Starting phenix.real_space_refine on Sun Sep 13 01:06:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u02_20594/09_2026/6u02_20594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u02_20594/09_2026/6u02_20594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6u02_20594/09_2026/6u02_20594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u02_20594/09_2026/6u02_20594.cif" model { file = "/net/cci-nas-00/data/ceres_data/6u02_20594/09_2026/6u02_20594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u02_20594/09_2026/6u02_20594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u02_20594/09_2026/6u02_20594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u02_20594/09_2026/6u02_20594.map" } resolution = 3.05 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= -0.000 sd= 0.160 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 120 5.16 5 C 12284 2.51 5 N 3336 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19672 Number of models: 1 Model: "" Number of chains: 5 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: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, E, J, C, F, I, D, G, K, N, O, P Time building chain proxies: 3.44, per 1000 atoms: 0.17 Number of scatterers: 19672 At special positions: 0 Unit cell: (198.79, 198.79, 84.46, 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 120 16.00 O 3932 8.00 N 3336 7.00 C 12284 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=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.04 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.02 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.02 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.02 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.02 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.02 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.02 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.02 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.04 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.09 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.09 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.09 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 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 M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 7 " - " MAN M 8 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 9 " " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 9 " " BMA P 3 " - " MAN P 7 " " MAN P 7 " - " MAN P 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 510 " - " ASN A 86 " " NAG A 511 " - " ASN A 146 " " NAG B 510 " - " ASN B 86 " " NAG B 511 " - " ASN B 146 " " NAG E 510 " - " ASN E 86 " " NAG E 511 " - " ASN E 146 " " NAG J 510 " - " ASN J 86 " " NAG J 511 " - " ASN J 146 " " NAG M 1 " - " ASN A 200 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN E 200 " " NAG P 1 " - " ASN J 200 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 723.8 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 48 sheets defined 7.0% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 109 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 'C' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 356 through 359 Processing helix chain 'E' and resid 463 through 468 Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 104 through 109 Processing helix chain 'J' and resid 142 through 146 Processing helix chain 'J' and resid 356 through 359 Processing helix chain 'J' and resid 463 through 468 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.131A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.725A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA A 420 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 125 removed outlier: 4.716A pdb=" N LEU A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR A 138 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA A 203 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 244 removed outlier: 7.433A pdb=" N THR A 252 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 254 " --> pdb=" O TRP A 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR A 256 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS A 278 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS A 280 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY A 282 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER A 372 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.643A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.606A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA B 420 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 125 removed outlier: 4.715A pdb=" N LEU B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 138 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA B 203 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 205 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR B 252 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 254 " --> pdb=" O TRP B 265 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR B 256 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.627A pdb=" N CYS B 278 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS B 280 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 282 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER B 372 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 399 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER C 67 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.607A pdb=" N MET D 34 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC7, first strand: chain 'E' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER E 445 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA E 420 " --> pdb=" O SER E 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 115 through 125 removed outlier: 4.715A pdb=" N LEU E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR E 138 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU E 158 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 179 through 184 removed outlier: 6.634A pdb=" N ALA E 203 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU E 214 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL E 205 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR E 252 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER E 267 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE E 254 " --> pdb=" O TRP E 