Starting phenix.real_space_refine on Thu Mar 5 05:57:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u02_20594/03_2026/6u02_20594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u02_20594/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6u02_20594/03_2026/6u02_20594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u02_20594/03_2026/6u02_20594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u02_20594/03_2026/6u02_20594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u02_20594/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 27 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 dihedrals: 6 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: 3.67, per 1000 atoms: 0.19 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: 1.80 Conformation dependent library (CDL) restraints added in 765.2 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: 0.99 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: 4.07 Time building geometry restraints manager: 2.27 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 - 21.67: 12088 21.67 - 43.35: 292 43.35 - 65.02: 80 65.02 - 86.70: 40 86.70 - 108.37: 20 Dihedral angle restraints: 12520 sinusoidal: 5464 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 12517 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.680 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 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 : 12.227 108.370 7900 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 covalent geometry : bond 0.02240 (20160) covalent geometry : angle 1.79095 (27412) SS BOND : bond 0.01923 ( 44) SS BOND : angle 3.40782 ( 88) hydrogen bonds : bond 0.16992 ( 652) hydrogen bonds : angle 8.80511 ( 1536) link_ALPHA1-2 : bond 0.03500 ( 8) link_ALPHA1-2 : angle 3.43187 ( 24) link_ALPHA1-3 : bond 0.03201 ( 8) link_ALPHA1-3 : angle 2.32301 ( 24) link_ALPHA1-6 : bond 0.02368 ( 8) link_ALPHA1-6 : angle 2.92899 ( 24) link_BETA1-4 : bond 0.03579 ( 8) link_BETA1-4 : angle 3.25865 ( 24) link_NAG-ASN : bond 0.02841 ( 12) link_NAG-ASN : angle 2.80047 ( 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 : 0.699 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: 0.1434 time to fit residues: 135.4026 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 : 0.591 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 325 ASN A 329 ASN L 37 GLN B 325 ASN B 329 ASN D 50 ASN D 81 GLN E 329 ASN F 37 GLN G 50 ASN J 325 ASN I 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091409 restraints weight = 25744.183| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.44 r_work: 0.2980 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20248 Z= 0.213 Angle : 0.767 8.844 27632 Z= 0.400 Chirality : 0.049 0.191 3064 Planarity : 0.006 0.058 3464 Dihedral : 8.956 75.797 3568 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.28 % Rotamer: Outliers : 2.61 % Allowed : 9.72 % Favored : 87.67 % 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: 0.20 (0.17), residues: 2428 helix: -2.10 (0.65), residues: 48 sheet: 0.48 (0.16), residues: 960 loop : 0.06 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 292 TYR 0.018 0.002 TYR G 79 PHE 0.038 0.002 PHE H 67 TRP 0.036 0.003 TRP J 206 HIS 0.004 0.002 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00477 (20160) covalent geometry : angle 0.75247 (27412) SS BOND : bond 0.00416 ( 44) SS BOND : angle 1.38304 ( 88) hydrogen bonds : bond 0.04306 ( 652) hydrogen bonds : angle 6.81356 ( 1536) link_ALPHA1-2 : bond 0.01260 ( 8) link_ALPHA1-2 : angle 1.61754 ( 24) link_ALPHA1-3 : bond 0.01050 ( 8) link_ALPHA1-3 : angle 2.01735 ( 24) link_ALPHA1-6 : bond 0.01121 ( 8) link_ALPHA1-6 : angle 1.47590 ( 24) link_BETA1-4 : bond 0.00802 ( 8) link_BETA1-4 : angle 2.74675 ( 24) link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 2.19833 ( 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 487 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 432 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 SER cc_start: 0.8256 (p) cc_final: 0.7757 (m) REVERT: L 11 LEU cc_start: 0.7515 (mt) cc_final: 0.7285 (mp) REVERT: L 24 ARG cc_start: 0.7459 (ttm110) cc_final: 0.7217 (tpp80) REVERT: L 54 LEU cc_start: 0.8408 (mt) cc_final: 0.8173 (mm) REVERT: L 82 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6209 (t0) REVERT: H 34 MET cc_start: 0.6804 (mmp) cc_final: 0.6570 (mmt) REVERT: H 91 TYR cc_start: 0.6174 (m-80) cc_final: 0.5913 (m-80) REVERT: B 372 SER cc_start: 0.7803 (p) cc_final: 0.7356 (m) REVERT: B 433 GLU cc_start: 0.8168 (mp0) cc_final: 0.7821 (mp0) REVERT: C 54 LEU cc_start: 0.8198 (mt) cc_final: 0.7976 (mm) REVERT: E 118 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.6640 (ttp-170) REVERT: E 119 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7452 (mt-10) REVERT: E 174 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7268 (mm-30) REVERT: E 372 SER cc_start: 0.7954 (p) cc_final: 0.7473 (m) REVERT: E 433 GLU cc_start: 0.8358 (mp0) cc_final: 0.8030 (mp0) REVERT: F 24 ARG cc_start: 0.7544 (tpp80) cc_final: 0.6919 (tpp80) REVERT: F 54 LEU cc_start: 0.8141 (mt) cc_final: 0.7936 (mm) REVERT: J 372 SER cc_start: 0.8235 (p) cc_final: 0.7762 (m) REVERT: I 24 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7535 (ttm110) REVERT: I 54 LEU cc_start: 0.8493 (mt) cc_final: 0.8200 (mm) REVERT: K 34 MET cc_start: 0.6821 (mmp) cc_final: 0.6566 (mmt) outliers start: 55 outliers final: 27 residues processed: 464 average time/residue: 0.1381 time to fit residues: 98.7206 Evaluate side-chains 379 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 350 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain B residue 205 VAL 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 74 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 70 SER 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 7 SER 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 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 126 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN H 50 ASN H 72 HIS B 294 ASN B 325 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 HIS E 294 ASN G 72 HIS J 294 ASN K 50 ASN K 72 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.089950 restraints weight = 26128.433| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.42 r_work: 0.3007 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 20248 Z= 0.191 Angle : 0.693 12.204 27632 Z= 0.364 Chirality : 0.047 0.320 3064 Planarity : 0.005 0.057 3464 Dihedral : 7.418 57.716 3568 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 2.89 % Allowed : 12.24 % Favored : 84.87 % 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: 0.37 (0.18), residues: 2428 helix: -2.41 (0.51), residues: 48 sheet: 0.58 (0.17), residues: 972 loop : 0.22 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 156 TYR 0.016 0.002 TYR B 155 PHE 0.037 0.002 PHE G 67 TRP 0.030 0.002 TRP J 206 HIS 0.004 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00443 (20160) covalent geometry : angle 0.67799 (27412) SS BOND : bond 0.00651 ( 44) SS BOND : angle 1.54863 ( 88) hydrogen bonds : bond 0.04185 ( 652) hydrogen bonds : angle 6.12483 ( 1536) link_ALPHA1-2 : bond 0.00783 ( 8) link_ALPHA1-2 : angle 2.67135 ( 24) link_ALPHA1-3 : bond 0.01152 ( 8) link_ALPHA1-3 : angle 0.87542 ( 24) link_ALPHA1-6 : bond 0.00906 ( 8) link_ALPHA1-6 : angle 1.16692 ( 24) link_BETA1-4 : bond 0.01024 ( 8) link_BETA1-4 : angle 1.99069 ( 24) link_NAG-ASN : bond 0.00244 ( 12) link_NAG-ASN : angle 1.89724 ( 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 465 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 404 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8280 (tm-30) REVERT: A 209 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7616 (mtp85) REVERT: L 24 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7342 (ttm110) REVERT: H 34 MET cc_start: 0.7825 (mmp) cc_final: 0.7501 (mmt) REVERT: B 110 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 119 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 441 ASN cc_start: 0.8541 (p0) cc_final: 0.8271 (p0) REVERT: C 24 ARG cc_start: 0.7686 (tpp80) cc_final: 0.7251 (tpp80) REVERT: C 54 LEU cc_start: 0.8529 (mt) cc_final: 0.8261 (mm) REVERT: E 110 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8197 (tm-30) REVERT: E 372 SER cc_start: 0.8576 (p) cc_final: 0.8069 (m) REVERT: F 24 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7252 (tpp80) REVERT: F 54 LEU cc_start: 0.8492 (mt) cc_final: 0.8245 (mm) REVERT: G 61 ASP cc_start: 0.7878 (m-30) cc_final: 0.7593 (m-30) REVERT: G 62 SER cc_start: 0.7053 (m) cc_final: 0.6832 (p) REVERT: J 110 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8330 (tm-30) REVERT: J 376 MET cc_start: 0.8257 (tpt) cc_final: 0.8039 (tpt) REVERT: J 463 LYS cc_start: 0.7133 (mttt) cc_final: 0.6644 (mmtt) REVERT: I 24 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7644 (ttm110) REVERT: K 34 MET cc_start: 0.7800 (mmp) cc_final: 0.7414 (mmt) outliers start: 61 outliers final: 27 residues processed: 440 average time/residue: 0.1466 time to fit residues: 99.4372 Evaluate side-chains 362 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 335 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 379 VAL Chi-restraints excluded: chain L residue 60 SER 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 245 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 21 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 SER 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 254 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 107 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 186 optimal weight: 0.0870 chunk 139 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN D 50 ASN D 52AGLN D 72 HIS E 329 ASN F 37 GLN G 50 ASN ** G 52AGLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090050 restraints weight = 25722.376| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.43 r_work: 0.2939 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.7553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 20248 Z= 0.180 Angle : 0.695 17.693 27632 Z= 0.355 Chirality : 0.048 0.285 3064 Planarity : 0.005 0.054 3464 Dihedral : 6.995 49.245 3568 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 3.56 % Allowed : 14.61 % Favored : 81.83 % 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: 0.35 (0.18), residues: 2428 helix: -2.40 (0.52), residues: 48 sheet: 0.59 (0.17), residues: 944 loop : 0.18 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 300 TYR 0.016 0.002 TYR A 121 PHE 0.023 0.002 PHE G 67 TRP 0.020 0.002 TRP G 33 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00435 (20160) covalent geometry : angle 0.67625 (27412) SS BOND : bond 0.00913 ( 44) SS BOND : angle 2.06752 ( 88) hydrogen bonds : bond 0.03610 ( 652) hydrogen bonds : angle 6.08053 ( 1536) link_ALPHA1-2 : bond 0.00683 ( 8) link_ALPHA1-2 : angle 2.10965 ( 24) link_ALPHA1-3 : bond 0.00689 ( 8) link_ALPHA1-3 : angle 1.30191 ( 24) link_ALPHA1-6 : bond 0.00639 ( 8) link_ALPHA1-6 : angle 1.35682 ( 24) link_BETA1-4 : bond 0.00608 ( 8) link_BETA1-4 : angle 2.06435 ( 24) link_NAG-ASN : bond 0.00381 ( 12) link_NAG-ASN : angle 1.99257 ( 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 467 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 392 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8231 (tm-30) REVERT: A 170 TYR cc_start: 0.8720 (m-80) cc_final: 0.8438 (m-80) REVERT: A 209 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7877 (mtp85) REVERT: A 251 ASP cc_start: 0.7568 (t0) cc_final: 0.7367 (t0) REVERT: A 254 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8185 (mt) REVERT: A 271 THR cc_start: 0.8013 (p) cc_final: 0.7788 (p) REVERT: L 24 ARG cc_start: 0.7692 (ttm110) cc_final: 0.7318 (ttm110) REVERT: L 31 THR cc_start: 0.8179 (p) cc_final: 0.7968 (p) REVERT: L 37 GLN cc_start: 0.8295 (tt0) cc_final: 0.7977 (tt0) REVERT: H 34 MET cc_start: 0.8210 (mmp) cc_final: 0.7838 (mmt) REVERT: H 67 PHE cc_start: 0.7104 (m-80) cc_final: 0.6520 (m-80) REVERT: B 110 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 170 TYR cc_start: 0.8679 (m-80) cc_final: 0.8473 (m-80) REVERT: B 339 ASP cc_start: 0.9095 (m-30) cc_final: 0.8860 (m-30) REVERT: B 463 LYS cc_start: 0.7263 (mttt) cc_final: 0.7009 (mttp) REVERT: C 24 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7119 (tpp80) REVERT: D 31 SER cc_start: 0.6568 (m) cc_final: 0.6331 (t) REVERT: D 101 ASP cc_start: 0.8114 (m-30) cc_final: 0.7882 (m-30) REVERT: E 110 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8096 (tm-30) REVERT: E 269 THR cc_start: 0.7626 (t) cc_final: 0.7328 (p) REVERT: F 24 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7347 (ttm110) REVERT: G 5 VAL cc_start: 0.8578 (p) cc_final: 0.8338 (m) REVERT: G 101 ASP cc_start: 0.8114 (m-30) cc_final: 0.7859 (m-30) REVERT: J 110 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8175 (tm-30) REVERT: J 170 TYR cc_start: 0.8695 (m-80) cc_final: 0.8411 (m-80) REVERT: J 271 THR cc_start: 0.8024 (p) cc_final: 0.7796 (p) REVERT: I 24 ARG cc_start: 0.8028 (ttm170) cc_final: 0.7585 (ttm110) REVERT: I 31 THR cc_start: 0.8278 (p) cc_final: 0.8061 (p) REVERT: I 37 GLN cc_start: 0.8437 (tt0) cc_final: 0.8182 (tt0) REVERT: K 34 MET cc_start: 0.8198 (mmp) cc_final: 0.7756 (mmt) REVERT: K 67 PHE cc_start: 0.7061 (m-80) cc_final: 0.6534 (m-80) REVERT: K 79 TYR cc_start: 0.7542 (m-80) cc_final: 0.7288 (m-80) outliers start: 75 outliers final: 45 residues processed: 430 average time/residue: 0.1512 time to fit residues: 98.6054 Evaluate side-chains 386 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 340 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 H residue 7 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 398 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 239 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain J residue 93 THR 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 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 Chi-restraints excluded: chain K residue 35 SER 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: 0.0570 chunk 144 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS A 333 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN E 333 ASN E 441 ASN F 37 GLN J 98 HIS J 274 HIS J 333 ASN J 441 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.081999 restraints weight = 26129.899| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.39 r_work: 0.2822 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.9553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 20248 Z= 0.231 Angle : 0.759 17.074 27632 Z= 0.391 Chirality : 0.049 0.305 3064 Planarity : 0.005 0.056 3464 Dihedral : 7.405 52.154 3568 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.88 % Rotamer: Outliers : 3.84 % Allowed : 15.42 % Favored : 80.74 % 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: 0.08 (0.17), residues: 2428 helix: -2.77 (0.45), residues: 48 sheet: 0.43 (0.17), residues: 976 loop : -0.02 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 82 TYR 0.026 0.002 TYR E 121 PHE 0.039 0.002 PHE G 67 TRP 0.026 0.002 TRP H 33 HIS 0.005 0.001 HIS E 98 Details of bonding type rmsd covalent geometry : bond 0.00562 (20160) covalent geometry : angle 0.73601 (27412) SS BOND : bond 0.00724 ( 44) SS BOND : angle 2.46135 ( 88) hydrogen bonds : bond 0.04226 ( 652) hydrogen bonds : angle 6.11328 ( 1536) link_ALPHA1-2 : bond 0.00596 ( 8) link_ALPHA1-2 : angle 2.63525 ( 24) link_ALPHA1-3 : bond 0.01202 ( 8) link_ALPHA1-3 : angle 1.02722 ( 24) link_ALPHA1-6 : bond 0.00579 ( 8) link_ALPHA1-6 : angle 1.32647 ( 24) link_BETA1-4 : bond 0.00920 ( 8) link_BETA1-4 : angle 2.12495 ( 24) link_NAG-ASN : bond 0.00193 ( 12) link_NAG-ASN : angle 2.24774 ( 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 418 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 337 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 HIS cc_start: 0.7193 (m-70) cc_final: 0.6845 (m-70) REVERT: A 190 MET cc_start: 0.8363 (ttm) cc_final: 0.8015 (ttp) REVERT: A 254 