Starting phenix.real_space_refine on Wed Nov 19 02:44:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pzz_20541/11_2025/6pzz_20541.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzz_20541/11_2025/6pzz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pzz_20541/11_2025/6pzz_20541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzz_20541/11_2025/6pzz_20541.map" model { file = "/net/cci-nas-00/data/ceres_data/6pzz_20541/11_2025/6pzz_20541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzz_20541/11_2025/6pzz_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-2.0-5881/lib/python3.9/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 dihedrals: 6 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 dihedrals: 27 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 dihedrals: 3 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: 3.88, 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: 2.05 Conformation dependent library (CDL) restraints added in 886.3 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: 0.93 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: 4.31 Time building geometry restraints manager: 2.65 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 - 21.52: 12174 21.52 - 43.03: 358 43.03 - 64.55: 60 64.55 - 86.07: 44 86.07 - 107.58: 16 Dihedral angle restraints: 12652 sinusoidal: 5540 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 12649 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: 1.680 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 12.057 107.584 7992 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 covalent geometry : bond 0.02406 (20260) covalent geometry : angle 1.88540 (27584) SS BOND : bond 0.00815 ( 44) SS BOND : angle 3.01812 ( 88) hydrogen bonds : bond 0.16540 ( 628) hydrogen bonds : angle 8.20706 ( 1536) link_ALPHA1-2 : bond 0.04887 ( 8) link_ALPHA1-2 : angle 5.41699 ( 24) link_ALPHA1-3 : bond 0.03571 ( 8) link_ALPHA1-3 : angle 3.87202 ( 24) link_ALPHA1-6 : bond 0.03408 ( 8) link_ALPHA1-6 : angle 4.66752 ( 24) link_BETA1-4 : bond 0.03048 ( 12) link_BETA1-4 : angle 3.38444 ( 36) link_NAG-ASN : bond 0.03350 ( 12) link_NAG-ASN : angle 3.47394 ( 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 : 0.776 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: 0.8338 (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: 0.1685 time to fit residues: 102.6312 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 : 0.685 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3297 r_free = 0.3297 target = 0.072502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058944 restraints weight = 58654.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061152 restraints weight = 23998.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.062531 restraints weight = 13167.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063357 restraints weight = 8654.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063945 restraints weight = 6552.858| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20352 Z= 0.163 Angle : 0.788 8.809 27816 Z= 0.396 Chirality : 0.048 0.323 3116 Planarity : 0.005 0.051 3484 Dihedral : 9.108 72.973 3672 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.84 % Favored : 97.99 % Rotamer: Outliers : 1.70 % Allowed : 7.45 % Favored : 90.85 % 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: -0.01 (0.16), residues: 2440 helix: 0.95 (1.09), residues: 24 sheet: 0.39 (0.16), residues: 964 loop : -0.24 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.027 0.002 TYR G 36 PHE 0.019 0.002 PHE J 96 TRP 0.027 0.002 TRP A 206 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00340 (20260) covalent geometry : angle 0.76371 (27584) SS BOND : bond 0.00201 ( 44) SS BOND : angle 0.85259 ( 88) hydrogen bonds : bond 0.04723 ( 628) hydrogen bonds : angle 6.62091 ( 1536) link_ALPHA1-2 : bond 0.01557 ( 8) link_ALPHA1-2 : angle 4.45489 ( 24) link_ALPHA1-3 : bond 0.01500 ( 8) link_ALPHA1-3 : angle 1.88922 ( 24) link_ALPHA1-6 : bond 0.02058 ( 8) link_ALPHA1-6 : angle 1.98812 ( 24) link_BETA1-4 : bond 0.00960 ( 12) link_BETA1-4 : angle 2.62343 ( 36) link_NAG-ASN : bond 0.00149 ( 12) link_NAG-ASN : angle 2.52930 ( 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 350 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 314 time to evaluate : 0.728 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 180 SER cc_start: 0.9282 (p) cc_final: 0.9017 (t) REVERT: A 310 MET cc_start: 0.8750 (ttm) cc_final: 0.8466 (mmm) REVERT: A 376 MET cc_start: 0.8709 (mmm) cc_final: 0.8481 (mmm) REVERT: A 446 MET cc_start: 0.9002 (mmm) cc_final: 0.8056 (mmm) REVERT: L 39 LYS cc_start: 0.9028 (mttt) cc_final: 0.8758 (mttp) REVERT: L 42 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8653 (mmmm) REVERT: L 55 GLN cc_start: 0.8086 (tp40) cc_final: 0.7677 (tp40) REVERT: L 89 GLN cc_start: 0.8634 (tt0) cc_final: 0.8304 (tm-30) REVERT: H 69 MET cc_start: 0.8397 (mtt) cc_final: 0.7768 (mtt) REVERT: H 72 ASP cc_start: 0.8524 (t0) cc_final: 0.8255 (p0) REVERT: H 102 TYR cc_start: 0.8266 (m-80) cc_final: 0.7884 (m-80) REVERT: B 180 SER cc_start: 0.9275 (p) cc_final: 0.9013 (t) REVERT: B 310 MET cc_start: 0.8754 (ttm) cc_final: 0.8466 (mmm) REVERT: B 376 MET cc_start: 0.8719 (mmm) cc_final: 0.8491 (mmm) REVERT: B 446 MET cc_start: 0.8962 (mmm) cc_final: 0.7986 (mmm) REVERT: E 39 LYS cc_start: 0.9037 (mttt) cc_final: 0.8766 (mttp) REVERT: E 42 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8594 (mmmm) REVERT: E 55 GLN cc_start: 0.7948 (tp40) cc_final: 0.7734 (tp40) REVERT: E 89 GLN cc_start: 0.8624 (tt0) cc_final: 0.8293 (tm-30) REVERT: F 72 ASP cc_start: 0.8395 (t70) cc_final: 0.8170 (p0) REVERT: F 102 TYR cc_start: 0.8193 (m-80) cc_final: 0.7264 (m-80) REVERT: C 180 SER cc_start: 0.9279 (p) cc_final: 0.9024 (t) REVERT: C 310 MET cc_start: 0.8759 (ttm) cc_final: 0.8473 (mmm) REVERT: C 376 MET cc_start: 0.8728 (mmm) cc_final: 0.8496 (mmm) REVERT: C 446 MET cc_start: 0.8958 (mmm) cc_final: 0.8015 (mmm) REVERT: G 39 LYS cc_start: 0.9045 (mttt) cc_final: 0.8779 (mttp) REVERT: G 42 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8650 (mmmm) REVERT: G 55 GLN cc_start: 0.7952 (tp40) cc_final: 0.7713 (tp40) REVERT: G 89 GLN cc_start: 0.8631 (tt0) cc_final: 0.8297 (tm-30) REVERT: I 69 MET cc_start: 0.8382 (mtt) cc_final: 0.7862 (mtt) REVERT: I 72 ASP cc_start: 0.8433 (t70) cc_final: 0.8163 (p0) REVERT: I 102 TYR cc_start: 0.8235 (m-80) cc_final: 0.7880 (m-80) REVERT: D 94 ILE cc_start: 0.9528 (mt) cc_final: 0.9269 (mm) REVERT: D 180 SER cc_start: 0.9300 (p) cc_final: 0.9053 (t) REVERT: D 310 MET cc_start: 0.8756 (ttm) cc_final: 0.8472 (mmm) REVERT: D 376 MET cc_start: 0.8734 (mmm) cc_final: 0.8510 (mmm) REVERT: D 446 MET cc_start: 0.8986 (mmm) cc_final: 0.8026 (mmm) REVERT: J 39 LYS cc_start: 0.9034 (mttt) cc_final: 0.8763 (mttp) REVERT: J 42 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8651 (mmmm) REVERT: J 89 GLN cc_start: 0.8636 (tt0) cc_final: 0.8304 (tm-30) REVERT: K 69 MET cc_start: 0.8407 (mtt) cc_final: 0.7904 (mtt) REVERT: K 72 ASP cc_start: 0.8409 (t70) cc_final: 0.8167 (p0) REVERT: K 102 TYR cc_start: 0.8250 (m-80) cc_final: 0.7851 (m-80) outliers start: 36 outliers final: 16 residues processed: 338 average time/residue: 0.1367 time to fit residues: 74.2117 Evaluate side-chains 251 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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: 9.9990 chunk 162 optimal weight: 0.0770 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 142 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056591 restraints weight = 59334.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058727 restraints weight = 24511.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060063 restraints weight = 13516.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.060918 restraints weight = 8924.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.061458 restraints weight = 6728.161| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20352 Z= 0.176 Angle : 0.688 7.779 27816 Z= 0.344 Chirality : 0.046 0.251 3116 Planarity : 0.005 0.042 3484 Dihedral : 8.517 68.395 3672 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 1.51 % Allowed : 9.67 % Favored : 88.82 % 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: -0.11 (0.16), residues: 2440 helix: 0.38 (0.87), residues: 24 sheet: 0.32 (0.16), residues: 936 loop : -0.29 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 66 TYR 0.030 0.002 TYR K 27 PHE 0.026 0.002 PHE J 96 TRP 0.020 0.002 TRP B 206 HIS 0.004 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00396 (20260) covalent geometry : angle 0.66640 (27584) SS BOND : bond 0.00516 ( 44) SS BOND : angle 0.93035 ( 88) hydrogen bonds : bond 0.03953 ( 628) hydrogen bonds : angle 6.19256 ( 1536) link_ALPHA1-2 : bond 0.01050 ( 8) link_ALPHA1-2 : angle 3.95682 ( 24) link_ALPHA1-3 : bond 0.01186 ( 8) link_ALPHA1-3 : angle 2.08385 ( 24) link_ALPHA1-6 : bond 0.01810 ( 8) link_ALPHA1-6 : angle 1.52932 ( 24) link_BETA1-4 : bond 0.00719 ( 12) link_BETA1-4 : angle 1.87526 ( 36) link_NAG-ASN : bond 0.00109 ( 12) link_NAG-ASN : angle 2.29067 ( 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 296 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 0.678 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: A 310 MET cc_start: 0.8756 (ttm) cc_final: 0.8375 (mmm) REVERT: L 39 LYS cc_start: 0.9060 (mttt) cc_final: 0.8823 (mttp) REVERT: L 42 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8113 (mmmm) REVERT: L 70 ASP cc_start: 0.8488 (m-30) cc_final: 0.8122 (p0) REVERT: H 48 MET cc_start: 0.8649 (mmm) cc_final: 0.8392 (mmm) REVERT: H 69 MET cc_start: 0.8493 (mtt) cc_final: 0.7946 (mtt) REVERT: H 80 MET cc_start: 0.8461 (tmm) cc_final: 0.7719 (ppp) REVERT: H 102 TYR cc_start: 0.8550 (m-80) cc_final: 0.8225 (m-80) REVERT: B 310 MET cc_start: 0.8735 (ttm) cc_final: 0.8371 (mmm) REVERT: E 42 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8660 (mmmm) REVERT: E 55 GLN cc_start: 0.7930 (tp40) cc_final: 0.7533 (tp40) REVERT: E 70 ASP cc_start: 0.8467 (m-30) cc_final: 0.8061 (p0) REVERT: F 48 MET cc_start: 0.8663 (mmm) cc_final: 0.8402 (mmm) REVERT: F 69 MET cc_start: 0.8465 (mtt) cc_final: 0.7942 (mtt) REVERT: F 80 MET cc_start: 0.8441 (tmm) cc_final: 0.7695 (ppp) REVERT: F 100 TYR cc_start: 0.6081 (t80) cc_final: 0.5712 (t80) REVERT: F 102 TYR cc_start: 0.8490 (m-80) cc_final: 0.8276 (m-80) REVERT: C 310 MET cc_start: 0.8755 (ttm) cc_final: 0.8383 (mmm) REVERT: G 42 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8669 (mmmm) REVERT: G 70 ASP cc_start: 0.8479 (m-30) cc_final: 0.8099 (p0) REVERT: I 48 MET cc_start: 0.8652 (mmm) cc_final: 0.8397 (mmm) REVERT: I 69 MET cc_start: 0.8464 (mtt) cc_final: 0.7928 (mtt) REVERT: I 80 MET cc_start: 0.8464 (tmm) cc_final: 0.7717 (ppp) REVERT: I 100 TYR cc_start: 0.6299 (t80) cc_final: 0.6034 (t80) REVERT: I 102 TYR cc_start: 0.8544 (m-80) cc_final: 0.8234 (m-80) REVERT: D 310 MET cc_start: 0.8746 (ttm) cc_final: 0.8386 (mmm) REVERT: D 446 MET cc_start: 0.9035 (mmm) cc_final: 0.7922 (mmm) REVERT: J 39 LYS cc_start: 0.9085 (mttt) cc_final: 0.8845 (mttp) REVERT: J 42 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8131 (mmmm) REVERT: J 70 ASP cc_start: 0.8492 (m-30) cc_final: 0.8127 (p0) REVERT: J 79 GLN cc_start: 0.7542 (tt0) cc_final: 0.7078 (pt0) REVERT: K 48 MET cc_start: 0.8642 (mmm) cc_final: 0.8388 (mmm) REVERT: K 69 MET cc_start: 0.8458 (mtt) cc_final: 0.7925 (mtt) REVERT: K 80 MET cc_start: 0.8452 (tmm) cc_final: 0.7714 (ppp) REVERT: K 102 TYR cc_start: 0.8471 (m-80) cc_final: 0.8134 (m-80) outliers start: 32 outliers final: 23 residues processed: 287 average time/residue: 0.1355 time to fit residues: 61.2943 Evaluate side-chains 219 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 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: 20.0000 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN E 37 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN G 37 GLN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN J 37 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.054062 restraints weight = 60207.