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP E 265 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR E 256 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS E 278 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR E 290 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS E 280 " --> pdb=" O THR E 288 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR E 288 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY E 282 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER E 372 " --> pdb=" O LEU E 399 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E 399 " --> pdb=" O SER E 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR E 374 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 393 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.607A pdb=" N MET G 34 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 6.726A pdb=" N SER J 445 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA J 420 " --> pdb=" O SER J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 125 removed outlier: 4.716A pdb=" N LEU J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR J 138 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU J 158 " --> pdb=" O GLU J 174 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 6.633A pdb=" N ALA J 203 " --> pdb=" O GLU J 214 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU J 214 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL J 205 " --> pdb=" O VAL J 212 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 236 through 244 removed outlier: 7.434A pdb=" N THR J 252 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER J 267 " --> pdb=" O THR J 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE J 254 " --> pdb=" O TRP J 265 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP J 265 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR J 256 " --> pdb=" O LEU J 263 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 4.626A pdb=" N CYS J 278 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR J 290 " --> pdb=" O CYS J 278 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS J 280 " --> pdb=" O THR J 288 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR J 288 " --> pdb=" O CYS J 280 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY J 282 " --> pdb=" O GLY J 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 353 through 354 removed outlier: 6.870A pdb=" N SER J 372 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU J 399 " --> pdb=" O SER J 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR J 374 " --> pdb=" O ILE J 397 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN J 393 " --> pdb=" O LYS J 378 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.644A pdb=" N SER I 67 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.251A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.606A pdb=" N MET K 34 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA K 40 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 11 684 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.16 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: 3633 1.31 - 1.45: 6238 1.45 - 1.58: 10129 1.58 - 1.71: 16 1.71 - 1.85: 144 Bond restraints: 20160 Sorted by residual: bond pdb=" C1 NAG A 510 " pdb=" O5 NAG A 510 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C1 NAG J 510 " pdb=" O5 NAG J 510 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C1 NAG B 510 " pdb=" O5 NAG B 510 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C1 NAG E 510 " pdb=" O5 NAG E 510 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.542 -0.136 2.00e-02 2.50e+03 4.63e+01 ... (remaining 20155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 22390 2.19 - 4.37: 4178 4.37 - 6.56: 714 6.56 - 8.74: 106 8.74 - 10.93: 24 Bond angle restraints: 27412 Sorted by residual: angle pdb=" C TYR A 341 " pdb=" N PRO A 342 " pdb=" CA PRO A 342 " ideal model delta sigma weight residual 120.03 129.26 -9.23 9.90e-01 1.02e+00 8.68e+01 angle pdb=" C TYR J 341 " pdb=" N PRO J 342 " pdb=" CA PRO J 342 " ideal model delta sigma weight residual 120.03 129.25 -9.22 9.90e-01 1.02e+00 8.67e+01 angle pdb=" C TYR B 341 " pdb=" N PRO B 342 " pdb=" CA PRO B 342 " ideal model delta sigma weight residual 120.03 129.24 -9.21 9.90e-01 1.02e+00 8.66e+01 angle pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta sigma weight residual 120.03 129.22 -9.19 9.90e-01 1.02e+00 8.62e+01 angle pdb=" C ASP A 330 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " ideal model delta sigma weight residual 120.98 130.76 -9.78 1.07e+00 8.73e-01 8.35e+01 ... (remaining 27407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11204 17.93 - 35.86: 330 35.86 - 53.78: 66 53.78 - 71.71: 40 71.71 - 89.64: 12 Dihedral angle restraints: 11652 sinusoidal: 4596 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS J 318 " pdb=" SG CYS J 318 " pdb=" SG CYS J 337 " pdb=" CB CYS J 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.69 -37.69 1 1.00e+01 1.00e-02 2.00e+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 93.00 130.68 -37.68 1 1.00e+01 1.00e-02 2.00e+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 93.00 130.65 -37.65 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 11649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2212 0.102 - 0.204: 716 0.204 - 0.306: 111 0.306 - 0.408: 21 0.408 - 0.510: 4 Chirality restraints: 3064 Sorted by residual: chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.32e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.30e+01 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.19e+01 ... (remaining 3061 not shown) Planarity restraints: 3476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 155 " -0.056 2.00e-02 2.50e+03 2.85e-02 1.63e+01 pdb=" CG TYR B 155 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 155 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 155 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 155 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 155 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 155 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 155 " -0.056 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR E 155 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR E 155 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR E 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR E 155 