Starting phenix.real_space_refine on Fri Sep 27 01:08:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/09_2024/6kpj_0748_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/09_2024/6kpj_0748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/09_2024/6kpj_0748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/09_2024/6kpj_0748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/09_2024/6kpj_0748_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/09_2024/6kpj_0748_trim.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.332 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 24 5.21 5 S 120 5.16 5 C 20316 2.51 5 N 5160 2.21 5 O 5976 1.98 5 H 31225 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62845 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "B" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "F" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "K" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 24.32, per 1000 atoms: 0.39 Number of scatterers: 62845 At special positions: 0 Unit cell: (143.64, 143.64, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 24 15.00 Mg 24 11.99 O 5976 8.00 N 5160 7.00 C 20316 6.00 H 31225 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.53 Conformation dependent library (CDL) restraints added in 4.1 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 12 sheets defined 67.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.593A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.868A pdb=" N MET A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.664A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 removed outlier: 3.725A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 91 through 97 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.592A pdb=" N PHE B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.868A pdb=" N MET B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.664A pdb=" N GLU B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 216 removed outlier: 3.724A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'C' and resid 25 through 37 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 82 through 91 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.593A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 141 removed outlier: 3.867A pdb=" N MET C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.665A pdb=" N GLU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 216 removed outlier: 3.726A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET C 250 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 91 through 97 Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.592A pdb=" N PHE D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 141 removed outlier: 3.868A pdb=" N MET D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.665A pdb=" N GLU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 216 removed outlier: 3.726A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 245 through 250 removed outlier: 4.160A pdb=" N MET D 250 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 268 through 286 removed outlier: 4.015A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 313 through 326 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.592A pdb=" N PHE E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.867A pdb=" N MET E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.664A pdb=" N GLU E 187 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 216 removed outlier: 3.725A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET E 250 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 286 " --> pdb=" O TYR E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 Processing helix chain 'E' and resid 300 through 312 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'F' and resid 25 through 37 Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 91 through 97 Processing helix chain 'F' and resid 108 through 113 removed outlier: 3.592A pdb=" N PHE F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 141 removed outlier: 3.868A pdb=" N MET F 137 " --> pdb=" O GLY F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.664A pdb=" N GLU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 216 removed outlier: 3.724A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 268 through 286 removed outlier: 4.017A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY F 286 " --> pdb=" O TYR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 313 through 326 Processing helix chain 'G' and resid 25 through 37 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 63 through 71 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.592A pdb=" N PHE G 113 " --> pdb=" O TYR G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 141 removed outlier: 3.868A pdb=" N MET G 137 " --> pdb=" O GLY G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.664A pdb=" N GLU G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 216 removed outlier: 3.726A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 Processing helix chain 'G' and resid 232 through 245 Processing helix chain 'G' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET G 250 " --> pdb=" O ILE G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 254 through 268 Processing helix chain 'G' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY G 286 " --> pdb=" O TYR G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 Processing helix chain 'G' and resid 300 through 312 Processing helix chain 'G' and resid 313 through 326 Processing helix chain 'H' and resid 25 through 37 Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 82 through 91 Processing helix chain 'H' and resid 91 through 97 Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.592A pdb=" N PHE H 113 " --> pdb=" O TYR H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 141 removed outlier: 3.868A pdb=" N MET H 137 " --> pdb=" O GLY H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.665A pdb=" N GLU H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 