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8434 (mt) REVERT: L 24 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7354 (ttm110) REVERT: L 37 GLN cc_start: 0.8734 (tt0) cc_final: 0.8516 (tt0) REVERT: L 96 TYR cc_start: 0.9193 (m-80) cc_final: 0.8853 (m-80) REVERT: H 34 MET cc_start: 0.8546 (mmp) cc_final: 0.8239 (mmt) REVERT: H 52 LYS cc_start: 0.7775 (tttt) cc_final: 0.7529 (tttt) REVERT: H 66 ARG cc_start: 0.5861 (mtm110) cc_final: 0.5564 (mtm110) REVERT: H 67 PHE cc_start: 0.8032 (m-10) cc_final: 0.7759 (m-80) REVERT: B 150 HIS cc_start: 0.7097 (m-70) cc_final: 0.6684 (m-70) REVERT: B 190 MET cc_start: 0.8332 (ttm) cc_final: 0.8066 (ttp) REVERT: B 254 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 271 THR cc_start: 0.8439 (p) cc_final: 0.8230 (p) REVERT: C 96 TYR cc_start: 0.9138 (m-80) cc_final: 0.8682 (m-80) REVERT: C 97 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7478 (m) REVERT: D 81 GLN cc_start: 0.6840 (tt0) cc_final: 0.6389 (tt0) REVERT: E 269 THR cc_start: 0.8018 (t) cc_final: 0.7580 (p) REVERT: E 271 THR cc_start: 0.8501 (p) cc_final: 0.8268 (p) REVERT: F 24 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7641 (ttm110) REVERT: F 96 TYR cc_start: 0.9137 (m-80) cc_final: 0.8693 (m-80) REVERT: F 97 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7468 (m) REVERT: G 70 SER cc_start: 0.7426 (OUTLIER) cc_final: 0.6634 (p) REVERT: J 150 HIS cc_start: 0.7158 (m-70) cc_final: 0.6850 (m-70) REVERT: J 190 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7827 (ttp) REVERT: J 269 THR cc_start: 0.8137 (t) cc_final: 0.7729 (p) REVERT: I 24 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7596 (ttm110) REVERT: I 96 TYR cc_start: 0.9215 (m-80) cc_final: 0.8993 (m-80) REVERT: I 105 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: K 52 LYS cc_start: 0.7762 (tttt) cc_final: 0.7518 (tttm) REVERT: K 66 ARG cc_start: 0.5850 (mtm110) cc_final: 0.5561 (mtm110) REVERT: K 67 PHE cc_start: 0.7958 (m-10) cc_final: 0.7700 (m-80) outliers start: 81 outliers final: 44 residues processed: 398 average time/residue: 0.1498 time to fit residues: 91.4376 Evaluate side-chains 341 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 439 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 62 SER 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 239 VAL 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 439 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 93 THR 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 280 CYS Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain J residue 190 MET Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 239 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 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 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 1 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 149 optimal weight: 0.0040 chunk 81 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN ** J 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.082735 restraints weight = 25274.287| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.37 r_work: 0.2836 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.9911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20248 Z= 0.149 Angle : 0.645 15.497 27632 Z= 0.331 Chirality : 0.046 0.286 3064 Planarity : 0.004 0.055 3464 Dihedral : 6.879 47.857 3568 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 2.94 % Allowed : 17.08 % Favored : 79.98 % 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: 0.10 (0.17), residues: 2428 helix: -2.73 (0.44), residues: 48 sheet: 0.47 (0.17), residues: 952 loop : -0.03 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 24 TYR 0.015 0.001 TYR B 121 PHE 0.031 0.002 PHE G 67 TRP 0.014 0.001 TRP H 33 HIS 0.006 0.001 HIS J 312 Details of bonding type rmsd covalent geometry : bond 0.00364 (20160) covalent geometry : angle 0.62479 (27412) SS BOND : bond 0.00679 ( 44) SS BOND : angle 2.11967 ( 88) hydrogen bonds : bond 0.03468 ( 652) hydrogen bonds : angle 5.97845 ( 1536) link_ALPHA1-2 : bond 0.00632 ( 8) link_ALPHA1-2 : angle 2.40131 ( 24) link_ALPHA1-3 : bond 0.01061 ( 8) link_ALPHA1-3 : angle 1.12787 ( 24) link_ALPHA1-6 : bond 0.00574 ( 8) link_ALPHA1-6 : angle 1.37953 ( 24) link_BETA1-4 : bond 0.00601 ( 8) link_BETA1-4 : angle 1.82063 ( 24) link_NAG-ASN : bond 0.00097 ( 12) link_NAG-ASN : angle 1.74100 ( 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 370 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 HIS cc_start: 0.7425 (m-70) cc_final: 0.7098 (m-70) REVERT: A 190 MET cc_start: 0.8350 (ttm) cc_final: 0.8028 (ttp) REVERT: A 251 ASP cc_start: 0.7700 (t0) cc_final: 0.7141 (m-30) REVERT: H 34 MET cc_start: 0.8573 (mmp) cc_final: 0.8211 (mmt) REVERT: B 93 THR cc_start: 0.8693 (m) cc_final: 0.8342 (p) REVERT: B 150 HIS cc_start: 0.7173 (m-70) cc_final: 0.6814 (m-70) REVERT: B 190 MET cc_start: 0.8287 (ttm) cc_final: 0.7916 (ttp) REVERT: B 271 THR cc_start: 0.8469 (p) cc_final: 0.8258 (p) REVERT: C 24 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7443 (ttm110) REVERT: C 31 THR cc_start: 0.8564 (p) cc_final: 0.8330 (p) REVERT: C 82 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.6569 (t0) REVERT: C 96 TYR cc_start: 0.9136 (m-80) cc_final: 0.8605 (m-80) REVERT: C 100 GLN cc_start: 0.8784 (mm-40) cc_final: 0.7325 (pm20) REVERT: D 67 PHE cc_start: 