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.056072 restraints weight = 25321.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.057346 restraints weight = 14241.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058165 restraints weight = 9574.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058703 restraints weight = 7324.110| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 20352 Z= 0.286 Angle : 0.744 8.097 27816 Z= 0.370 Chirality : 0.047 0.187 3116 Planarity : 0.005 0.051 3484 Dihedral : 8.548 64.745 3672 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 2.08 % Allowed : 10.38 % 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: -0.23 (0.16), residues: 2440 helix: -0.31 (0.80), residues: 24 sheet: 0.36 (0.17), residues: 900 loop : -0.44 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 284 TYR 0.020 0.002 TYR J 36 PHE 0.016 0.002 PHE G 96 TRP 0.030 0.002 TRP A 456 HIS 0.005 0.002 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00648 (20260) covalent geometry : angle 0.72424 (27584) SS BOND : bond 0.00310 ( 44) SS BOND : angle 0.89967 ( 88) hydrogen bonds : bond 0.04182 ( 628) hydrogen bonds : angle 6.06741 ( 1536) link_ALPHA1-2 : bond 0.01106 ( 8) link_ALPHA1-2 : angle 3.71511 ( 24) link_ALPHA1-3 : bond 0.00986 ( 8) link_ALPHA1-3 : angle 2.37526 ( 24) link_ALPHA1-6 : bond 0.01523 ( 8) link_ALPHA1-6 : angle 1.84408 ( 24) link_BETA1-4 : bond 0.00548 ( 12) link_BETA1-4 : angle 1.71607 ( 36) link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 2.38205 ( 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 253 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.750 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: A 411 MET cc_start: 0.8777 (mtm) cc_final: 0.8493 (mtp) REVERT: A 446 MET cc_start: 0.9091 (mmm) cc_final: 0.8038 (mmm) REVERT: H 48 MET cc_start: 0.8686 (mmm) cc_final: 0.8484 (mmm) REVERT: H 69 MET cc_start: 0.8512 (mtt) cc_final: 0.7990 (mtt) REVERT: H 80 MET cc_start: 0.8409 (tmm) cc_final: 0.7707 (ppp) REVERT: H 102 TYR cc_start: 0.8565 (m-80) cc_final: 0.8232 (m-80) REVERT: B 411 MET cc_start: 0.8793 (mtm) cc_final: 0.8514 (mtp) REVERT: B 414 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: B 446 MET cc_start: 0.9081 (mmm) cc_final: 0.8003 (mmm) REVERT: E 38 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8026 (tm-30) REVERT: E 55 GLN cc_start: 0.8070 (tp40) cc_final: 0.7846 (tp40) REVERT: E 70 ASP cc_start: 0.8391 (m-30) cc_final: 0.8104 (p0) REVERT: F 48 MET cc_start: 0.8674 (mmm) cc_final: 0.8463 (mmm) REVERT: F 69 MET cc_start: 0.8483 (mtt) cc_final: 0.7969 (mtt) REVERT: F 102 TYR cc_start: 0.8580 (m-80) cc_final: 0.8317 (m-80) REVERT: C 411 MET cc_start: 0.8778 (mtm) cc_final: 0.8500 (mtp) REVERT: C 446 MET cc_start: 0.9083 (mmm) cc_final: 0.8037 (mmm) REVERT: G 42 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8749 (mmmm) REVERT: I 48 MET cc_start: 0.8667 (mmm) cc_final: 0.8462 (mmm) REVERT: I 69 MET cc_start: 0.8482 (mtt) cc_final: 0.7976 (mtt) REVERT: I 102 TYR cc_start: 0.8590 (m-80) cc_final: 0.8271 (m-80) REVERT: D 411 MET cc_start: 0.8769 (mtm) cc_final: 0.8509 (mtp) REVERT: D 446 MET cc_start: 0.9100 (mmm) cc_final: 0.7973 (mmm) REVERT: J 70 ASP cc_start: 0.8410 (m-30) cc_final: 0.8111 (p0) REVERT: K 69 MET cc_start: 0.8479 (mtt) cc_final: 0.7958 (mtt) REVERT: K 80 MET cc_start: 0.8402 (tmm) cc_final: 0.7699 (ppp) REVERT: K 102 TYR cc_start: 0.8517 (m-80) cc_final: 0.8183 (m-80) outliers start: 44 outliers final: 35 residues processed: 246 average time/residue: 0.1368 time to fit residues: 54.0788 Evaluate side-chains 220 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 149 ILE Chi-restraints excluded: chain A residue 230 CYS 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 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 149 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 414 GLU 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 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 149 ILE 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 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 149 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 37 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: 5.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 30.0000 chunk 24 optimal weight: 0.5980 chunk 225 optimal weight: 7.9990 chunk 221 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3208 r_free = 0.3208 target = 0.068386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.054832 restraints weight = 59221.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.056879 restraints weight = 24790.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.058166 restraints weight = 13812.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.058975 restraints weight = 9239.