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 155 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 155 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 155 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 155 " 0.056 2.00e-02 2.50e+03 2.83e-02 1.60e+01 pdb=" CG TYR J 155 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR J 155 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR J 155 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR J 155 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR J 155 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR J 155 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR J 155 " 0.033 2.00e-02 2.50e+03 ... (remaining 3473 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 9692 2.94 - 3.43: 16837 3.43 - 3.92: 34456 3.92 - 4.41: 41521 4.41 - 4.90: 67558 Nonbonded interactions: 170064 Sorted by model distance: nonbonded pdb=" N ASP B 434 " pdb=" OD1 ASP B 434 " model vdw 2.449 3.120 nonbonded pdb=" N ASP J 416 " pdb=" OD1 ASP J 416 " model vdw 2.450 3.120 nonbonded pdb=" N ASP J 434 " pdb=" OD1 ASP J 434 " model vdw 2.450 3.120 nonbonded pdb=" N ASP E 416 " pdb=" OD1 ASP E 416 " model vdw 2.450 3.120 nonbonded pdb=" N ASP A 434 " pdb=" OD1 ASP A 434 " model vdw 2.451 3.120 ... (remaining 170059 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 'E' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'D' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.460 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.138 20248 Z= 1.169 Angle : 1.806 10.926 27632 Z= 1.185 Chirality : 0.101 0.510 3064 Planarity : 0.009 0.044 3464 Dihedral : 10.460 89.641 7032 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.31 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.75 (0.17), residues: 2428 helix: -2.15 (0.51), residues: 48 sheet: 1.08 (0.17), residues: 892 loop : 0.31 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 292 TYR 0.056 0.008 TYR B 155 PHE 0.032 0.008 PHE B 241 TRP 0.045 0.008 TRP A 456 HIS 0.006 0.002 HIS E 274 Details of bonding type rmsd/Z covalent geometry : bond 0.02240 / 1.17 (20160) covalent geometry : angle 1.79095 / 1.18 (27412) SS BOND : bond 0.01923 / 1.47 ( 44) SS BOND : angle 3.40782 / 2.43 ( 88) hydrogen bonds : bond 0.16992 / 11.59 ( 652) hydrogen bonds : angle 8.80511 / 6.19 ( 1536) link_ALPHA1-2 : bond 0.03500 / 1.89 ( 8) link_ALPHA1-2 : angle 3.43187 / 2.18 ( 24) link_ALPHA1-3 : bond 0.03201 / 1.73 ( 8) link_ALPHA1-3 : angle 2.32301 / 1.49 ( 24) link_ALPHA1-6 : bond 0.02368 / 1.28 ( 8) link_ALPHA1-6 : angle 2.92899 / 1.92 ( 24) link_BETA1-4 : bond 0.03579 / 1.93 ( 8) link_BETA1-4 : angle 3.25865 / 1.92 ( 24) link_NAG-ASN : bond 0.02841 / 1.86 ( 12) link_NAG-ASN : angle 2.80047 / 1.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.7720 (p) cc_final: 0.7407 (m) REVERT: L 54 LEU cc_start: 0.7564 (mt) cc_final: 0.7143 (mt) REVERT: B 372 SER cc_start: 0.6967 (p) cc_final: 0.6711 (m) REVERT: E 372 SER cc_start: 0.7259 (p) cc_final: 0.6968 (m) REVERT: J 372 SER cc_start: 0.7742 (p) cc_final: 0.7410 (m) REVERT: I 54 LEU cc_start: 0.7628 (mt) cc_final: 0.7229 (mt) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.1362 time to fit residues: 129.9629 Evaluate side-chains 366 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 329 ASN L 37 GLN H 72 HIS B 325 ASN B 329 ASN D 50 ASN D 72 HIS D 81 GLN E 329 ASN F 37 GLN G 50 ASN G 72 HIS J 325 ASN I 37 GLN K 72 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092877 restraints weight = 24856.401| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.35 r_work: 0.2972 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20248 Z= 0.189 Angle : 0.722 8.584 27632 Z= 0.380 Chirality : 0.047 0.206 3064 Planarity : 0.005 0.054 3464 Dihedral : 5.341 21.734 2700 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 2.70 % Allowed : 9.54 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2428 helix: -2.02 (0.66), residues: 48 sheet: 0.51 (0.16), residues: 980 loop : 0.13 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 430 TYR 0.017 0.002 TYR G 79 PHE 0.033 0.002 PHE H 67 TRP 0.031 0.003 TRP J 206 HIS 0.006 0.002 HIS G 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (20160) covalent geometry : angle 0.70729 / 0.38 (27412) SS BOND : bond 0.00635 / 0.45 ( 44) SS BOND : angle 1.49873 / 1.00 ( 88) hydrogen bonds : bond 0.04453 / 2.97 ( 652) hydrogen bonds : angle 6.80013 / 4.73 ( 1536) link_ALPHA1-2 : bond 0.01558 / 0.88 ( 8) link_ALPHA1-2 : angle 1.38805 / 0.99 ( 24) link_ALPHA1-3 : bond 0.00717 / 0.39 ( 8) link_ALPHA1-3 : angle 1.49131 / 1.10 ( 24) link_ALPHA1-6 : bond 0.01132 / 0.62 ( 8) link_ALPHA1-6 : angle 1.77424 / 1.23 ( 24) link_BETA1-4 : bond 0.01041 / 0.56 ( 8) link_BETA1-4 : angle 2.68667 / 1.86 ( 24) link_NAG-ASN : bond 0.00294 / 0.18 ( 12) link_NAG-ASN : angle 2.00070 / 1.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 428 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 372 SER cc_start: 0.8207 (p) cc_final: 0.7697 (m) REVERT: L 11 LEU cc_start: 0.7506 (mt) cc_final: 0.7260 (mp) REVERT: L 24 ARG cc_start: 0.7446 (ttm110) cc_final: 0.7109 (tpp80) REVERT: L 54 LEU cc_start: 0.8367 (mt) cc_final: 0.8130 (mm) REVERT: L 82 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6255 (t0) REVERT: H 34 MET cc_start: 0.6718 (mmp) cc_final: 0.6464 (mmt) REVERT: B 372 SER cc_start: 0.7685 (p) cc_final: 0.7292 (m) REVERT: B 413 TYR cc_start: 0.7986 (m-80) cc_final: 0.7779 (m-80) REVERT: B 433 GLU cc_start: 0.8195 (mp0) cc_final: 0.7827 (mp0) REVERT: C 24 ARG cc_start: 0.7462 (tpp80) cc_final: 0.6981 (tpp80) REVERT: C 54 LEU cc_start: 0.8129 (mt) cc_final: 0.7929 (mm) REVERT: D 55 SER cc_start: 0.6746 (t) cc_final: 0.6529 (m) REVERT: E 118 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6636 (ttp-170) REVERT: E 372 SER cc_start: 0.7832 (p) cc_final: 0.7381 (m) REVERT: E 413 TYR cc_start: 0.8054 (m-80) cc_final: 0.7844 (m-80) REVERT: E 433 GLU cc_start: 0.8288 (mp0) cc_final: 0.7942 (mp0) REVERT: F 24 ARG cc_start: 0.7536 (tpp80) cc_final: 0.6881 (tpp80) REVERT: J 372 SER cc_start: 0.8179 (p) cc_final: 0.7675 (m) REVERT: I 24 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7544 (ttm110) REVERT: I 54 LEU cc_start: 0.8452 (mt) cc_final: 0.8156 (mm) REVERT: K 34 MET cc_start: 0.6687 (mmp) cc_final: 0.6413 (mmt) REVERT: K 89 VAL cc_start: 0.7614 (t) cc_final: 0.7225 (p) outliers start: 