08081 / 1.84 ( 24) link_ALPHA1-3 : bond 0.00751 / 0.41 ( 8) link_ALPHA1-3 : angle 2.35740 / 1.57 ( 24) link_ALPHA1-6 : bond 0.00684 / 0.37 ( 8) link_ALPHA1-6 : angle 1.68076 / 1.18 ( 24) link_BETA1-4 : bond 0.00586 / 0.39 ( 12) link_BETA1-4 : angle 1.38528 / 0.94 ( 36) link_NAG-ASN : bond 0.00042 / 0.03 ( 12) link_NAG-ASN : angle 1.71278 / 1.16 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.25 seconds wall clock time: 56 minutes 21.91 seconds (3381.91 seconds total)