0.6382 (m-80) cc_final: 0.6121 (m-80) REVERT: D 81 GLN cc_start: 0.6771 (tt0) cc_final: 0.6320 (tt0) REVERT: E 121 TYR cc_start: 0.8791 (p90) cc_final: 0.8391 (p90) REVERT: E 128 GLU cc_start: 0.7124 (tt0) cc_final: 0.6838 (pt0) REVERT: E 154 GLN cc_start: 0.7416 (mt0) cc_final: 0.6790 (mt0) REVERT: E 190 MET cc_start: 0.8235 (ttm) cc_final: 0.7913 (ttp) REVERT: E 209 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8252 (mtp85) REVERT: E 269 THR cc_start: 0.8082 (t) cc_final: 0.7645 (p) REVERT: E 271 THR cc_start: 0.8503 (p) cc_final: 0.8261 (p) REVERT: F 24 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7653 (ttm110) REVERT: F 31 THR cc_start: 0.8587 (p) cc_final: 0.8368 (p) REVERT: F 96 TYR cc_start: 0.9133 (m-80) cc_final: 0.8608 (m-80) REVERT: G 5 VAL cc_start: 0.8660 (p) cc_final: 0.8408 (m) REVERT: J 150 HIS cc_start: 0.7317 (m-70) cc_final: 0.7035 (m-70) REVERT: J 190 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7743 (ttp) REVERT: J 269 THR cc_start: 0.8166 (t) cc_final: 0.7716 (p) REVERT: I 24 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7611 (ttm110) REVERT: I 96 TYR cc_start: 0.9191 (m-80) cc_final: 0.8921 (m-80) REVERT: K 66 ARG cc_start: 0.5593 (mtm110) cc_final: 0.5305 (mtm110) REVERT: K 81 GLN cc_start: 0.6957 (tt0) cc_final: 0.6653 (tt0) outliers start: 62 outliers final: 36 residues processed: 342 average time/residue: 0.1459 time to fit residues: 77.0156 Evaluate side-chains 317 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 439 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 245 SER 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 82 ASP Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 62 SER 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 367 SER Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 190 MET 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 439 THR Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 60 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 206 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 172 optimal weight: 0.0670 chunk 33 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 441 ASN E 170AASN E 441 ASN F 37 GLN ** G 52AGLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.084552 restraints weight = 25605.671| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.39 r_work: 0.2856 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 1.0098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20248 Z= 0.119 Angle : 0.612 14.172 27632 Z= 0.313 Chirality : 0.045 0.289 3064 Planarity : 0.004 0.053 3464 Dihedral : 6.459 46.868 3568 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.24 % Rotamer: Outliers : 2.18 % Allowed : 17.74 % Favored : 80.08 % 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: 0.19 (0.17), residues: 2428 helix: -2.54 (0.47), residues: 48 sheet: 0.50 (0.17), residues: 972 loop : 0.04 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 24 TYR 0.015 0.001 TYR D 32 PHE 0.034 0.002 PHE K 67 TRP 0.012 0.001 TRP J 206 HIS 0.007 0.001 HIS J 312 Details of bonding type rmsd covalent geometry : bond 0.00285 (20160) covalent geometry : angle 0.59402 (27412) SS BOND : bond 0.00647 ( 44) SS BOND : angle 1.88732 ( 88) hydrogen bonds : bond 0.03176 ( 652) hydrogen bonds : angle 5.84035 ( 1536) link_ALPHA1-2 : bond 0.00734 ( 8) link_ALPHA1-2 : angle 2.48510 ( 24) link_ALPHA1-3 : bond 0.01118 ( 8) link_ALPHA1-3 : angle 1.03961 ( 24) link_ALPHA1-6 : bond 0.00672 ( 8) link_ALPHA1-6 : angle 1.36179 ( 24) link_BETA1-4 : bond 0.00635 ( 8) link_BETA1-4 : angle 1.60399 ( 24) link_NAG-ASN : bond 0.00079 ( 12) link_NAG-ASN : angle 1.59106 ( 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 332 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8773 (p90) cc_final: 0.8057 (p90) REVERT: A 150 HIS cc_start: 0.7388 (m-70) cc_final: 0.7000 (m-70) REVERT: A 190 MET cc_start: 0.8320 (ttm) cc_final: 0.7860 (ttp) REVERT: A 251 ASP cc_start: 0.7764 (t0) cc_final: 0.7174 (m-30) REVERT: B 93 THR cc_start: 0.8673 (m) cc_final: 0.8342 (p) REVERT: B 150 HIS cc_start: 0.7177 (m-70) cc_final: 0.6794 (m-70) REVERT: B 190 MET cc_start: 0.8299 (ttm) cc_final: 0.7999 (ttp) REVERT: B 251 ASP cc_start: 0.7663 (t0) cc_final: 0.6997 (m-30) REVERT: B 271 THR cc_start: 0.8474 (p) cc_final: 0.8260 (p) REVERT: C 24 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7361 (ttm110) REVERT: C 31 THR cc_start: 0.8528 (p) cc_final: 0.8299 (p) REVERT: C 82 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.6566 (t0) REVERT: D 38 ARG cc_start: 0.7662 (ptt180) cc_final: 0.7366 (ptt180) REVERT: D 81 GLN cc_start: 0.6719 (tt0) cc_final: 0.6302 (tt0) REVERT: E 93 THR cc_start: 0.8691 (m) cc_final: 0.8355 (p) REVERT: E 128 GLU cc_start: 0.7023 (tt0) cc_final: 0.6743 (pt0) REVERT: E 150 HIS cc_start: 0.7193 (m-70) cc_final: 0.6635 (m-70) REVERT: E 154 GLN cc_start: 0.7382 (mt0) cc_final: 0.6778 (mt0) REVERT: E 190 MET cc_start: 0.8231 (ttm) cc_final: 0.7952 (ttp) REVERT: E 209 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8282 (mtp85) REVERT: E 269 THR cc_start: 0.8097 (t) cc_final: 0.7658 (p) REVERT: E 271 THR cc_start: 0.8533 (p) cc_final: 0.8293 (p) REVERT: F 24 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7602 (ttm110) REVERT: G 66 ARG cc_start: 0.4716 (mtm110) cc_final: 0.4499 (mtm110) REVERT: J 121 TYR cc_start: 0.8711 (p90) cc_final: 