57 outliers final: 31 residues processed: 461 average time/residue: 0.1409 time to fit residues: 100.8157 Evaluate side-chains 386 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 353 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 126 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.6359 > 50:) chunk 2 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN L 37 GLN H 50 ASN B 294 ASN E 294 ASN J 294 ASN K 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.094643 restraints weight = 25413.628| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.21 r_work: 0.3016 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 20248 Z= 0.199 Angle : 0.702 12.202 27632 Z= 0.368 Chirality : 0.046 0.236 3064 Planarity : 0.005 0.050 3464 Dihedral : 4.895 16.874 2700 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 3.65 % Allowed : 11.10 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.40 (0.18), residues: 2428 helix: -2.35 (0.54), residues: 48 sheet: 0.63 (0.17), residues: 972 loop : 0.20 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 428 TYR 0.022 0.002 TYR F 36 PHE 0.031 0.002 PHE D 67 TRP 0.025 0.002 TRP J 265 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (20160) covalent geometry : angle 0.67460 / 0.36 (27412) SS BOND : bond 0.01093 / 0.79 ( 44) SS BOND : angle 2.84601 / 1.66 ( 88) hydrogen bonds : bond 0.04084 / 2.69 ( 652) hydrogen bonds : angle 6.10937 / 4.21 ( 1536) link_ALPHA1-2 : bond 0.00951 / 0.56 ( 8) link_ALPHA1-2 : angle 2.06944 / 1.39 ( 24) link_ALPHA1-3 : bond 0.00779 / 0.42 ( 8) link_ALPHA1-3 : angle 1.20106 / 0.85 ( 24) link_ALPHA1-6 : bond 0.00822 / 0.45 ( 8) link_ALPHA1-6 : angle 1.32687 / 0.95 ( 24) link_BETA1-4 : bond 0.00974 / 0.52 ( 8) link_BETA1-4 : angle 2.10366 / 1.41 ( 24) link_NAG-ASN : bond 0.00268 / 0.18 ( 12) link_NAG-ASN : angle 1.97529 / 1.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 393 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 209 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7493 (mtp85) REVERT: A 441 ASN cc_start: 0.8678 (p0) cc_final: 0.8467 (p0) REVERT: L 24 ARG cc_start: 0.7660 (ttm110) cc_final: 0.7338 (ttm110) REVERT: L 37 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: L 54 LEU cc_start: 0.8892 (mt) cc_final: 0.8615 (mm) REVERT: H 34 MET cc_start: 0.7778 (mmp) cc_final: 0.7415 (mmt) REVERT: H 101 ASP cc_start: 0.8045 (m-30) cc_final: 0.7677 (m-30) REVERT: B 110 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 119 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8054 (mt-10) REVERT: B 372 SER cc_start: 0.8493 (p) cc_final: 0.7968 (m) REVERT: B 441 ASN cc_start: 0.8531 (p0) cc_final: 0.8295 (p0) REVERT: C 24 ARG cc_start: 0.7620 (tpp80) cc_final: 0.7206 (tpp80) REVERT: C 54 LEU cc_start: 0.8494 (mt) cc_final: 0.8194 (mm) REVERT: D 34 MET cc_start: 0.6974 (mmp) cc_final: 0.6755 (mmp) REVERT: D 55 SER cc_start: 0.7486 (t) cc_final: 0.7087 (m) REVERT: E 110 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8160 (tm-30) REVERT: E 118 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7263 (ttp-170) REVERT: F 24 ARG cc_start: 0.7670 (tpp80) cc_final: 0.7233 (tpp80) REVERT: G 34 MET cc_start: 0.6960 (mmp) cc_final: 0.6702 (mmp) REVERT: G 57 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7274 (mptt) REVERT: J 110 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8303 (tm-30) REVERT: J 463 LYS cc_start: 0.7180 (mttt) cc_final: 0.6786 (mmtt) REVERT: I 24 ARG cc_start: 0.8146 (ttm170) cc_final: 0.7617 (ttm110) REVERT: K 34 MET cc_start: 0.7815 (mmp) cc_final: 0.7460 (mmt) REVERT: K 101 ASP cc_start: 0.7984 (m-30) cc_final: 0.7660 (m-30) outliers start: 77 outliers final: 34 residues processed: 438 average time/residue: 0.1354 time to fit residues: 93.0820 Evaluate side-chains 361 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 324 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 107 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 182 optimal weight: 0.0060 chunk 174 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 chunk 186 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 52AGLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 52AGLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN E 274 HIS G 50 ASN ** G 52AGLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.089442 restraints weight = 26245.744| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.41 r_work: 0.2968 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 20248 Z= 0.164 Angle : 0.664 17.920 27632 Z= 0.343 Chirality : 0.046 0.292 3064 Planarity : 0.005 0.056 3464 Dihedral : 4.820 24.075 2700 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.06 % Favored : 97.78 % Rotamer: Outliers : 2.99 % Allowed : 14.66 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.36 (0.18), residues: 2428 helix: -2.33 (0.55), residues: 48 sheet: 0.61 (0.17), residues: 932 loop : 0.18 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 300 TYR 0.020 0.001 TYR L 36 PHE 0.048 0.002 PHE D 67 TRP 0.018 0.001 TRP D 33 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (20160) covalent geometry : angle 0.64212 / 0.34 (27412) SS BOND : bond 0.00825 / 0.55 ( 44) SS BOND : angle 2.34704 / 1.42 ( 88) hydrogen bonds : bond 0.03756 / 2.47 ( 652) hydrogen bonds : angle 6.05385 / 4.17 ( 1536) link_ALPHA1-2 : bond 0.01085 / 0.57 ( 8) link_ALPHA1-2 : angle 1.75906 / 1.23 ( 24) link_ALPHA1-3 : bond 0.00543 / 0.31 ( 8) link_ALPHA1-3 : angle 1.27475 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00630 / 0.34 ( 8) link_ALPHA1-6 : angle 1.44973 / 1.05 ( 24) link_BETA1-4 : bond 0.00728 / 0.40 ( 8) link_BETA1-4 : angle 2.07084 / 1.41 ( 24) link_NAG-ASN : bond 0.00294 / 0.19 ( 12) link_NAG-ASN : angle 1.86234 / 1.15 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 382 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 170 TYR cc_start: 0.8680 (m-80) cc_final: 0.8412 (m-80) REVERT: A 209 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7915 (mtp85) REVERT: A 254 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8192 (mt) REVERT: A 430 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8025 (mtp85) REVERT: A 441 ASN cc_start: 0.8873 (p0) cc_final: 0.8668 (p0) REVERT: L 24 ARG cc_start: 0.7781 (ttm110) cc_final: 0.7395 (ttm110) REVERT: L 31 THR cc_start: 0.8270 (p) cc_final: 0.8058 (p) REVERT: H 34 MET cc_start: 0.8221 (mmp) cc_final: 