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059529 restraints weight = 7081.682| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20352 Z= 0.194 Angle : 0.680 7.909 27816 Z= 0.337 Chirality : 0.046 0.177 3116 Planarity : 0.004 0.051 3484 Dihedral : 8.091 59.689 3672 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.90 % Rotamer: Outliers : 2.31 % Allowed : 12.22 % Favored : 85.47 % 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: -0.30 (0.17), residues: 2440 helix: -0.64 (0.69), residues: 24 sheet: 0.40 (0.17), residues: 912 loop : -0.56 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 284 TYR 0.020 0.002 TYR G 92 PHE 0.013 0.002 PHE L 96 TRP 0.024 0.002 TRP C 456 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00429 (20260) covalent geometry : angle 0.66031 (27584) SS BOND : bond 0.00206 ( 44) SS BOND : angle 0.87001 ( 88) hydrogen bonds : bond 0.03678 ( 628) hydrogen bonds : angle 5.92730 ( 1536) link_ALPHA1-2 : bond 0.01032 ( 8) link_ALPHA1-2 : angle 3.72253 ( 24) link_ALPHA1-3 : bond 0.01151 ( 8) link_ALPHA1-3 : angle 2.28162 ( 24) link_ALPHA1-6 : bond 0.01697 ( 8) link_ALPHA1-6 : angle 1.54603 ( 24) link_BETA1-4 : bond 0.00564 ( 12) link_BETA1-4 : angle 1.49840 ( 36) link_NAG-ASN : bond 0.00179 ( 12) link_NAG-ASN : angle 2.15198 ( 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 265 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.799 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: L 6 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: L 70 ASP cc_start: 0.8413 (m-30) cc_final: 0.8103 (p0) REVERT: L 79 GLN cc_start: 0.7693 (pt0) cc_final: 0.7316 (pt0) REVERT: H 69 MET cc_start: 0.8483 (mtt) cc_final: 0.7994 (mtt) REVERT: H 102 TYR cc_start: 0.8631 (m-80) cc_final: 0.8320 (m-80) REVERT: E 6 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: E 42 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8117 (mmmm) REVERT: E 70 ASP cc_start: 0.8413 (m-30) cc_final: 0.8101 (p0) REVERT: E 79 GLN cc_start: 0.7712 (pt0) cc_final: 0.7369 (pt0) REVERT: F 69 MET cc_start: 0.8441 (mtt) cc_final: 0.7960 (mtt) REVERT: F 102 TYR cc_start: 0.8563 (m-80) cc_final: 0.8324 (m-80) REVERT: G 6 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: G 42 LYS cc_start: 0.9082 (mmmt) cc_final: 0.8867 (mmmm) REVERT: G 70 ASP cc_start: 0.8437 (m-30) cc_final: 0.8066 (p0) REVERT: G 79 GLN cc_start: 0.7705 (pt0) cc_final: 0.7377 (pt0) REVERT: I 69 MET cc_start: 0.8441 (mtt) cc_final: 0.7952 (mtt) REVERT: I 102 TYR cc_start: 0.8627 (m-80) cc_final: 0.8323 (m-80) REVERT: D 446 MET cc_start: 0.9145 (mmm) cc_final: 0.8219 (mmm) REVERT: J 6 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7331 (mt0) REVERT: J 70 ASP cc_start: 0.8420 (m-30) cc_final: 0.8078 (p0) REVERT: K 48 MET cc_start: 0.8622 (mmm) cc_final: 0.8387 (mmm) REVERT: K 69 MET cc_start: 0.8410 (mtt) cc_final: 0.7911 (mtt) REVERT: K 102 TYR cc_start: 0.8564 (m-80) cc_final: 0.8248 (m-80) outliers start: 49 outliers final: 38 residues processed: 255 average time/residue: 0.1312 time to fit residues: 53.3844 Evaluate side-chains 221 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 149 ILE 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 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 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 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 97 THR 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 149 ILE 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 6 GLN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 97 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 188 optimal weight: 0.0570 chunk 20 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055729 restraints weight = 58536.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.057792 restraints weight = 24271.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.059094 restraints weight = 13459.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059932 restraints weight = 8963.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060420 restraints weight = 6800.955| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20352 Z= 0.147 Angle : 0.651 7.401 27816 Z= 0.320 Chirality : 0.045 0.180 3116 Planarity : 0.004 0.049 3484 Dihedral : 7.663 55.885 3672 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 2.12 % Allowed : 12.69 % Favored : 85.19 % 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: -0.20 (0.17), residues: 2440 helix: -0.99 (0.64), residues: 24 sheet: 0.58 (0.17), residues: 912 loop : -0.57 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 61 TYR 0.018 0.002 TYR L 92 PHE 0.013 0.001 PHE L 96 TRP 0.020 0.002 TRP A 456 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00329 (20260) covalent geometry : angle 0.63337 (27584) SS BOND : bond 0.00179 ( 44) SS BOND : angle 0.78908 ( 88) hydrogen bonds : bond 0.03377 ( 628) hydrogen bonds : angle 5.76361 ( 1536) link_ALPHA1-2 : bond 0.00939 ( 8) link_ALPHA1-2 : angle 3.59701 ( 24) link_ALPHA1-3 : bond 0.01188 ( 8) link_ALPHA1-3 : angle 2.18334 ( 24) link_ALPHA1-6 : bond 0.01724 ( 8) link_ALPHA1-6 : angle 1.47038 ( 24) link_BETA1-4 : bond 0.00604 ( 12) link_BETA1-4 : angle 1.41366 ( 36) link_NAG-ASN : bond 0.00046 ( 12) link_NAG-ASN : angle 1.92960 ( 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 259 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.777 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: A 310 MET cc_start: 0.8531 (mmt) cc_final: 0.8070 (tpp) REVERT: A 446 MET cc_start: 0.9157 (mmm) cc_final: 0.8219 (mmm) REVERT: L 6 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: L 70 ASP cc_start: 0.8440 (m-30) cc_final: 