216 removed outlier: 3.726A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 Processing helix chain 'H' and resid 232 through 245 Processing helix chain 'H' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET H 250 " --> pdb=" O ILE H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 253 No H-bonds generated for 'chain 'H' and resid 251 through 253' Processing helix chain 'H' and resid 254 through 268 Processing helix chain 'H' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 Processing helix chain 'H' and resid 300 through 312 Processing helix chain 'H' and resid 313 through 326 Processing helix chain 'I' and resid 25 through 36 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 63 through 71 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 91 through 97 Processing helix chain 'I' and resid 108 through 113 removed outlier: 3.592A pdb=" N PHE I 113 " --> pdb=" O TYR I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 141 removed outlier: 3.869A pdb=" N MET I 137 " --> pdb=" O GLY I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.664A pdb=" N GLU I 187 " --> pdb=" O SER I 183 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 216 removed outlier: 3.725A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 Processing helix chain 'I' and resid 232 through 245 Processing helix chain 'I' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET I 250 " --> pdb=" O ILE I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 253 No H-bonds generated for 'chain 'I' and resid 251 through 253' Processing helix chain 'I' and resid 254 through 268 Processing helix chain 'I' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY I 286 " --> pdb=" O TYR I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 Processing helix chain 'I' and resid 300 through 312 Processing helix chain 'I' and resid 313 through 326 Processing helix chain 'J' and resid 25 through 36 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 63 through 71 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 91 through 97 Processing helix chain 'J' and resid 108 through 113 removed outlier: 3.592A pdb=" N PHE J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 141 removed outlier: 3.868A pdb=" N MET J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.665A pdb=" N GLU J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 216 removed outlier: 3.725A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 Processing helix chain 'J' and resid 232 through 245 Processing helix chain 'J' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET J 250 " --> pdb=" O ILE J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 253 No H-bonds generated for 'chain 'J' and resid 251 through 253' Processing helix chain 'J' and resid 254 through 268 Processing helix chain 'J' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY J 286 " --> pdb=" O TYR J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 Processing helix chain 'J' and resid 300 through 312 Processing helix chain 'J' and resid 313 through 326 Processing helix chain 'K' and resid 25 through 37 Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 63 through 71 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 91 through 97 Processing helix chain 'K' and resid 108 through 113 removed outlier: 3.593A pdb=" N PHE K 113 " --> pdb=" O TYR K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 141 removed outlier: 3.868A pdb=" N MET K 137 " --> pdb=" O GLY K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 Processing helix chain 'K' and resid 183 through 197 removed outlier: 3.664A pdb=" N GLU K 187 " --> pdb=" O SER K 183 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 216 removed outlier: 3.724A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 Processing helix chain 'K' and resid 232 through 245 Processing helix chain 'K' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET K 250 " --> pdb=" O ILE K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 253 No H-bonds generated for 'chain 'K' and resid 251 through 253' Processing helix chain 'K' and resid 254 through 268 Processing helix chain 'K' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY K 286 " --> pdb=" O TYR K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 Processing helix chain 'K' and resid 300 through 312 Processing helix chain 'K' and resid 313 through 326 Processing helix chain 'L' and resid 25 through 36 Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 63 through 71 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 91 through 97 Processing helix chain 'L' and resid 108 through 113 removed outlier: 3.591A pdb=" N PHE L 113 " --> pdb=" O TYR L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 141 removed outlier: 3.867A pdb=" N MET L 137 " --> pdb=" O GLY L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 183 through 197 removed outlier: 3.664A pdb=" N GLU L 187 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 216 removed outlier: 3.725A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 Processing helix chain 'L' and resid 232 through 245 Processing helix chain 'L' and resid 245 through 250 removed outlier: 4.161A pdb=" N MET L 250 " --> pdb=" O ILE L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 253 No H-bonds generated for 'chain 'L' and resid 251 through 253' Processing helix chain 'L' and resid 254 through 268 Processing helix chain 'L' and resid 268 through 286 removed outlier: 4.016A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY L 286 " --> pdb=" O TYR L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 Processing helix chain 'L' and resid 300 through 312 Processing helix chain 'L' and resid 313 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 101 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE A 125 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 103 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 127 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE A 105 