0.7865 (mmt) REVERT: B 110 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 170 TYR cc_start: 0.8638 (m-80) cc_final: 0.8380 (m-80) REVERT: B 222 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7945 (mp) REVERT: B 441 ASN cc_start: 0.8826 (p0) cc_final: 0.8570 (p0) REVERT: B 463 LYS cc_start: 0.7403 (mttt) cc_final: 0.7163 (mttp) REVERT: C 24 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7098 (tpp80) REVERT: D 82 MET cc_start: 0.7519 (mtm) cc_final: 0.7226 (mtm) REVERT: E 110 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8111 (tm-30) REVERT: E 170 TYR cc_start: 0.8676 (m-80) cc_final: 0.8412 (m-80) REVERT: E 463 LYS cc_start: 0.7349 (mttt) cc_final: 0.7138 (mttm) REVERT: F 24 ARG cc_start: 0.7843 (tpp80) cc_final: 0.7208 (tpp80) REVERT: G 101 ASP cc_start: 0.8218 (m-30) cc_final: 0.8011 (m-30) REVERT: J 110 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8182 (tm-30) REVERT: J 170 TYR cc_start: 0.8670 (m-80) cc_final: 0.8393 (m-80) REVERT: J 376 MET cc_start: 0.8490 (tpt) cc_final: 0.8254 (tpp) REVERT: J 463 LYS cc_start: 0.7435 (mttt) cc_final: 0.7221 (mttp) REVERT: I 24 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7651 (ttm110) REVERT: I 37 GLN cc_start: 0.8420 (tt0) cc_final: 0.8097 (tt0) REVERT: K 34 MET cc_start: 0.8222 (mmp) cc_final: 0.7892 (mmt) outliers start: 63 outliers final: 37 residues processed: 406 average time/residue: 0.1524 time to fit residues: 94.4267 Evaluate side-chains 371 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 332 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 252 THR Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 298 SER Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 0.1980 chunk 144 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 212 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 50 ASN B 274 HIS ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN E 441 ASN F 37 GLN J 274 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.087733 restraints weight = 25852.270| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.43 r_work: 0.2911 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 20248 Z= 0.159 Angle : 0.657 16.414 27632 Z= 0.338 Chirality : 0.045 0.261 3064 Planarity : 0.004 0.057 3464 Dihedral : 4.748 24.003 2700 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.95 % Rotamer: Outliers : 3.32 % Allowed : 15.89 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.17), residues: 2428 helix: -2.36 (0.54), residues: 48 sheet: 0.56 (0.17), residues: 948 loop : 0.16 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 82 TYR 0.030 0.002 TYR A 418 PHE 0.023 0.002 PHE D 67 TRP 0.019 0.001 TRP H 33 HIS 0.003 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (20160) covalent geometry : angle 0.63728 / 0.33 (27412) SS BOND : bond 0.00775 / 0.55 ( 44) SS BOND : angle 2.08737 / 1.27 ( 88) hydrogen bonds : bond 0.03593 / 2.32 ( 652) hydrogen bonds : angle 5.79411 / 4.02 ( 1536) link_ALPHA1-2 : bond 0.00666 / 0.40 ( 8) link_ALPHA1-2 : angle 2.09724 / 1.41 ( 24) link_ALPHA1-3 : bond 0.00604 / 0.33 ( 8) link_ALPHA1-3 : angle 1.21816 / 0.91 ( 24) link_ALPHA1-6 : bond 0.00527 / 0.28 ( 8) link_ALPHA1-6 : angle 1.36858 / 1.01 ( 24) link_BETA1-4 : bond 0.00698 / 0.38 ( 8) link_BETA1-4 : angle 1.95050 / 1.29 ( 24) link_NAG-ASN : bond 0.00129 / 0.08 ( 12) link_NAG-ASN : angle 1.85744 / 1.17 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 382 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8511 (tm-30) REVERT: A 150 HIS cc_start: 0.6749 (m-70) cc_final: 0.6402 (m-70) REVERT: A 170 TYR cc_start: 0.8776 (m-80) cc_final: 0.8552 (m-80) REVERT: A 190 MET cc_start: 0.8128 (ttm) cc_final: 0.7670 (ttp) REVERT: A 271 THR cc_start: 0.8239 (p) cc_final: 0.7990 (p) REVERT: L 24 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7288 (ttm110) REVERT: L 31 THR cc_start: 0.8319 (p) cc_final: 0.8031 (p) REVERT: L 97 THR cc_start: 0.7655 (m) cc_final: 0.7429 (m) REVERT: H 67 PHE cc_start: 0.7203 (m-80) cc_final: 0.6839 (m-80) REVERT: B 110 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 150 HIS cc_start: 0.6655 (m-70) cc_final: 0.6298 (m-70) REVERT: B 170 TYR cc_start: 0.8788 (m-80) cc_final: 0.8521 (m-80) REVERT: B 190 MET cc_start: 0.7961 (ttm) cc_final: 0.7513 (ttp) REVERT: B 254 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8099 (mt) REVERT: B 271 THR cc_start: 0.8032 (p) cc_final: 0.7799 (p) REVERT: C 24 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7196 (ttm110) REVERT: C 31 THR cc_start: 0.8209 (p) cc_final: 0.7916 (p) REVERT: E 110 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8442 (tm-30) REVERT: E 170 TYR cc_start: 0.8806 (m-80) cc_final: 0.8569 (m-80) REVERT: E 251 ASP cc_start: 0.7866 (t0) cc_final: 0.7553 (t0) REVERT: E 254 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8085 (mt) REVERT: E 269 THR cc_start: 0.7861 (t) cc_final: 0.7469 (p) REVERT: E 271 THR cc_start: 0.8086 (p) cc_final: 0.7847 (p) REVERT: F 24 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7256 (ttm110) REVERT: F 31 THR cc_start: 0.8209 (p) cc_final: 0.7920 (p) REVERT: F 82 ASP cc_start: 0.7421 (t0) cc_final: 0.6327 (t0) REVERT: G 5 VAL cc_start: 0.8706 (p) cc_final: 0.8488 (m) REVERT: G 82 MET cc_start: 0.7831 (mtm) cc_final: 0.7441 (mtm) REVERT: J 110 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8550 (tm-30) REVERT: J 170 TYR cc_start: 0.8770 (m-80) cc_final: 0.8532 (m-80) REVERT: J 190 MET cc_start: 0.7997 (ttm) cc_final: 0.7524 (ttp) REVERT: J 269 THR cc_start: 0.7980 (t) cc_final: 0.7544 (p) REVERT: J 271 THR cc_start: 0.8214 (p) cc_final: 0.7952 (p) REVERT: I 24 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7691 (ttm110) REVERT: I 37 GLN cc_start: 0.8544 (tt0) cc_final: 0.8326 (tt0) REVERT: I 97 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7384 (m) REVERT: K 67 PHE cc_start: 0.7238 (m-80) cc_final: 0.6835 (m-80) outliers start: 70 outliers final: 49 residues processed: 420 average time/residue: 0.1518 time to fit residues: 98.0097 Evaluate side-chains 384 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 252 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain K residue 70 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 1 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 176 optimal weight: 0.0070 chunk 36 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN B 333 