0.8088 (p0) REVERT: H 48 MET cc_start: 0.8653 (mmm) cc_final: 0.8448 (mmm) REVERT: H 69 MET cc_start: 0.8453 (mtt) cc_final: 0.8089 (mmt) REVERT: H 102 TYR cc_start: 0.8642 (m-80) cc_final: 0.8345 (m-80) REVERT: B 310 MET cc_start: 0.8537 (mmt) cc_final: 0.8071 (tpp) REVERT: B 446 MET cc_start: 0.9156 (mmm) cc_final: 0.8191 (mmm) REVERT: E 6 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: E 70 ASP cc_start: 0.8427 (m-30) cc_final: 0.8006 (p0) REVERT: F 48 MET cc_start: 0.8633 (mmm) cc_final: 0.8422 (mmm) REVERT: F 69 MET cc_start: 0.8418 (mtt) cc_final: 0.8060 (mmt) REVERT: F 102 TYR cc_start: 0.8643 (m-80) cc_final: 0.8415 (m-80) REVERT: C 310 MET cc_start: 0.8546 (mmt) cc_final: 0.8078 (tpp) REVERT: C 446 MET cc_start: 0.9152 (mmm) cc_final: 0.8218 (mmm) REVERT: G 6 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7288 (mt0) REVERT: G 42 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8814 (mmmm) REVERT: G 70 ASP cc_start: 0.8428 (m-30) cc_final: 0.8008 (p0) REVERT: I 48 MET cc_start: 0.8640 (mmm) cc_final: 0.8424 (mmm) REVERT: I 69 MET cc_start: 0.8417 (mtt) cc_final: 0.8059 (mmt) REVERT: I 102 TYR cc_start: 0.8667 (m-80) cc_final: 0.8351 (m-80) REVERT: D 310 MET cc_start: 0.8540 (mmt) cc_final: 0.8075 (tpp) REVERT: D 446 MET cc_start: 0.9165 (mmm) cc_final: 0.8222 (mmm) REVERT: J 6 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7291 (mt0) REVERT: J 70 ASP cc_start: 0.8427 (m-30) cc_final: 0.7975 (p0) REVERT: K 48 MET cc_start: 0.8691 (mmm) cc_final: 0.8464 (mmm) REVERT: K 69 MET cc_start: 0.8412 (mtt) cc_final: 0.8057 (mmt) REVERT: K 102 TYR cc_start: 0.8608 (m-80) cc_final: 0.8324 (m-80) outliers start: 45 outliers final: 37 residues processed: 248 average time/residue: 0.1369 time to fit residues: 54.0793 Evaluate side-chains 223 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 A residue 444 VAL Chi-restraints excluded: chain L residue 6 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 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 B residue 444 VAL Chi-restraints excluded: chain E residue 6 GLN 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 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 C residue 444 VAL 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 444 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 97 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: 0.0050 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 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 = 0.3245 r_free = 0.3245 target = 0.070240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.056720 restraints weight = 58551.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.058815 restraints weight = 24150.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.060135 restraints weight = 13306.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060970 restraints weight = 8805.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.061455 restraints weight = 6668.122| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4069 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= 0.119 Angle : 0.637 6.916 27816 Z= 0.313 Chirality : 0.045 0.181 3116 Planarity : 0.004 0.046 3484 Dihedral : 7.228 55.532 3672 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 1.98 % Allowed : 13.68 % Favored : 84.34 % 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: -0.23 (0.17), residues: 2440 helix: -1.60 (0.53), residues: 24 sheet: 0.58 (0.17), residues: 884 loop : -0.57 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 61 TYR 0.020 0.001 TYR G 36 PHE 0.044 0.002 PHE L 62 TRP 0.016 0.001 TRP C 206 HIS 0.002 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00265 (20260) covalent geometry : angle 0.62027 (27584) SS BOND : bond 0.00174 ( 44) SS BOND : angle 0.77787 ( 88) hydrogen bonds : bond 0.03147 ( 628) hydrogen bonds : angle 5.65546 ( 1536) link_ALPHA1-2 : bond 0.00885 ( 8) link_ALPHA1-2 : angle 3.51834 ( 24) link_ALPHA1-3 : bond 0.01256 ( 8) link_ALPHA1-3 : angle 2.10058 ( 24) link_ALPHA1-6 : bond 0.01762 ( 8) link_ALPHA1-6 : angle 1.36514 ( 24) link_BETA1-4 : bond 0.00650 ( 12) link_BETA1-4 : angle 1.35148 ( 36) link_NAG-ASN : bond 0.00083 ( 12) link_NAG-ASN : angle 1.77899 ( 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 258 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 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: A 310 MET cc_start: 0.8479 (mmt) cc_final: 0.8017 (tpp) REVERT: A 446 MET cc_start: 0.9167 (mmm) cc_final: 0.8202 (mmm) REVERT: L 17 ASP cc_start: 0.8124 (m-30) cc_final: 0.7848 (m-30) REVERT: L 70 ASP cc_start: 0.8416 (m-30) cc_final: 0.7973 (p0) REVERT: H 48 MET cc_start: 0.8695 (mmm) cc_final: 0.8479 (mmm) REVERT: H 69 MET cc_start: 0.8416 (mtt) cc_final: 0.8065 (mmt) REVERT: H 102 TYR cc_start: 0.8659 (m-80) cc_final: 0.8337 (m-80) REVERT: B 310 MET cc_start: 0.8474 (mmt) cc_final: 0.8009 (tpp) REVERT: B 446 MET cc_start: 0.9156 (mmm) cc_final: 0.8196 (mmm) REVERT: E 17 ASP cc_start: 0.8126 (m-30) cc_final: 0.7852 (m-30) REVERT: E 37 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: E 55 GLN cc_start: 0.8186 (tp40) cc_final: 0.7977 (tp40) REVERT: E 70 ASP cc_start: 0.8410 (m-30) cc_final: 0.7971 (p0) REVERT: F 48 MET cc_start: 0.8702 (mmm) cc_final: 0.8489 (mmm) REVERT: F 69 MET cc_start: 0.8389 (mtt) cc_final: 0.8038 (mmt) REVERT: F 102 TYR cc_start: 0.8646 (m-80) cc_final: 0.8417 (m-80) REVERT: C 310 MET cc_start: 0.8475 (mmt) cc_final: 0.8011 (tpp) REVERT: C 446 MET cc_start: 0.9161 (mmm) cc_final: 0.8200 (mmm) REVERT: G 17 ASP cc_start: 0.8003 (m-30) cc_final: 0.7739 (m-30) REVERT: G 37 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: G 42 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8790 (mmmm) REVERT: G 70 ASP cc_start: 0.8410 (m-30) cc_final: 0.7969 (p0) REVERT: I 48 MET cc_start: 0.8701 (mmm) cc_final: 0.8488 (mmm) REVERT: I 69 MET cc_start: 0.8392 (mtt) cc_final: 0.8039 (mmt) REVERT: I 102 TYR cc_start: 0.8671 (m-80) cc_final: 0.8342 (m-80) REVERT: D 310 MET cc_start: 0.8468 (mmt) cc_final: 0.8006 (tpp) REVERT: D 446 MET cc_start: 0.9174 (mmm) cc_final: 0.8207 (mmm) REVERT: J 70 ASP cc_start: 0.8412 (m-30) cc_final: 0.7971 (p0) REVERT: K 3 GLN cc_start: 0.8636 (mt0) cc_final: 0.8297 (mm-40) REVERT: K 48 MET cc_start: 0.8733 (mmm) cc_final: 0.8510 (mmm) REVERT: K 69 MET cc_start: 0.8405 (mtt) cc_final: 0.7988 (mmt) REVERT: K 102 TYR cc_start: 0.8598 (m-80) cc_final: 0.8328 (m-80) outliers start: 42 outliers final: 31 residues processed: 247 average time/residue: 0.1361 time to fit residues: 54.0775 Evaluate side-chains 226 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 180 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS 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 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 37 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: 0.9990 chunk 114 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055533 restraints weight = 59519.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057559 restraints weight = 24978.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058855 restraints weight = 13966.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.059672 restraints weight = 9320.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060200 restraints weight = 7095.754| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4184 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= 0.173 Angle : 0.656 6.617 27816 Z= 0.321 Chirality : 0.045 0.184 3116 Planarity : 0.004 0.049 3484 Dihedral : 7.201 55.051 3672 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Rotamer: Outliers : 2.26 % Allowed : 13.16 % Favored : 84.58 % 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: -0.32 (0.17), residues: 2440 helix: -1.45 (0.60), residues: 24 sheet: 0.35 (0.17), residues: 916 loop : -0.53 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 61 TYR 0.021 0.002 TYR A 423 PHE 0.025 0.002 PHE G 62 TRP 0.014 0.001 TRP C 456 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00393 (20260) covalent geometry : angle 0.63865 (27584) SS BOND : bond 0.00248 ( 44) SS BOND : angle 0.97459 ( 88) hydrogen bonds : bond 0.03309 ( 628) hydrogen bonds : angle 5.62194 ( 1536) link_ALPHA1-2 : bond 0.00819 ( 8) link_ALPHA1-2 : angle 3.31457 ( 24) link_ALPHA1-3 : bond 0.01076 ( 8) link_ALPHA1-3 : angle 2.12244 ( 24) link_ALPHA1-6 : bond 0.01571 ( 8) link_ALPHA1-6 : angle 1.40541 ( 24) link_BETA1-4 : bond 0.00548 ( 12) link_BETA1-4 : angle 1.41075 ( 36) link_NAG-ASN : bond 0.00121 ( 12) link_NAG-ASN : angle 1.92987 ( 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 251 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9166 (mmm) cc_final: 0.8214 (mmm) REVERT: L 17 ASP cc_start: 0.8069 (m-30) cc_final: 0.7786 (m-30) REVERT: L 37 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8719 (tt0) REVERT: L 70 ASP cc_start: 0.8420 (m-30) cc_final: 0.7961 (p0) REVERT: H 48 MET cc_start: 0.8711 (mmm) cc_final: 0.8481 (mmm) REVERT: H 69 MET cc_start: 0.8448 (mtt) cc_final: 0.7960 (mtt) REVERT: H 80 MET cc_start: 0.8301 (tmm) cc_final: 0.7424 (ppp) REVERT: H 102 TYR cc_start: 0.8718 (m-80) cc_final: 0.8380 (m-80) REVERT: B 446 MET cc_start: 0.9156 (mmm) cc_final: 0.8212 (mmm) REVERT: E 17 ASP cc_start: 0.8080 (m-30) cc_final: 0.7796 (m-30) REVERT: E 70 ASP cc_start: 0.8425 (m-30) cc_final: 0.7964 (p0) REVERT: F 48 MET cc_start: 0.8705 (mmm) cc_final: 0.8496 (mmm) REVERT: F 69 MET cc_start: 0.8386 (mtt) cc_final: 0.7946 (mmt) REVERT: F 102 TYR cc_start: 0.8662 (m-80) cc_final: 0.8429 (m-80) REVERT: C 446 MET cc_start: 0.9161 (mmm) cc_final: 0.8215 (mmm) REVERT: G 17 ASP cc_start: 0.8074 (m-30) cc_final: 0.7790 (m-30) REVERT: G 42 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8782 (mmmm) REVERT: G 70 ASP cc_start: 0.8411 (m-30) cc_final: 0.7952 (p0) REVERT: I 48 MET cc_start: 0.8701 (mmm) cc_final: 0.8491 (mmm) REVERT: I 69 MET cc_start: 0.8386 (mtt) cc_final: 0.7942 (mmt) REVERT: I 102 TYR cc_start: 0.8721 (m-80) cc_final: 0.8379 (m-80) REVERT: D 446 MET cc_start: 0.9177 (mmm) cc_final: 0.8220 (mmm) REVERT: J 17 ASP cc_start: 0.8127 (m-30) cc_final: 0.7842 (m-30) REVERT: J 70 ASP cc_start: 0.8422 (m-30) cc_final: 0.7963 (p0) REVERT: K 3 GLN cc_start: 0.8673 (mt0) cc_final: 0.8326 (mm-40) REVERT: K 48 MET cc_start: 0.8734 (mmm) cc_final: 0.8513 (mmm) REVERT: K 69 MET cc_start: 0.8399 (mtt) cc_final: 0.7986 (mmt) REVERT: K 80 MET cc_start: 0.8294 (tmm) cc_final: 0.7514 (ppp) REVERT: K 102 TYR cc_start: 0.8673 (m-80) cc_final: 0.8380 (m-80) outliers start: 48 outliers final: 41 residues processed: 242 average time/residue: 0.1366 time to fit residues: 53.1052 Evaluate side-chains 227 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 444 VAL Chi-restraints excluded: chain L residue 11 LEU 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 149 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 11 LEU 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 149 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 106 ILE 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 379 VAL Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 VAL 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 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: 0.7980 chunk 191 optimal weight: 0.0970 chunk 157 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.069019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.055545 restraints weight = 59650.