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 148 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 9.020A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE B 101 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE B 125 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 103 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 127 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE B 105 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 148 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE C 101 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE C 125 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 103 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL C 127 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE C 105 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 148 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL D 43 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE D 101 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE D 125 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU D 103 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 127 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE D 105 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL D 148 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 61 through 62 removed outlier: 9.020A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE E 101 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE E 125 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU E 103 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL E 127 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE E 105 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 148 " --> pdb=" O VAL E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE F 101 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE F 125 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU F 103 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL F 127 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE F 105 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 148 " --> pdb=" O VAL F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 62 removed outlier: 9.020A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE G 101 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE G 125 " --> pdb=" O PHE G 101 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU G 103 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL G 127 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE G 105 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL G 148 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE H 101 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE H 125 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU H 103 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL H 127 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE H 105 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL H 148 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE I 101 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE I 125 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU I 103 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL I 127 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE I 105 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL I 148 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE J 101 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE J 125 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU J 103 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL J 127 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE J 105 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL J 148 " --> pdb=" O VAL J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE K 101 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE K 125 " --> pdb=" O PHE K 101 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU K 103 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL K 127 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE K 105 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL K 148 " --> pdb=" O VAL K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 61 through 62 removed outlier: 9.021A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE L 101 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE L 125 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU L 103 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL L 127 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE L 105 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL L 148 " --> pdb=" O VAL L 180 " (cutoff:3.500A) 1760 hydrogen bonds defined for protein. 5244 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: 24.02 Time building geometry restraints manager: 16.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 0.99: 31208 0.99 - 1.19: 5 1.19 - 1.39: 13078 1.39 - 1.60: 18914 1.60 - 1.80: 300 Bond restraints: 63505 Sorted by residual: bond pdb=" C1B NAI A 402 " pdb=" C2B NAI A 402 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1B NAI G 402 " pdb=" C2B NAI G 402 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1B NAI D 403 " pdb=" C2B NAI D 403 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1B NAI F 403 " pdb=" C2B NAI F 403 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1B NAI H 403 " pdb=" C2B NAI H 403 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 ... (remaining 63500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.88: 114677 11.88 - 23.76: 72 23.76 - 35.64: 185 35.64 - 47.52: 86 47.52 - 59.39: 10 Bond angle restraints: 115030 Sorted by residual: angle pdb=" C GLN K 30 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 125.01 65.62 59.39 3.00e+00 1.11e-01 3.92e+02 angle pdb=" C GLN L 30 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 125.01 65.69 59.32 3.00e+00 1.11e-01 3.91e+02 angle pdb=" C LYS K 55 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 124.93 65.73 59.20 3.00e+00 1.11e-01 3.89e+02 angle pdb=" CA LYS K 56 