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 ASN ** J 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 = 0.3283 r_free = 0.3283 target = 0.108946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.079678 restraints weight = 26467.387| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.32 r_work: 0.2779 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 1.0009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 20248 Z= 0.266 Angle : 0.754 16.788 27632 Z= 0.392 Chirality : 0.049 0.306 3064 Planarity : 0.005 0.079 3464 Dihedral : 5.194 25.731 2700 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 3.42 % Allowed : 16.27 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -0.02 (0.17), residues: 2428 helix: -2.95 (0.39), residues: 48 sheet: 0.37 (0.17), residues: 980 loop : -0.10 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 61 TYR 0.023 0.002 TYR F 36 PHE 0.032 0.003 PHE D 67 TRP 0.024 0.002 TRP G 33 HIS 0.007 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.27 (20160) covalent geometry : angle 0.72725 / 0.38 (27412) SS BOND : bond 0.00747 / 0.53 ( 44) SS BOND : angle 2.78168 / 1.88 ( 88) hydrogen bonds : bond 0.04277 / 2.78 ( 652) hydrogen bonds : angle 6.18202 / 4.31 ( 1536) link_ALPHA1-2 : bond 0.00323 / 0.18 ( 8) link_ALPHA1-2 : angle 2.25782 / 1.58 ( 24) link_ALPHA1-3 : bond 0.00437 / 0.25 ( 8) link_ALPHA1-3 : angle 1.25766 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00308 / 0.17 ( 8) link_ALPHA1-6 : angle 1.50328 / 1.10 ( 24) link_BETA1-4 : bond 0.00588 / 0.32 ( 8) link_BETA1-4 : angle 2.43133 / 1.62 ( 24) link_NAG-ASN : bond 0.00310 / 0.18 ( 12) link_NAG-ASN : angle 2.27534 / 1.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 316 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8281 (ttm) cc_final: 0.7838 (ttp) REVERT: A 269 THR cc_start: 0.8083 (t) cc_final: 0.7585 (p) REVERT: L 97 THR cc_start: 0.7674 (OUTLIER) cc_final: 0.7449 (m) REVERT: B 170 ASN cc_start: 0.8393 (t0) cc_final: 0.8138 (t0) REVERT: B 190 MET cc_start: 0.8234 (ttm) cc_final: 0.7813 (ttp) REVERT: B 254 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8287 (mt) REVERT: C 24 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7617 (ttm110) REVERT: E 190 MET cc_start: 0.8314 (ttm) cc_final: 0.8042 (ttp) REVERT: E 254 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8357 (mt) REVERT: E 269 THR cc_start: 0.8011 (t) cc_final: 0.7590 (p) REVERT: E 356 ASP cc_start: 0.8510 (t0) cc_final: 0.8289 (t0) REVERT: F 24 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7638 (ttm110) REVERT: F 97 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.7486 (m) REVERT: J 170 ASN cc_start: 0.8269 (t0) cc_final: 0.8045 (t0) REVERT: J 190 MET cc_start: 0.8265 (ttm) cc_final: 0.7758 (ttp) REVERT: J 227 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: J 269 THR cc_start: 0.8035 (t) cc_final: 0.7565 (p) REVERT: J 376 MET cc_start: 0.8697 (mmm) cc_final: 0.8430 (mmm) REVERT: I 24 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7600 (ttm110) REVERT: I 96 TYR cc_start: 0.9157 (m-80) cc_final: 0.8929 (m-80) REVERT: K 52 LYS cc_start: 0.7538 (tttt) cc_final: 0.7300 (tttp) REVERT: K 66 ARG cc_start: 0.5635 (mtm110) cc_final: 0.5350 (mtm110) outliers start: 72 outliers final: 38 residues processed: 362 average time/residue: 0.1441 time to fit residues: 80.6008 Evaluate side-chains 328 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 252 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 60 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.081367 restraints weight = 25478.518| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.39 r_work: 0.2811 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 1.0266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 20248 Z= 0.139 Angle : 0.637 15.164 27632 Z= 0.329 Chirality : 0.044 0.293 3064 Planarity : 0.004 0.056 3464 Dihedral : 4.837 24.285 2700 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.35 % Favored : 97.49 % Rotamer: Outliers : 2.47 % Allowed : 16.75 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.07 (0.17), residues: 2428 helix: -2.75 (0.41), residues: 48 sheet: 0.48 (0.17), residues: 972 loop : -0.09 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 24 TYR 0.014 0.001 TYR E 121 PHE 0.037 0.002 PHE D 67 TRP 0.012 0.001 TRP J 206 HIS 0.007 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (20160) covalent geometry : angle 0.61459 / 0.32 (27412) SS BOND : bond 0.00719 / 0.51 ( 44) SS BOND : angle 2.26287 / 1.45 ( 88) hydrogen bonds : bond 0.03522 / 2.28 ( 652) hydrogen bonds : angle 5.90835 / 4.10 ( 1536) link_ALPHA1-2 : bond 0.00707 / 0.40 ( 8) link_ALPHA1-2 : angle 2.18465 / 1.47 ( 24) link_ALPHA1-3 : bond 0.00656 / 0.36 ( 8) link_ALPHA1-3 : angle 1.16683 / 0.88 ( 24) link_ALPHA1-6 : bond 0.00437 / 0.24 ( 8) link_ALPHA1-6 : angle 1.43287 / 1.06 ( 24) link_BETA1-4 : bond 0.00573 / 0.31 ( 8) link_BETA1-4 : angle 1.93274 / 1.30 ( 24) link_NAG-ASN : bond 0.00049 / 0.03 ( 12) link_NAG-ASN : angle 1.81540 / 1.15 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 274 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8343 (ttm) cc_final: 0.7861 (ttp) REVERT: A 251 ASP cc_start: 0.7706 (t0) cc_final: 0.7184 (m-30) REVERT: A 269 THR cc_start: 0.8165 (t) cc_final: 0.7713 (p) REVERT: H 38 ARG cc_start: 0.7859 (ptt180) cc_final: 0.7542 (ptt180) REVERT: B 170 ASN cc_start: 0.8314 (t0) cc_final: 0.8067 (t0) REVERT: B 190 MET cc_start: 0.8238 (ttm) cc_final: 0.7773 (ttp) REVERT: B 209 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8276 (mtp85) REVERT: B 251 ASP cc_start: 0.7620 (t0) cc_final: 0.7072 (m-30) REVERT: C 24 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7632 (ttm110) REVERT: C 79 GLN cc_start: 0.7972 (mt0) cc_final: 0.7558 (mp10) REVERT: C 100 GLN cc_start: 0.8861 (mm-40) cc_final: 0.7447 (pm20) REVERT: E 190 MET cc_start: 0.8279 (ttm) cc_final: 0.7933 (ttp) REVERT: E 209 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8300 (mtp85) REVERT: E 269 THR cc_start: 0.8120 (t) cc_final: 0.7702 (p) REVERT: E 376 MET cc_start: 0.8464 (mmm) cc_final: 0.8248 (mmm) REVERT: F 24 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7643 (ttm110) REVERT: F 82 ASP cc_start: 0.7503 (t0) cc_final: 0.6842 (t0) REVERT: G 5 VAL cc_start: 0.8658 (p) cc_final: 0.8390 (m) REVERT: G 81 GLN cc_start: 0.6734 (tt0) cc_final: 0.6394 (tt0) REVERT: J 