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057571 restraints weight = 24921.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.058855 restraints weight = 13851.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059677 restraints weight = 9202.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060161 restraints weight = 6967.668| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20352 Z= 0.182 Angle : 0.666 7.633 27816 Z= 0.326 Chirality : 0.046 0.185 3116 Planarity : 0.004 0.051 3484 Dihedral : 7.109 53.600 3672 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.43 % Favored : 95.41 % Rotamer: Outliers : 2.22 % Allowed : 13.07 % Favored : 84.72 % 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: -0.30 (0.17), residues: 2440 helix: -1.49 (0.56), residues: 24 sheet: 0.34 (0.17), residues: 948 loop : -0.52 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 61 TYR 0.023 0.002 TYR G 36 PHE 0.028 0.002 PHE E 62 TRP 0.014 0.001 TRP B 206 HIS 0.004 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00412 (20260) covalent geometry : angle 0.64945 (27584) SS BOND : bond 0.00272 ( 44) SS BOND : angle 0.88841 ( 88) hydrogen bonds : bond 0.03364 ( 628) hydrogen bonds : angle 5.63318 ( 1536) link_ALPHA1-2 : bond 0.00810 ( 8) link_ALPHA1-2 : angle 3.30778 ( 24) link_ALPHA1-3 : bond 0.01074 ( 8) link_ALPHA1-3 : angle 2.16622 ( 24) link_ALPHA1-6 : bond 0.01523 ( 8) link_ALPHA1-6 : angle 1.38424 ( 24) link_BETA1-4 : bond 0.00511 ( 12) link_BETA1-4 : angle 1.37958 ( 36) link_NAG-ASN : bond 0.00150 ( 12) link_NAG-ASN : angle 1.96895 ( 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 244 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.790 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 156 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7801 (ttm-80) REVERT: A 310 MET cc_start: 0.8535 (mmt) cc_final: 0.8333 (tpp) REVERT: A 446 MET cc_start: 0.9184 (mmm) cc_final: 0.8247 (mmm) REVERT: L 17 ASP cc_start: 0.8114 (m-30) cc_final: 0.7836 (m-30) REVERT: L 70 ASP cc_start: 0.8414 (m-30) cc_final: 0.7941 (p0) REVERT: H 48 MET cc_start: 0.8746 (mmm) cc_final: 0.8526 (mmm) REVERT: H 69 MET cc_start: 0.8444 (mtt) cc_final: 0.7987 (mtt) REVERT: H 80 MET cc_start: 0.8302 (tmm) cc_final: 0.7416 (ppp) REVERT: H 102 TYR cc_start: 0.8731 (m-80) cc_final: 0.8390 (m-80) REVERT: B 310 MET cc_start: 0.8541 (mmt) cc_final: 0.8340 (tpp) REVERT: B 446 MET cc_start: 0.9172 (mmm) cc_final: 0.8247 (mmm) REVERT: E 17 ASP cc_start: 0.8060 (m-30) cc_final: 0.7782 (m-30) REVERT: E 37 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: E 70 ASP cc_start: 0.8416 (m-30) cc_final: 0.7939 (p0) REVERT: F 69 MET cc_start: 0.8391 (mtt) cc_final: 0.7948 (mmt) REVERT: F 102 TYR cc_start: 0.8685 (m-80) cc_final: 0.8436 (m-80) REVERT: C 310 MET cc_start: 0.8553 (mmt) cc_final: 0.8335 (tpp) REVERT: C 446 MET cc_start: 0.9178 (mmm) cc_final: 0.8258 (mmm) REVERT: G 17 ASP cc_start: 0.8045 (m-30) cc_final: 0.7782 (m-30) REVERT: G 37 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: G 42 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8783 (mmmm) REVERT: G 70 ASP cc_start: 0.8415 (m-30) cc_final: 0.7941 (p0) REVERT: I 69 MET cc_start: 0.8389 (mtt) cc_final: 0.7960 (mmt) REVERT: I 102 TYR cc_start: 0.8736 (m-80) cc_final: 0.8393 (m-80) REVERT: D 156 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7786 (ttm-80) REVERT: D 310 MET cc_start: 0.8546 (mmt) cc_final: 0.8325 (tpp) REVERT: D 446 MET cc_start: 0.9198 (mmm) cc_final: 0.8238 (mmm) REVERT: J 17 ASP cc_start: 0.8007 (m-30) cc_final: 0.7746 (m-30) REVERT: J 70 ASP cc_start: 0.8418 (m-30) cc_final: 0.7940 (p0) REVERT: K 3 GLN cc_start: 0.8680 (mt0) cc_final: 0.8335 (mm-40) REVERT: K 48 MET cc_start: 0.8726 (mmm) cc_final: 0.8516 (mmm) REVERT: K 69 MET cc_start: 0.8392 (mtt) cc_final: 0.7983 (mmt) REVERT: K 80 MET cc_start: 0.8309 (tmm) cc_final: 0.7510 (ppp) REVERT: K 102 TYR cc_start: 0.8677 (m-80) cc_final: 0.8367 (m-80) outliers start: 47 outliers final: 42 residues processed: 232 average time/residue: 0.1422 time to fit residues: 52.4368 Evaluate side-chains 224 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 444 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 58 VAL 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 149 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 11 LEU 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 149 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 444 VAL 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 106 ILE 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 379 VAL Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 VAL 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 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 66 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 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: 0.0870 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.067949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054432 restraints weight = 60304.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.056457 restraints weight = 24881.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057735 restraints weight = 13729.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.058553 restraints weight = 9093.