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 114.63 55.53 59.10 3.00e+00 1.11e-01 3.88e+02 angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.71 55.72 58.99 3.00e+00 1.11e-01 3.87e+02 ... (remaining 115025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 27031 17.52 - 35.03: 2150 35.03 - 52.55: 623 52.55 - 70.07: 159 70.07 - 87.59: 26 Dihedral angle restraints: 29989 sinusoidal: 16636 harmonic: 13353 Sorted by residual: dihedral pdb=" CA VAL I 214 " pdb=" C VAL I 214 " pdb=" N LYS I 215 " pdb=" CA LYS I 215 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA VAL D 214 " pdb=" C VAL D 214 " pdb=" N LYS D 215 " pdb=" CA LYS D 215 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA VAL E 214 " pdb=" C VAL E 214 " pdb=" N LYS E 215 " pdb=" CA LYS E 215 " ideal model delta harmonic sigma weight residual -180.00 -163.27 -16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 29986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3883 0.071 - 0.141: 736 0.141 - 0.212: 72 0.212 - 0.282: 49 0.282 - 0.353: 24 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CB VAL L 127 " pdb=" CA VAL L 127 " pdb=" CG1 VAL L 127 " pdb=" CG2 VAL L 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB VAL I 127 " pdb=" CA VAL I 127 " pdb=" CG1 VAL I 127 " pdb=" CG2 VAL I 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB VAL J 127 " pdb=" CA VAL J 127 " pdb=" CG1 VAL J 127 " pdb=" CG2 VAL J 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 4761 not shown) Planarity restraints: 9268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 128 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO J 129 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO J 129 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 129 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 128 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 129 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 128 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO I 129 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO I 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 129 " -0.028 5.00e-02 4.00e+02 ... (remaining 9265 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.89: 551 1.89 - 2.57: 63068 2.57 - 3.25: 190059 3.25 - 3.92: 234151 3.92 - 4.60: 387836 Nonbonded interactions: 875665 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb="MG MG C 404 " model vdw 1.218 1.300 nonbonded pdb="MG MG A 401 " pdb="MG MG A 404 " model vdw 1.222 1.300 nonbonded pdb="MG MG G 401 " pdb="MG MG G 404 " model vdw 1.238 1.300 nonbonded pdb="MG MG I 401 " pdb="MG MG I 404 " model vdw 1.243 1.300 nonbonded pdb="MG MG E 401 " pdb="MG MG E 404 " model vdw 1.257 1.300 ... (remaining 875660 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'C' and (resid 2 through 329 or resid 401)) selection = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'H' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'I' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'J' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 329 or res \ id 401)) selection = (chain 'L' and (resid 2 through 329 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.820 Extract box with map and model: 1.730 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 108.470 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.014 0.244 32280 Z= 0.895 Angle : 0.935 14.258 43704 Z= 0.429 Chirality : 0.060 0.353 4764 Planarity : 0.004 0.051 5484 Dihedral : 13.400 87.586 12504 Min Nonbonded Distance : 1.218 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.10), residues: 3912 helix: -2.36 (0.08), residues: 2448 sheet: -2.56 (0.18), residues: 504 loop : -3.76 (0.14), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 198 HIS 0.003 0.001 HIS E 140 PHE 0.012 0.002 PHE J 288 TYR 0.008 0.001 TYR L 87 ARG 0.001 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8106 (mp10) REVERT: C 30 GLN cc_start: 0.8591 (mt0) cc_final: 0.8287 (mm110) REVERT: D 308 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8261 (mm-30) REVERT: E 187 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7753 (tm-30) REVERT: F 187 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8135 (tm-30) REVERT: G 3 LYS cc_start: 0.9117 (mttt) cc_final: 0.8781 (mmpt) REVERT: H 187 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7866 (tm-30) REVERT: J 187 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8031 (tm-30) REVERT: K 308 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8207 (mm-30) REVERT: L 187 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7895 (tm-30) outliers start: 0 outliers final: 2 residues processed: 442 average time/residue: 3.5206 time to fit residues: 1771.7304 Evaluate side-chains 341 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 339 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain G residue 104 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 37 ASN A 278 ASN B 30 GLN B 37 ASN C 37 ASN C 278 ASN D 30 GLN D 37 ASN D 278 ASN E 37 ASN E 278 ASN F 30 GLN F 37 ASN F 278 ASN G 30 GLN G 37 ASN G 249 GLN H 30 GLN H 37 ASN I 30 GLN I 37 ASN I 278 ASN J 30 GLN J 37 ASN J 278 ASN K 30 GLN K 37 ASN K 40 ASN K 278 ASN L 30 GLN L 37 ASN L 278 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32280 Z= 0.256 Angle : 0.731 16.644 43704 Z= 0.375 Chirality : 0.132 1.736 4764 Planarity : 0.004 0.079 5484 Dihedral : 9.289 77.325 5057 Min Nonbonded Distance : 1.128 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.78 % Allowed : 8.18 % Favored : 90.04 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.12), residues: 3912 helix: -0.40 (0.10), residues: 2424 sheet: -1.94 (0.19), residues: 504 loop : -2.78 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 198 HIS 0.005 0.001 HIS E 196 PHE 0.010 0.001 PHE K 288 TYR 0.010 0.001 TYR L 217 ARG 0.007 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 353 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 215 LYS cc_start: 0.9161 (mppt) cc_final: 0.8818 (mttp) REVERT: D 308 