0.8035 (p90) REVERT: J 150 HIS cc_start: 0.7430 (m-70) cc_final: 0.7088 (m-70) REVERT: J 190 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7829 (ttp) REVERT: J 269 THR cc_start: 0.8148 (t) cc_final: 0.7752 (p) REVERT: I 24 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7586 (ttm110) REVERT: K 81 GLN cc_start: 0.6986 (tt0) cc_final: 0.6701 (tt0) outliers start: 46 outliers final: 26 residues processed: 319 average time/residue: 0.1397 time to fit residues: 69.1979 Evaluate side-chains 295 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 439 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS 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 82 ASP Chi-restraints excluded: chain D residue 7 SER 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 439 THR Chi-restraints excluded: chain J residue 190 MET 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 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 231 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 128 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52AGLN B 170AASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 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 = 0.3346 r_free = 0.3346 target = 0.111759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.083172 restraints weight = 25283.446| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.38 r_work: 0.2844 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 1.0387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20248 Z= 0.133 Angle : 0.617 14.482 27632 Z= 0.314 Chirality : 0.045 0.274 3064 Planarity : 0.004 0.054 3464 Dihedral : 6.297 46.307 3568 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 2.37 % Allowed : 17.17 % 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: 0.20 (0.17), residues: 2428 helix: -2.49 (0.47), residues: 48 sheet: 0.56 (0.17), residues: 968 loop : 0.01 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 24 TYR 0.012 0.001 TYR B 121 PHE 0.029 0.002 PHE G 67 TRP 0.011 0.001 TRP H 33 HIS 0.007 0.001 HIS J 312 Details of bonding type rmsd covalent geometry : bond 0.00328 (20160) covalent geometry : angle 0.59339 (27412) SS BOND : bond 0.00657 ( 44) SS BOND : angle 2.31716 ( 88) hydrogen bonds : bond 0.03198 ( 652) hydrogen bonds : angle 5.73577 ( 1536) link_ALPHA1-2 : bond 0.00694 ( 8) link_ALPHA1-2 : angle 2.46960 ( 24) link_ALPHA1-3 : bond 0.01082 ( 8) link_ALPHA1-3 : angle 1.03377 ( 24) link_ALPHA1-6 : bond 0.00628 ( 8) link_ALPHA1-6 : angle 1.40107 ( 24) link_BETA1-4 : bond 0.00616 ( 8) link_BETA1-4 : angle 1.66970 ( 24) link_NAG-ASN : bond 0.00051 ( 12) link_NAG-ASN : angle 1.61076 ( 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 328 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8783 (p90) cc_final: 0.8080 (p90) REVERT: A 190 MET cc_start: 0.8338 (ttm) cc_final: 0.7863 (ttp) REVERT: A 251 ASP cc_start: 0.7745 (t0) cc_final: 0.7281 (m-30) REVERT: L 5 THR cc_start: 0.8036 (p) cc_final: 0.7829 (p) REVERT: L 24 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7349 (ttm110) REVERT: L 96 TYR cc_start: 0.9238 (m-80) cc_final: 0.8776 (m-80) REVERT: H 67 PHE cc_start: 0.7586 (m-80) cc_final: 0.7321 (m-10) REVERT: B 93 THR cc_start: 0.8722 (m) cc_final: 0.8356 (p) REVERT: B 150 HIS cc_start: 0.7437 (m-70) cc_final: 0.7065 (m-70) REVERT: B 190 MET cc_start: 0.8327 (ttm) cc_final: 0.7866 (ttp) REVERT: B 251 ASP cc_start: 0.7666 (t0) cc_final: 0.7084 (m-30) REVERT: B 271 THR cc_start: 0.8543 (p) cc_final: 0.8323 (p) REVERT: C 24 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7501 (ttm110) REVERT: C 31 THR cc_start: 0.8612 (p) cc_final: 0.8395 (p) REVERT: C 82 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6552 (t0) REVERT: C 96 TYR cc_start: 0.9223 (m-80) cc_final: 0.8808 (m-80) REVERT: D 38 ARG cc_start: 0.7812 (ptt180) cc_final: 0.7505 (ptt180) REVERT: D 81 GLN cc_start: 0.6800 (tt0) cc_final: 0.6364 (tt0) REVERT: E 93 THR cc_start: 0.8781 (m) cc_final: 0.8400 (p) REVERT: E 128 GLU cc_start: 0.7045 (tt0) cc_final: 0.6723 (pt0) REVERT: E 150 HIS cc_start: 0.7424 (m-70) cc_final: 0.6810 (m-70) REVERT: E 190 MET cc_start: 0.8245 (ttm) cc_final: 0.7977 (ttp) REVERT: E 269 THR cc_start: 0.8157 (t) cc_final: 0.7718 (p) REVERT: E 271 THR cc_start: 0.8617 (p) cc_final: 0.8379 (p) REVERT: F 24 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7618 (ttm110) REVERT: F 96 TYR cc_start: 0.9201 (m-80) cc_final: 0.8775 (m-80) REVERT: G 32 TYR cc_start: 0.8267 (m-80) cc_final: 0.7922 (m-80) REVERT: G 66 ARG cc_start: 0.4851 (mtm110) cc_final: 0.4628 (mtm110) REVERT: J 150 HIS cc_start: 0.7490 (m-70) cc_final: 0.7136 (m-70) REVERT: J 190 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7843 (ttp) REVERT: J 269 THR cc_start: 0.8184 (t) cc_final: 0.7799 (p) REVERT: I 24 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7530 (ttm110) REVERT: K 52 LYS cc_start: 0.7762 (tttt) cc_final: 0.7520 (tttp) REVERT: K 81 GLN cc_start: 0.7098 (tt0) cc_final: 0.6861 (tt0) outliers start: 50 outliers final: 36 residues processed: 310 average time/residue: 0.1462 time to fit residues: 69.3700 Evaluate side-chains 304 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 271 THR 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 35 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 101 ASP 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 