121 TYR cc_start: 0.8841 (p90) cc_final: 0.8042 (p90) REVERT: J 150 HIS cc_start: 0.7572 (m-70) cc_final: 0.6820 (m-70) REVERT: J 190 MET cc_start: 0.8267 (ttm) cc_final: 0.7802 (ttp) REVERT: J 269 THR cc_start: 0.8164 (t) cc_final: 0.7686 (p) REVERT: I 24 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7589 (ttm110) REVERT: I 96 TYR cc_start: 0.9185 (m-80) cc_final: 0.8867 (m-80) REVERT: K 66 ARG cc_start: 0.5539 (mtm110) cc_final: 0.5252 (mtm110) outliers start: 52 outliers final: 30 residues processed: 301 average time/residue: 0.1484 time to fit residues: 69.0794 Evaluate side-chains 290 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 260 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 252 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain K residue 35 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 231 optimal weight: 0.0270 chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.079409 restraints weight = 25487.476| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.24 r_work: 0.2790 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 1.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20248 Z= 0.181 Angle : 0.660 14.769 27632 Z= 0.340 Chirality : 0.046 0.299 3064 Planarity : 0.004 0.054 3464 Dihedral : 4.851 23.251 2700 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.29 % Favored : 96.54 % Rotamer: Outliers : 2.09 % Allowed : 17.03 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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 (0.17), residues: 2428 helix: -2.89 (0.37), residues: 48 sheet: 0.46 (0.17), residues: 1000 loop : -0.15 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 24 TYR 0.015 0.001 TYR J 121 PHE 0.035 0.002 PHE D 67 TRP 0.016 0.001 TRP K 33 HIS 0.009 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (20160) covalent geometry : angle 0.63736 / 0.33 (27412) SS BOND : bond 0.00677 / 0.48 ( 44) SS BOND : angle 2.26570 / 1.44 ( 88) hydrogen bonds : bond 0.03644 / 2.37 ( 652) hydrogen bonds : angle 5.93589 / 4.12 ( 1536) link_ALPHA1-2 : bond 0.00560 / 0.31 ( 8) link_ALPHA1-2 : angle 2.27795 / 1.57 ( 24) link_ALPHA1-3 : bond 0.00568 / 0.31 ( 8) link_ALPHA1-3 : angle 1.20720 / 0.92 ( 24) link_ALPHA1-6 : bond 0.00326 / 0.18 ( 8) link_ALPHA1-6 : angle 1.49377 / 1.10 ( 24) link_BETA1-4 : bond 0.00579 / 0.31 ( 8) link_BETA1-4 : angle 2.12085 / 1.42 ( 24) link_NAG-ASN : bond 0.00150 / 0.08 ( 12) link_NAG-ASN : angle 1.90889 / 1.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASN cc_start: 0.8319 (t0) cc_final: 0.7944 (t0) REVERT: A 190 MET cc_start: 0.8371 (ttm) cc_final: 0.7907 (ttp) REVERT: A 251 ASP cc_start: 0.7782 (t0) cc_final: 0.7265 (m-30) REVERT: A 269 THR cc_start: 0.8192 (t) cc_final: 0.7710 (p) REVERT: L 5 THR cc_start: 0.8113 (p) cc_final: 0.7912 (p) REVERT: L 24 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7322 (ttm110) REVERT: H 38 ARG cc_start: 0.7932 (ptt180) cc_final: 0.7711 (ptt180) REVERT: H 66 ARG cc_start: 0.6345 (mtp85) cc_final: 0.6136 (mtm110) REVERT: B 170 ASN cc_start: 0.8285 (t0) cc_final: 0.7947 (t0) REVERT: B 190 MET cc_start: 0.8292 (ttm) cc_final: 0.7841 (ttp) REVERT: B 209 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8392 (mtp85) REVERT: B 227 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: B 251 ASP cc_start: 0.7663 (t0) cc_final: 0.7173 (m-30) REVERT: B 269 THR cc_start: 0.8166 (t) cc_final: 0.7711 (p) REVERT: D 38 ARG cc_start: 0.7822 (ptt180) cc_final: 0.7488 (ptt180) REVERT: E 190 MET cc_start: 0.8259 (ttm) cc_final: 0.7881 (ttp) REVERT: E 209 ARG cc_start: 0.8634 (mtp85) cc_final: 0.8400 (mtp85) REVERT: E 269 THR cc_start: 0.8146 (t) cc_final: 0.7701 (p) REVERT: F 24 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7525 (ttm110) REVERT: F 82 ASP cc_start: 0.7563 (t0) cc_final: 0.6891 (t0) REVERT: G 81 GLN cc_start: 0.6967 (tt0) cc_final: 0.6673 (tt0) REVERT: J 121 TYR cc_start: 0.8867 (p90) cc_final: 0.8077 (p90) REVERT: J 190 MET cc_start: 0.8305 (ttm) cc_final: 0.7847 (ttp) REVERT: J 227 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: J 269 THR cc_start: 0.8161 (t) cc_final: 0.7668 (p) REVERT: I 24 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7592 (ttm110) REVERT: I 96 TYR cc_start: 0.9284 (m-80) cc_final: 0.8961 (m-80) REVERT: K 39 GLN cc_start: 0.8391 (tt0) cc_final: 0.7863 (tt0) outliers start: 44 outliers final: 35 residues processed: 281 average time/residue: 0.1491 time to fit residues: 64.6709 Evaluate side-chains 278 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 252 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 101 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 161 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.077354 restraints weight = 26057.163| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.30 r_work: 0.2745 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 1.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 20248 Z= 0.229 Angle : 0.703 17.112 27632 Z= 0.362 Chirality : 0.048 0.320 3064 Planarity : 0.005 0.055 3464 Dihedral : 5.072 21.828 2700 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Rotamer: Outliers : 2.51 % Allowed : 16.46 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -0.14 (0.17), residues: 2428 helix: -3.02 (0.38), residues: 48 sheet: 0.39 (0.17), residues: 1000 loop : -0.28 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.019 0.002 TYR E 121 PHE 0.052 0.003 PHE D 67 TRP 0.014 0.001 TRP D 33 HIS 0.018 0.002 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (20160) covalent geometry : angle 0.68004 / 0.36 (27412) SS BOND : bond 0.00791 / 0.56 ( 44) SS BOND : angle 2.36812 / 1.52 ( 88) hydrogen bonds : bond 0.04010 / 2.60 ( 652) hydrogen bonds : angle 6.02026 / 4.21 ( 1536) link_ALPHA1-2 : bond 0.00457 / 0.25 ( 8) link_ALPHA1-2 : angle 2.35750 / 1.61 ( 24) link_ALPHA1-3 : bond 0.00636 / 0.35 ( 8) link_ALPHA1-3 : angle 1.17885 / 0.89 ( 24) link_ALPHA1-6 : bond 0.00314 / 0.17 ( 8) link_ALPHA1-6 : angle 1.48738 / 1.10 ( 24) link_BETA1-4 : bond 0.00545 / 0.29 ( 8) link_BETA1-4 : angle 2.29901 / 1.53 ( 24) link_NAG-ASN : bond 0.00146 / 0.08 ( 12) link_NAG-ASN : angle 1.94601 / 1.23 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8447 (ttm) cc_final: 0.7959 (ttp) REVERT: A 251 ASP cc_start: 0.7849 (t0) cc_final: 0.7416 (m-30) REVERT: A 269 THR cc_start: 0.8315 (t) cc_final: 0.7796 (p) REVERT: H 25 