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8485 (mm-30) REVERT: E 187 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8125 (tm-30) REVERT: F 99 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8288 (mppt) REVERT: G 3 LYS cc_start: 0.9181 (mttt) cc_final: 0.8849 (mmpt) REVERT: H 131 MET cc_start: 0.6398 (mtm) cc_final: 0.5028 (mtm) REVERT: I 249 GLN cc_start: 0.9555 (tm-30) cc_final: 0.9351 (pp30) REVERT: J 3 LYS cc_start: 0.9208 (mttt) cc_final: 0.8839 (mmpt) REVERT: J 99 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8208 (mppt) REVERT: L 131 MET cc_start: 0.6502 (mtm) cc_final: 0.5189 (mtm) REVERT: L 187 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8258 (tm-30) outliers start: 57 outliers final: 29 residues processed: 372 average time/residue: 3.2432 time to fit residues: 1388.7973 Evaluate side-chains 345 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 314 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 346 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN B 249 GLN B 278 ASN C 30 GLN C 249 GLN E 30 GLN F 25 ASN F 30 GLN F 249 GLN G 30 GLN G 249 GLN G 278 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN H 278 ASN I 30 GLN J 30 GLN J 249 GLN L 30 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 32280 Z= 0.495 Angle : 0.784 16.350 43704 Z= 0.410 Chirality : 0.131 1.657 4764 Planarity : 0.003 0.040 5484 Dihedral : 9.333 88.729 5052 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.43 % Allowed : 9.80 % Favored : 87.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 3912 helix: -0.13 (0.10), residues: 2460 sheet: -1.54 (0.20), residues: 504 loop : -2.36 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 198 HIS 0.009 0.002 HIS C 196 PHE 0.015 0.002 PHE L 288 TYR 0.016 0.001 TYR E 217 ARG 0.003 0.000 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 339 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8280 (mp10) REVERT: B 96 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: B 249 GLN cc_start: 0.9662 (OUTLIER) cc_final: 0.9400 (pp30) REVERT: C 96 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: C 249 GLN cc_start: 0.9674 (OUTLIER) cc_final: 0.9438 (pp30) REVERT: E 315 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.9065 (ttm) REVERT: F 249 GLN cc_start: 0.9671 (OUTLIER) cc_final: 0.9402 (pp30) REVERT: G 3 LYS cc_start: 0.9288 (mttt) cc_final: 0.8898 (mmpt) REVERT: G 249 GLN cc_start: 0.9676 (OUTLIER) cc_final: 0.9438 (pp30) REVERT: H 96 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: H 131 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.5539 (mtm) REVERT: J 96 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8482 (mp10) REVERT: J 249 GLN cc_start: 0.9656 (OUTLIER) cc_final: 0.9389 (pp30) REVERT: J 312 GLN cc_start: 0.8914 (mm110) cc_final: 0.8708 (mm110) REVERT: K 215 LYS cc_start: 0.9132 (mttt) cc_final: 0.8924 (mttp) REVERT: L 96 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8271 (mp10) REVERT: L 131 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.5605 (mtm) outliers start: 78 outliers final: 44 residues processed: 367 average time/residue: 3.2099 time to fit residues: 1368.0293 Evaluate side-chains 345 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 287 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 131 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 332 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN B 30 GLN B 297 GLN C 30 GLN D 30 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN F 25 ASN F 30 GLN G 30 GLN H 30 GLN I 30 GLN J 30 GLN ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32280 Z= 0.186 Angle : 0.687 17.265 43704 Z= 0.352 Chirality : 0.134 1.698 4764 Planarity : 0.003 0.040 5484 Dihedral : 8.160 86.521 5052 Min Nonbonded Distance : 1.167 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.28 % Allowed : 10.58 % Favored : 87.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 3912 helix: 0.62 (0.10), residues: 2412 sheet: -1.20 (0.21), residues: 504 loop : -1.99 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 198 HIS 0.002 0.001 HIS A 140 PHE 0.009 0.001 PHE L 288 TYR 0.008 0.001 TYR E 217 ARG 0.002 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 346 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8900 (mttp) REVERT: C 96 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: D 96 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: E 315 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8971 (ttm) REVERT: G 3 LYS cc_start: 0.9270 (mttt) cc_final: 0.8889 (mmpt) REVERT: H 131 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.5211 (mtm) REVERT: H 216 GLU cc_start: 0.7989 (mp0) cc_final: 0.7768 (mp0) REVERT: J 3 LYS cc_start: 0.9243 (mttt) cc_final: 0.8882 (mmpt) REVERT: L 131 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.5210 (mtm) outliers start: 73 outliers final: 33 residues processed: 375 average time/residue: 2.8891 time to fit residues: 1262.8038 Evaluate side-chains 326 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 287 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 250 MET Chi-restraints excluded: chain L residue 251 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 333 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN C 30 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN F 25 ASN F 30 GLN G 30 GLN H 37 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 32280 Z= 0.237 Angle : 0.685 17.122 43704 Z= 0.352 Chirality : 0.134 1.695 4764 Planarity : 0.003 0.037 5484 Dihedral : 7.524 88.657 5052 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.69 % Allowed : 12.33 % Favored : 85.