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 G residue 101 ASP Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 190 MET 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 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain K residue 94 SER 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: 0.6980 chunk 108 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52AGLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.081767 restraints weight = 25182.405| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.27 r_work: 0.2818 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 1.0653 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= 0.170 Angle : 0.658 14.526 27632 Z= 0.333 Chirality : 0.046 0.289 3064 Planarity : 0.004 0.052 3464 Dihedral : 6.457 45.136 3568 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.01 % Favored : 96.83 % Rotamer: Outliers : 1.99 % Allowed : 17.60 % Favored : 80.41 % 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: 0.15 (0.17), residues: 2428 helix: -2.58 (0.43), residues: 48 sheet: 0.54 (0.17), residues: 988 loop : -0.05 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 24 TYR 0.014 0.001 TYR J 418 PHE 0.032 0.002 PHE G 67 TRP 0.016 0.001 TRP D 36 HIS 0.008 0.001 HIS J 312 Details of bonding type rmsd covalent geometry : bond 0.00423 (20160) covalent geometry : angle 0.63359 (27412) SS BOND : bond 0.00692 ( 44) SS BOND : angle 2.49223 ( 88) hydrogen bonds : bond 0.03447 ( 652) hydrogen bonds : angle 5.78448 ( 1536) link_ALPHA1-2 : bond 0.00588 ( 8) link_ALPHA1-2 : angle 2.55833 ( 24) link_ALPHA1-3 : bond 0.01087 ( 8) link_ALPHA1-3 : angle 1.02394 ( 24) link_ALPHA1-6 : bond 0.00540 ( 8) link_ALPHA1-6 : angle 1.42775 ( 24) link_BETA1-4 : bond 0.00646 ( 8) link_BETA1-4 : angle 1.86329 ( 24) link_NAG-ASN : bond 0.00080 ( 12) link_NAG-ASN : angle 1.75582 ( 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 306 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ASN cc_start: 0.8389 (t0) cc_final: 0.8006 (t0) REVERT: A 190 MET cc_start: 0.8375 (ttm) cc_final: 0.7903 (ttp) REVERT: A 251 ASP cc_start: 0.7690 (t0) cc_final: 0.7283 (m-30) REVERT: A 269 THR cc_start: 0.8251 (t) cc_final: 0.7785 (p) REVERT: H 32 TYR cc_start: 0.8466 (m-80) cc_final: 0.7893 (m-80) REVERT: H 38 ARG cc_start: 0.7903 (ptt180) cc_final: 0.7678 (ptt180) REVERT: H 66 ARG cc_start: 0.6331 (mtp85) cc_final: 0.6105 (mtm110) REVERT: B 150 HIS cc_start: 0.7460 (m-70) cc_final: 0.7130 (m-70) REVERT: B 190 MET cc_start: 0.8342 (ttm) cc_final: 0.7855 (ttp) REVERT: B 251 ASP cc_start: 0.7690 (t0) cc_final: 0.7211 (m-30) REVERT: C 24 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7483 (ttm110) REVERT: C 82 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.6619 (t0) REVERT: D 38 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7552 (ptt180) REVERT: E 128 GLU cc_start: 0.7137 (tt0) cc_final: 0.6804 (pt0) REVERT: E 154 GLN cc_start: 0.7600 (mt0) cc_final: 0.7100 (mt0) REVERT: E 190 MET cc_start: 0.8291 (ttm) cc_final: 0.8014 (ttp) REVERT: E 269 THR cc_start: 0.8198 (t) cc_final: 0.7734 (p) REVERT: E 271 THR cc_start: 0.8586 (p) cc_final: 0.8377 (p) REVERT: F 24 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7645 (ttm110) REVERT: G 66 ARG cc_start: 0.5158 (mtm110) cc_final: 0.4926 (mtm110) REVERT: G 81 GLN cc_start: 0.6777 (tt0) cc_final: 0.6574 (tt0) REVERT: J 150 HIS cc_start: 0.7526 (m-70) cc_final: 0.7216 (m-70) REVERT: J 190 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7889 (ttp) REVERT: J 269 THR cc_start: 0.8226 (t) cc_final: 0.7831 (p) REVERT: I 24 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7550 (ttm110) REVERT: K 39 GLN cc_start: 0.8407 (tt0) cc_final: 0.7934 (tt0) REVERT: K 52 LYS cc_start: 0.7889 (tttt) cc_final: 0.7673 (tttp) REVERT: K 81 GLN cc_start: 0.7268 (tt0) cc_final: 0.7003 (tt0) outliers start: 42 outliers final: 33 residues processed: 294 average time/residue: 0.1443 time to fit residues: 65.1946 Evaluate side-chains 287 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 101 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 439 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 190 MET 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 439 THR Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 214 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 174 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52AGLN B 441 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.082568 restraints weight = 25304.727| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.37 r_work: 0.2832 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 1.