SER cc_start: 0.7860 (t) cc_final: 0.7653 (t) REVERT: H 38 ARG cc_start: 0.8019 (ptt180) cc_final: 0.7813 (ptt180) REVERT: H 56 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 190 MET cc_start: 0.8394 (ttm) cc_final: 0.7927 (ttp) REVERT: B 209 ARG cc_start: 0.8679 (mtp85) cc_final: 0.8437 (mtp85) REVERT: B 251 ASP cc_start: 0.7807 (t0) cc_final: 0.7281 (m-30) REVERT: B 269 THR cc_start: 0.8293 (t) cc_final: 0.7832 (p) REVERT: C 96 TYR cc_start: 0.9320 (m-80) cc_final: 0.8949 (m-80) REVERT: D 38 ARG cc_start: 0.7911 (ptt180) cc_final: 0.7665 (ptt180) REVERT: E 190 MET cc_start: 0.8360 (ttm) cc_final: 0.8000 (ttp) REVERT: E 209 ARG cc_start: 0.8678 (mtp85) cc_final: 0.8448 (mtp85) REVERT: E 269 THR cc_start: 0.8245 (t) cc_final: 0.7746 (p) REVERT: G 52 LYS cc_start: 0.7755 (tttt) cc_final: 0.7520 (tttp) REVERT: J 190 MET cc_start: 0.8414 (ttm) cc_final: 0.7949 (ttp) REVERT: J 269 THR cc_start: 0.8242 (t) cc_final: 0.7721 (p) REVERT: I 24 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7589 (ttm110) REVERT: I 96 TYR cc_start: 0.9331 (m-80) cc_final: 0.9005 (m-80) REVERT: K 52 LYS cc_start: 0.7753 (tttt) cc_final: 0.7500 (tttp) outliers start: 53 outliers final: 45 residues processed: 274 average time/residue: 0.1423 time to fit residues: 60.6588 Evaluate side-chains 266 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 252 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 214 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 206 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN H 50 ASN B 441 ASN E 441 ASN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.080903 restraints weight = 25809.625| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.30 r_work: 0.2798 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 1.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 20248 Z= 0.129 Angle : 0.615 14.835 27632 Z= 0.316 Chirality : 0.044 0.283 3064 Planarity : 0.004 0.054 3464 Dihedral : 4.712 20.945 2700 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 1.57 % Allowed : 17.98 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.04 (0.17), residues: 2428 helix: -2.86 (0.38), residues: 48 sheet: 0.54 (0.16), residues: 1004 loop : -0.19 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 24 TYR 0.012 0.001 TYR E 121 PHE 0.035 0.002 PHE D 67 TRP 0.012 0.001 TRP J 206 HIS 0.007 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (20160) covalent geometry : angle 0.59689 / 0.31 (27412) SS BOND : bond 0.00670 / 0.48 ( 44) SS BOND : angle 1.84248 / 1.15 ( 88) hydrogen bonds : bond 0.03379 / 2.20 ( 652) hydrogen bonds : angle 5.87479 / 4.08 ( 1536) link_ALPHA1-2 : bond 0.00726 / 0.40 ( 8) link_ALPHA1-2 : angle 2.21273 / 1.47 ( 24) link_ALPHA1-3 : bond 0.00731 / 0.40 ( 8) link_ALPHA1-3 : angle 1.16787 / 0.88 ( 24) link_ALPHA1-6 : bond 0.00462 / 0.25 ( 8) link_ALPHA1-6 : angle 1.44896 / 1.07 ( 24) link_BETA1-4 : bond 0.00548 / 0.30 ( 8) link_BETA1-4 : angle 1.90203 / 1.29 ( 24) link_NAG-ASN : bond 0.00119 / 0.08 ( 12) link_NAG-ASN : angle 1.60489 / 1.02 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8332 (ttm) cc_final: 0.7914 (ttp) REVERT: A 251 ASP cc_start: 0.7647 (t0) cc_final: 0.7383 (m-30) REVERT: A 269 THR cc_start: 0.8253 (t) cc_final: 0.7733 (p) REVERT: H 25 SER cc_start: 0.7693 (t) cc_final: 0.7466 (t) REVERT: H 56 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 190 MET cc_start: 0.8286 (ttm) cc_final: 0.7898 (ttp) REVERT: B 251 ASP cc_start: 0.7602 (t0) cc_final: 0.7357 (m-30) REVERT: B 269 THR cc_start: 0.8201 (t) cc_final: 0.7749 (p) REVERT: C 24 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7655 (ttm110) REVERT: D 38 ARG cc_start: 0.7852 (ptt180) cc_final: 0.7615 (ptt180) REVERT: D 56 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7943 (mt-10) REVERT: D 67 PHE cc_start: 0.6514 (m-80) cc_final: 0.6202 (m-80) REVERT: E 190 MET cc_start: 0.8310 (ttm) cc_final: 0.7991 (ttp) REVERT: E 269 THR cc_start: 0.8203 (t) cc_final: 0.7698 (p) REVERT: F 82 ASP cc_start: 0.7605 (t0) cc_final: 0.6882 (t0) REVERT: G 67 PHE cc_start: 0.6346 (m-80) cc_final: 0.6035 (m-80) REVERT: J 190 MET cc_start: 0.8314 (ttm) cc_final: 0.7915 (ttp) REVERT: J 269 THR cc_start: 0.8229 (t) cc_final: 0.7708 (p) REVERT: I 24 ARG cc_start: 0.7716 (ttm170) cc_final: 0.7470 (ttm110) REVERT: I 96 TYR cc_start: 0.9254 (m-80) cc_final: 0.8834 (m-80) outliers start: 33 outliers final: 26 residues processed: 259 average time/residue: 0.1532 time to fit residues: 60.4399 Evaluate side-chains 252 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 252 THR Chi-restraints excluded: chain J residue 280 CYS Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 14 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52AGLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.080512 restraints weight = 25836.585| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.30 r_work: 0.2790 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 1.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20248 Z= 0.146 Angle : 0.617 14.602 27632 Z= 0.318 Chirality : 0.045 0.281 3064 Planarity : 0.004 0.054 3464 Dihedral : 4.678 21.245 2700 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.12 % Rotamer: Outliers : 1.38 % Allowed : 18.03 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.07 (0.17), residues: 2428 helix: -2.71 (0.40), residues: 48 sheet: 0.59 (0.17), residues: 1004 loop : -0.20 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 24 TYR 0.014 0.001 TYR E 121 PHE 0.034 0.002 PHE D 67 TRP 0.012 0.001 TRP H 33 HIS 0.009 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (20160) covalent geometry : angle 0.59744 / 0.31 (27412) SS BOND : bond 0.00658 / 0.47 ( 44) SS BOND : angle 1.95792 / 1.22 ( 88) hydrogen bonds : bond 0.03416 / 2.22 ( 652) hydrogen bonds : angle 5.80757 / 4.04 ( 1536) link_ALPHA1-2 : bond 0.00665 / 0.37 ( 8) link_ALPHA1-2 : angle 2.22019 / 1.50 ( 24) link_ALPHA1-3 : bond 0.00651 / 0.35 ( 8) link_ALPHA1-3 : angle 1.20623 / 0.91 ( 24) link_ALPHA1-6 : bond 0.00405 / 0.22 ( 8) link_ALPHA1-6 : angle 1.47524 / 1.09 ( 24) link_BETA1-4 : bond 0.00577 / 0.31 ( 8) link_BETA1-4 : angle 2.03144 / 1.37 ( 24) link_NAG-ASN : bond 0.00068 / 0.04 ( 12) link_NAG-ASN : angle 1.69299 / 1.08 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5402.70 seconds wall clock time: 93 minutes 16.77 seconds (5596.77 seconds total)