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 3912 helix: 0.93 (0.10), residues: 2424 sheet: -1.01 (0.21), residues: 504 loop : -1.76 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 198 HIS 0.003 0.001 HIS L 196 PHE 0.010 0.001 PHE L 288 TYR 0.007 0.001 TYR E 229 ARG 0.001 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 300 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 LYS cc_start: 0.9230 (mppt) cc_final: 0.8929 (mttp) REVERT: C 215 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8996 (mttp) REVERT: E 11 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8496 (p0) REVERT: E 215 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8932 (mttp) REVERT: E 315 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8980 (ttm) REVERT: G 3 LYS cc_start: 0.9277 (mttt) cc_final: 0.8893 (mmpt) REVERT: G 11 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8491 (p0) REVERT: G 96 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8309 (mp10) REVERT: H 131 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5144 (mtm) REVERT: H 315 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8942 (ttm) REVERT: I 215 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9025 (mttp) REVERT: J 3 LYS cc_start: 0.9239 (mttt) cc_final: 0.8883 (mmpt) REVERT: J 11 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8505 (p0) REVERT: K 11 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8499 (p0) REVERT: K 315 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8961 (ttm) REVERT: L 11 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8548 (p0) REVERT: L 131 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5114 (mtm) outliers start: 54 outliers final: 23 residues processed: 319 average time/residue: 3.1018 time to fit residues: 1153.9833 Evaluate side-chains 322 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 315 MET Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 215 LYS Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN C 30 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN F 25 ASN F 30 GLN G 30 GLN H 30 GLN H 37 ASN I 30 GLN J 30 GLN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN L 30 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32280 Z= 0.200 Angle : 0.675 17.225 43704 Z= 0.344 Chirality : 0.134 1.699 4764 Planarity : 0.003 0.037 5484 Dihedral : 7.014 87.795 5052 Min Nonbonded Distance : 1.150 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.44 % Allowed : 12.73 % Favored : 85.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.13), residues: 3912 helix: 1.23 (0.10), residues: 2448 sheet: -0.88 (0.22), residues: 504 loop : -1.50 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 198 HIS 0.002 0.001 HIS L 196 PHE 0.009 0.001 PHE D 288 TYR 0.006 0.001 TYR E 229 ARG 0.001 0.000 ARG H 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 294 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8903 (ttm) REVERT: D 315 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8928 (ttm) REVERT: E 11 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8522 (p0) REVERT: F 215 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8960 (mttp) REVERT: G 3 LYS cc_start: 0.9271 (mttt) cc_final: 0.8889 (mmpt) REVERT: G 11 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8512 (p0) REVERT: G 34 MET cc_start: 0.8955 (mtp) cc_final: 0.8711 (tpp) REVERT: G 315 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8889 (ttt) REVERT: H 11 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8531 (p0) REVERT: H 131 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5055 (mtm) REVERT: H 315 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8895 (ttm) REVERT: I 11 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8535 (p0) REVERT: I 215 LYS cc_start: 0.9290 (mppt) cc_final: 0.9075 (mtmp) REVERT: I 315 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8938 (ttm) REVERT: J 3 LYS cc_start: 0.9237 (mttt) cc_final: 0.8888 (mmpt) REVERT: K 11 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8509 (p0) REVERT: K 131 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6209 (mmm) REVERT: K 315 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8926 (ttm) outliers start: 46 outliers final: 18 residues processed: 313 average time/residue: 3.0972 time to fit residues: 1128.8002 Evaluate side-chains 322 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 290 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 315 MET Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 315 MET Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 4.9990 chunk 41 optimal weight: 0.0050 chunk 211 optimal weight: 4.9990 chunk 271 optimal weight: 0.2980 chunk 210 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 225 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN C 30 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN F 25 ASN F 30 GLN H 30 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32280 Z= 0.201 Angle : 0.673 17.222 43704 Z= 0.342 Chirality : 0.134 1.698 4764 Planarity : 0.003 0.035 5484 Dihedral : 6.853 88.306 5052 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.34 % Allowed : 13.14 % Favored : 85.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3912 helix: 1.41 (0.10), residues: 2460 sheet: -0.76 (0.22), residues: 504 loop : -1.52 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 198 HIS 0.002 0.001 HIS A 196 PHE 0.009 0.001 PHE H 288 TYR 0.007 0.001 TYR E 229 ARG 0.001 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 295 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8889 (ttm) REVERT: C 315 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8931 (ttm) REVERT: D 26 GLN cc_start: 0.8550 (mm110) cc_final: 0.8272 (mp10) REVERT: D 315 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8906 (ttm) REVERT: E 11 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8539 (p0) REVERT: E 315 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8908 (ttm) REVERT: F 215 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8958 (mttp) REVERT: F 315 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8903 (ttm) REVERT: G 3 LYS cc_start: 0.9260 (mttt) cc_final: 0.8888 (mmpt) REVERT: G 11 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8529 (p0) REVERT: G 34 MET cc_start: 0.8945 (mtp) cc_final: 0.8690 (tpp) REVERT: G 315 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8854 (ttm) REVERT: H 11 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8536 (p0) REVERT: H 315 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8880 (ttm) REVERT: I 11 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8550 (p0) REVERT: I 26 GLN cc_start: 0.8578 (mm110) cc_final: 0.8292 (mp10) REVERT: I 315 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8892 (ttm) REVERT: J 3 LYS cc_start: 0.9268 (mttt) cc_final: 0.8883 (mmpt) REVERT: K 11 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8525 (p0) REVERT: K 34 MET cc_start: 0.9090 (tpp) cc_final: 0.8856 (mpp) REVERT: K 315 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8913 (ttm) REVERT: L 11 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8550 (p0) REVERT: L 131 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.4992 (mtm) REVERT: L 315 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8905 (ttm) outliers start: 43 outliers final: 16 residues processed: 310 average time/residue: 3.0732 time to fit residues: 1103.8802 Evaluate side-chains 327 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 293 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 315 MET Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 315 MET Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain L residue 315 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 0.0170 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 290 optimal weight: 8.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 30 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 30 GLN G 30 GLN H 30 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32280 Z= 0.208 Angle : 0.678 17.179 43704 Z= 0.344 Chirality : 0.134 1.698 4764 Planarity : 0.003 0.034 5484 Dihedral : 6.839 89.189 5052 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.22 % Allowed : 13.08 % Favored : 85.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3912 helix: 1.51 (0.10), residues: 2460 sheet: -0.70 (0.23), residues: 504 loop : -1.40 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 198 HIS 0.002 0.001 HIS H 196 PHE 0.010 0.001 PHE L 288 TYR 0.006 0.001 TYR E 229 ARG 0.001 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 290 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6396 (mtm) cc_final: 0.5169 (mtm) REVERT: A 315 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8847 (ttm) REVERT: C 215 LYS cc_start: 0.9289 (mppt) cc_final: 0.8986 (mttp) REVERT: D 26 GLN cc_start: 0.8517 (mm110) cc_final: 0.8241 (mp10) REVERT: D 315 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8872 (ttm) REVERT: E 11 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8550 (p0) REVERT: E 215 LYS cc_start: 0.9258 (mppt) cc_final: 0.9015 (mttp) REVERT: E 315 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8954 (ttp) REVERT: F 26 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: F 215 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8981 (mtpt) REVERT: F 315 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8863 (ttm) REVERT: G 3 LYS cc_start: 0.9259 (mttt) cc_final: 0.8886 (mmpt) REVERT: G 34 MET cc_start: 0.8941 (mtp) cc_final: 0.8675 (tpp) REVERT: G 315 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8853 (ttm) REVERT: H 11 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8542 (p0) REVERT: H 131 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5097 (mtm) REVERT: H 315 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8827 (ttm) REVERT: I 11 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8529 (p0) REVERT: I 26 GLN cc_start: 0.8506 (mm110) cc_final: 0.8228 (mp10) REVERT: I 315 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8885 (ttm) REVERT: J 3 LYS cc_start: 0.9262 (mttt) cc_final: 0.8885 (mmpt) REVERT: J 315 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8907 (ttm) REVERT: K 11 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8537 (p0) REVERT: K 34 MET cc_start: 0.9061 (tpp) cc_final: 0.8803 (mpp) REVERT: K 315 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8880 (ttm) REVERT: L 11 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8566 (p0) REVERT: L 131 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.4957 (mtm) REVERT: L 315 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8902 (ttm) outliers start: 39 outliers final: 16 residues processed: 305 average time/residue: 3.1801 time to fit residues: 1128.8864 Evaluate side-chains 324 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 315 MET Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 315 MET Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain L residue 315 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 344 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 270 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 343 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN C 30 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 30 GLN G 249 GLN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN K 30 GLN ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32280 Z= 0.317 Angle : 0.715 17.005 43704 Z= 0.368 Chirality : 0.134 1.699 4764 Planarity : 0.003 0.035 5484 Dihedral : 7.241 89.863 5052 Min Nonbonded Distance : 1.111 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.15 % Allowed : 13.36 % Favored : 85.49 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3912 helix: 1.23 (0.10), residues: 2484 sheet: -0.74 (0.23), residues: 504 loop : -1.27 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 198 HIS 0.004 0.001 HIS H 196 PHE 0.015 0.002 PHE J 288 TYR 0.010 0.001 TYR E 229 ARG 0.002 0.000 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 282 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.5350 (mtm) REVERT: A 315 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8932 (ttm) REVERT: B 215 LYS cc_start: 0.9283 (mppt) cc_final: 0.8990 (mttp) REVERT: C 215 LYS cc_start: 0.9302 (mppt) cc_final: 0.9050 (mttp) REVERT: D 315 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8958 (ttm) REVERT: E 11 