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 20248 Z= 0.134 Angle : 0.624 13.797 27632 Z= 0.317 Chirality : 0.045 0.277 3064 Planarity : 0.004 0.054 3464 Dihedral : 6.245 45.438 3568 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.51 % Favored : 97.32 % Rotamer: Outliers : 1.85 % Allowed : 17.69 % 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: 0.22 (0.17), residues: 2428 helix: -2.49 (0.45), residues: 48 sheet: 0.63 (0.17), residues: 968 loop : -0.02 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 24 TYR 0.012 0.001 TYR E 121 PHE 0.031 0.002 PHE G 67 TRP 0.011 0.001 TRP H 33 HIS 0.007 0.001 HIS J 312 Details of bonding type rmsd covalent geometry : bond 0.00330 (20160) covalent geometry : angle 0.60011 (27412) SS BOND : bond 0.00728 ( 44) SS BOND : angle 2.42517 ( 88) hydrogen bonds : bond 0.03275 ( 652) hydrogen bonds : angle 5.73580 ( 1536) link_ALPHA1-2 : bond 0.00683 ( 8) link_ALPHA1-2 : angle 2.54301 ( 24) link_ALPHA1-3 : bond 0.01114 ( 8) link_ALPHA1-3 : angle 1.01698 ( 24) link_ALPHA1-6 : bond 0.00605 ( 8) link_ALPHA1-6 : angle 1.38892 ( 24) link_BETA1-4 : bond 0.00603 ( 8) link_BETA1-4 : angle 1.72204 ( 24) link_NAG-ASN : bond 0.00070 ( 12) link_NAG-ASN : angle 1.57538 ( 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 302 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8774 (p90) cc_final: 0.8131 (p90) REVERT: A 190 MET cc_start: 0.8284 (ttm) cc_final: 0.7854 (ttp) REVERT: A 251 ASP cc_start: 0.7629 (t0) cc_final: 0.7290 (m-30) REVERT: A 269 THR cc_start: 0.8265 (t) cc_final: 0.7811 (p) REVERT: L 5 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7719 (p) REVERT: L 96 TYR cc_start: 0.9369 (m-80) cc_final: 0.8795 (m-80) REVERT: L 100 GLN cc_start: 0.8795 (mm-40) cc_final: 0.7681 (pm20) REVERT: H 25 SER cc_start: 0.7301 (t) cc_final: 0.6934 (t) REVERT: H 32 TYR cc_start: 0.8434 (m-80) cc_final: 0.7910 (m-80) REVERT: H 38 ARG cc_start: 0.7894 (ptt180) cc_final: 0.7668 (ptt180) REVERT: H 56 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 150 HIS cc_start: 0.7477 (m-70) cc_final: 0.7087 (m-70) REVERT: B 190 MET cc_start: 0.8239 (ttm) cc_final: 0.7811 (ttp) REVERT: B 251 ASP cc_start: 0.7638 (t0) cc_final: 0.7173 (m-30) REVERT: C 24 ARG cc_start: 0.7758 (ttm110) cc_final: 0.7482 (ttm110) REVERT: C 82 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.6639 (t0) REVERT: C 96 TYR cc_start: 0.9309 (m-80) cc_final: 0.8927 (m-80) REVERT: D 38 ARG cc_start: 0.7847 (ptt180) cc_final: 0.7505 (ptt180) REVERT: D 81 GLN cc_start: 0.7038 (tt0) cc_final: 0.6637 (tt0) REVERT: E 128 GLU cc_start: 0.7220 (tt0) cc_final: 0.6831 (pt0) REVERT: E 190 MET cc_start: 0.8199 (ttm) cc_final: 0.7883 (ttp) REVERT: E 269 THR cc_start: 0.8186 (t) cc_final: 0.7723 (p) REVERT: E 271 THR cc_start: 0.8610 (p) cc_final: 0.8392 (p) REVERT: F 24 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7636 (ttm110) REVERT: F 96 TYR cc_start: 0.9334 (m-80) cc_final: 0.8924 (m-80) REVERT: G 67 PHE cc_start: 0.6468 (m-80) cc_final: 0.5887 (m-80) REVERT: G 81 GLN cc_start: 0.6851 (tt0) cc_final: 0.6596 (tt0) REVERT: J 121 TYR cc_start: 0.8738 (p90) cc_final: 0.8117 (p90) REVERT: J 150 HIS cc_start: 0.7545 (m-70) cc_final: 0.7163 (m-70) REVERT: J 190 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7895 (ttp) REVERT: J 269 THR cc_start: 0.8230 (t) cc_final: 0.7830 (p) REVERT: I 24 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7554 (ttm110) REVERT: I 100 GLN cc_start: 0.8709 (mm-40) cc_final: 0.7599 (pt0) REVERT: I 105 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: K 39 GLN cc_start: 0.8395 (tt0) cc_final: 0.7926 (tt0) REVERT: K 56 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7956 (mt-10) REVERT: K 81 GLN cc_start: 0.7246 (tt0) cc_final: 0.6952 (tt0) outliers start: 39 outliers final: 31 residues processed: 291 average time/residue: 0.1405 time to fit residues: 62.7885 Evaluate side-chains 284 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR 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 B residue 127 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 180 SER 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 G residue 101 ASP Chi-restraints excluded: chain J residue 190 MET 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 105 GLU Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 14 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 49 optimal weight: 0.0000 chunk 74 optimal weight: 0.0040 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52AGLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.082916 restraints weight = 25734.896| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.42 r_work: 0.2828 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 1.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 20248 Z= 0.135 Angle : 0.629 13.497 27632 Z= 0.318 Chirality : 0.045 0.272 3064 Planarity : 0.004 0.052 3464 Dihedral : 6.214 45.323 3568 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 1.94 % Allowed : 17.88 % Favored : 80.17 % 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: 0.25 (0.17), residues: 2428 helix: -2.48 (0.46), residues: 48 sheet: 0.65 (0.17), residues: 988 loop : -0.02 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 24 TYR 0.012 0.001 TYR E 121 PHE 0.031 0.002 PHE G 67 TRP 0.011 0.001 TRP H 33 HIS 0.007 0.001 HIS J 312 Details of bonding type rmsd covalent geometry : bond 0.00331 (20160) covalent geometry : angle 0.60420 (27412) SS BOND : bond 0.00718 ( 44) SS BOND : angle 2.43574 ( 88) hydrogen bonds : bond 0.03273 ( 652) hydrogen bonds : angle 5.71281 ( 1536) link_ALPHA1-2 : bond 0.00680 ( 8) link_ALPHA1-2 : angle 2.56516 ( 24) link_ALPHA1-3 : bond 0.01089 ( 8) link_ALPHA1-3 : angle 1.01210 ( 24) link_ALPHA1-6 : bond 0.00599 ( 8) link_ALPHA1-6 : angle 1.40475 ( 24) link_BETA1-4 : bond 0.00623 ( 8) link_BETA1-4 : angle 1.74666 ( 24) link_NAG-ASN : bond 0.00069 ( 12) link_NAG-ASN : angle 1.57434 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5397.57 seconds wall clock time: 93 minutes 14.12 seconds (5594.12 seconds total)