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059044 restraints weight = 6886.580| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 20352 Z= 0.245 Angle : 0.709 9.487 27816 Z= 0.349 Chirality : 0.047 0.187 3116 Planarity : 0.005 0.053 3484 Dihedral : 7.302 52.280 3672 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.34 % Rotamer: Outliers : 2.03 % Allowed : 13.25 % Favored : 84.72 % 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: -0.41 (0.17), residues: 2440 helix: -1.36 (0.60), residues: 24 sheet: 0.19 (0.17), residues: 968 loop : -0.54 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 61 TYR 0.030 0.002 TYR L 36 PHE 0.025 0.002 PHE E 62 TRP 0.016 0.002 TRP C 456 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00552 (20260) covalent geometry : angle 0.69319 (27584) SS BOND : bond 0.00284 ( 44) SS BOND : angle 0.86391 ( 88) hydrogen bonds : bond 0.03625 ( 628) hydrogen bonds : angle 5.68193 ( 1536) link_ALPHA1-2 : bond 0.00844 ( 8) link_ALPHA1-2 : angle 3.28264 ( 24) link_ALPHA1-3 : bond 0.00931 ( 8) link_ALPHA1-3 : angle 2.28908 ( 24) link_ALPHA1-6 : bond 0.01374 ( 8) link_ALPHA1-6 : angle 1.52757 ( 24) link_BETA1-4 : bond 0.00472 ( 12) link_BETA1-4 : angle 1.42559 ( 36) link_NAG-ASN : bond 0.00313 ( 12) link_NAG-ASN : angle 2.13635 ( 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 225 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8599 (mmt) cc_final: 0.8388 (tpp) REVERT: A 446 MET cc_start: 0.9203 (mmm) cc_final: 0.8879 (mmm) REVERT: L 17 ASP cc_start: 0.8179 (m-30) cc_final: 0.7890 (m-30) REVERT: L 70 ASP cc_start: 0.8426 (m-30) cc_final: 0.7925 (p0) REVERT: H 48 MET cc_start: 0.8743 (mmm) cc_final: 0.8537 (mmm) REVERT: H 69 MET cc_start: 0.8452 (mtt) cc_final: 0.8001 (mtt) REVERT: H 102 TYR cc_start: 0.8763 (m-80) cc_final: 0.8418 (m-80) REVERT: B 310 MET cc_start: 0.8610 (mmt) cc_final: 0.8394 (tpp) REVERT: B 376 MET cc_start: 0.8846 (mmm) cc_final: 0.8489 (mmm) REVERT: B 446 MET cc_start: 0.9195 (mmm) cc_final: 0.8872 (mmm) REVERT: E 17 ASP cc_start: 0.8198 (m-30) cc_final: 0.7910 (m-30) REVERT: E 37 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8643 (tt0) REVERT: F 69 MET cc_start: 0.8409 (mtt) cc_final: 0.7963 (mtt) REVERT: F 102 TYR cc_start: 0.8714 (m-80) cc_final: 0.8442 (m-80) REVERT: C 310 MET cc_start: 0.8604 (mmt) cc_final: 0.8395 (tpp) REVERT: C 446 MET cc_start: 0.9200 (mmm) cc_final: 0.8870 (mmm) REVERT: G 17 ASP cc_start: 0.8182 (m-30) cc_final: 0.7897 (m-30) REVERT: G 37 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: G 42 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8799 (mmmm) REVERT: I 69 MET cc_start: 0.8411 (mtt) cc_final: 0.7952 (mtt) REVERT: I 102 TYR cc_start: 0.8791 (m-80) cc_final: 0.8437 (m-80) REVERT: D 310 MET cc_start: 0.8594 (mmt) cc_final: 0.8382 (tpp) REVERT: D 446 MET cc_start: 0.9207 (mmm) cc_final: 0.8882 (mmm) REVERT: J 17 ASP cc_start: 0.8042 (m-30) cc_final: 0.7773 (m-30) REVERT: J 70 ASP cc_start: 0.8437 (m-30) cc_final: 0.7931 (p0) REVERT: K 3 GLN cc_start: 0.8626 (mt0) cc_final: 0.8314 (mm-40) REVERT: K 48 MET cc_start: 0.8750 (mmm) cc_final: 0.8538 (mmm) REVERT: K 69 MET cc_start: 0.8396 (mtt) cc_final: 0.7949 (mtt) REVERT: K 102 TYR cc_start: 0.8732 (m-80) cc_final: 0.8412 (m-80) outliers start: 43 outliers final: 40 residues processed: 213 average time/residue: 0.1304 time to fit residues: 45.8581 Evaluate side-chains 216 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 444 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 58 VAL 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 149 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 11 LEU 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 149 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 444 VAL 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 106 ILE 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 D residue 444 VAL 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 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: 4.9990 chunk 128 optimal weight: 0.2980 chunk 187 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.068280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.054725 restraints weight = 60127.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056758 restraints weight = 24848.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.058042 restraints weight = 13672.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058843 restraints weight = 9050.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.059371 restraints weight = 6894.236| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20352 Z= 0.206 Angle : 0.700 13.832 27816 Z= 0.341 Chirality : 0.046 0.186 3116 Planarity : 0.004 0.052 3484 Dihedral : 7.180 50.850 3672 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 2.12 % Allowed : 13.30 % Favored : 84.58 % 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: -0.49 (0.17), residues: 2440 helix: -1.38 (0.62), residues: 24 sheet: 0.11 (0.16), residues: 976 loop : -0.57 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 61 TYR 0.020 0.002 TYR E 36 PHE 0.026 0.002 PHE E 62 TRP 0.016 0.002 TRP D 456 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00467 (20260) covalent geometry : angle 0.68478 (27584) SS BOND : bond 0.00244 ( 44) SS BOND : angle 0.78355 ( 88) hydrogen bonds : bond 0.03485 ( 628) hydrogen bonds : angle 5.73304 ( 1536) link_ALPHA1-2 : bond 0.00819 ( 8) link_ALPHA1-2 : angle 3.30711 ( 24) link_ALPHA1-3 : bond 0.01015 ( 8) link_ALPHA1-3 : angle 2.29853 ( 24) link_ALPHA1-6 : bond 0.01440 ( 8) link_ALPHA1-6 : angle 1.43670 ( 24) link_BETA1-4 : bond 0.00494 ( 12) link_BETA1-4 : angle 1.36134 ( 36) link_NAG-ASN : bond 0.00225 ( 12) link_NAG-ASN : angle 2.04662 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.80 seconds wall clock time: 55 minutes 9.31 seconds (3309.31 seconds total)