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8553 (p0) REVERT: E 315 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8966 (ttm) REVERT: F 315 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8909 (ttm) REVERT: G 3 LYS cc_start: 0.9261 (mttt) cc_final: 0.8893 (mmpt) REVERT: G 34 MET cc_start: 0.8943 (mtp) cc_final: 0.8671 (tpp) REVERT: G 315 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8910 (ttm) REVERT: H 11 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8549 (p0) REVERT: H 131 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5257 (mtm) REVERT: H 315 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8942 (ttm) REVERT: I 11 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8525 (p0) REVERT: I 315 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8914 (ttm) REVERT: J 3 LYS cc_start: 0.9263 (mttt) cc_final: 0.8894 (mmpt) REVERT: J 315 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8902 (ttm) REVERT: K 11 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8541 (p0) REVERT: K 315 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8960 (ttm) REVERT: L 11 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8552 (p0) REVERT: L 131 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5214 (mtm) REVERT: L 315 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8971 (ttm) outliers start: 37 outliers final: 19 residues processed: 297 average time/residue: 3.1309 time to fit residues: 1081.9788 Evaluate side-chains 318 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 281 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 315 MET Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 315 MET Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain L residue 315 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 5.9990 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN C 30 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 30 GLN G 30 GLN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN L 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32280 Z= 0.258 Angle : 0.701 17.158 43704 Z= 0.358 Chirality : 0.134 1.695 4764 Planarity : 0.003 0.034 5484 Dihedral : 7.197 89.654 5052 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.12 % Allowed : 13.30 % Favored : 85.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3912 helix: 1.43 (0.10), residues: 2448 sheet: -0.70 (0.23), residues: 504 loop : -1.30 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 198 HIS 0.003 0.001 HIS I 140 PHE 0.011 0.001 PHE H 288 TYR 0.007 0.001 TYR G 300 ARG 0.001 0.000 ARG I 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 279 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.5330 (mtm) REVERT: A 315 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8886 (ttm) REVERT: B 215 LYS cc_start: 0.9269 (mppt) cc_final: 0.8972 (mttp) REVERT: C 215 LYS cc_start: 0.9291 (mppt) cc_final: 0.9021 (mttp) REVERT: D 315 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8913 (ttm) REVERT: E 11 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8566 (p0) REVERT: E 315 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8918 (ttm) REVERT: F 26 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: F 315 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8868 (ttm) REVERT: G 3 LYS cc_start: 0.9252 (mttt) cc_final: 0.8889 (mmpt) REVERT: G 34 MET cc_start: 0.8917 (mtp) cc_final: 0.8667 (tpp) REVERT: G 315 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8865 (ttm) REVERT: H 11 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8554 (p0) REVERT: H 131 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5219 (mtm) REVERT: H 315 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8894 (ttm) REVERT: I 11 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8540 (p0) REVERT: I 315 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8936 (ttm) REVERT: J 3 LYS cc_start: 0.9258 (mttt) cc_final: 0.8897 (mmpt) REVERT: J 315 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8949 (ttm) REVERT: K 11 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8551 (p0) REVERT: K 34 MET cc_start: 0.8984 (mpp) cc_final: 0.8756 (mmt) REVERT: K 131 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6314 (mmm) REVERT: K 315 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8921 (ttm) REVERT: L 11 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8538 (p0) REVERT: L 131 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5151 (mtm) REVERT: L 315 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8947 (ttm) outliers start: 36 outliers final: 15 residues processed: 293 average time/residue: 3.0515 time to fit residues: 1035.8261 Evaluate side-chains 313 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 278 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain G residue 315 MET Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 315 MET Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 251 VAL Chi-restraints excluded: chain L residue 315 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 30 GLN G 30 GLN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.077033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.057238 restraints weight = 238535.148| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.18 r_work: 0.2629 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 32280 Z= 0.335 Angle : 0.720 17.021 43704 Z= 0.372 Chirality : 0.135 1.697 4764 Planarity : 0.003 0.035 5484 Dihedral : 7.423 89.065 5052 Min Nonbonded Distance : 1.108 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.12 % Allowed : 13.39 % Favored : 85.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3912 helix: 1.20 (0.10), residues: 2484 sheet: -0.72 (0.23), residues: 504 loop : -1.31 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 198 HIS 0.004 0.001 HIS D 196 PHE 0.015 0.002 PHE H 288 TYR 0.010 0.001 TYR E 229 ARG 0.002 0.000 ARG H 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18953.90 seconds wall clock time: 321 minutes 52.89 seconds (19312.89 seconds total)