Starting phenix.real_space_refine on Sat Mar 16 11:57:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iug_9734/03_2024/6iug_9734_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iug_9734/03_2024/6iug_9734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iug_9734/03_2024/6iug_9734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iug_9734/03_2024/6iug_9734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iug_9734/03_2024/6iug_9734_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iug_9734/03_2024/6iug_9734_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9225 2.51 5 N 2450 2.21 5 O 2795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14585 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2889 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "B" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2889 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "C" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2889 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "D" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2889 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "E" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2889 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.92, per 1000 atoms: 0.54 Number of scatterers: 14585 At special positions: 0 Unit cell: (93.544, 93.544, 191.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 O 2795 8.00 N 2450 7.00 C 9225 6.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.8 seconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 15 sheets defined 36.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 261 through 264 No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 319 through 322 No H-bonds generated for 'chain 'A' and resid 319 through 322' Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 353 through 356 removed outlier: 3.748A pdb=" N GLN A 356 " --> pdb=" O THR A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 369 through 373 removed outlier: 4.281A pdb=" N VAL A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 373' Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 261 through 264 No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 276 through 286 Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 319 through 322 No H-bonds generated for 'chain 'B' and resid 319 through 322' Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 353 through 356 removed outlier: 3.748A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 356' Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 369 through 373 removed outlier: 4.281A pdb=" N VAL B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS B 373 " --> pdb=" O SER B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 373' Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 261 through 264 No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 276 through 286 Processing helix chain 'C' and resid 293 through 296 No H-bonds generated for 'chain 'C' and resid 293 through 296' Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 319 through 322 No H-bonds generated for 'chain 'C' and resid 319 through 322' Processing helix chain 'C' and resid 340 through 350 Processing helix chain 'C' and resid 353 through 356 removed outlier: 3.748A pdb=" N GLN C 356 " --> pdb=" O THR C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 356' Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 369 through 373 removed outlier: 4.281A pdb=" N VAL C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 373 " --> pdb=" O SER C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 373' Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'D' and resid 205 through 218 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 261 through 264 No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 276 through 286 Processing helix chain 'D' and resid 293 through 296 No H-bonds generated for 'chain 'D' and resid 293 through 296' Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 319 through 322 No H-bonds generated for 'chain 'D' and resid 319 through 322' Processing helix chain 'D' and resid 340 through 350 Processing helix chain 'D' and resid 353 through 356 removed outlier: 3.748A pdb=" N GLN D 356 " --> pdb=" O THR D 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 353 through 356' Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 369 through 373 removed outlier: 4.281A pdb=" N VAL D 372 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS D 373 " --> pdb=" O SER D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 373' Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 115 through 127 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 184 through 195 Processing helix chain 'E' and resid 205 through 218 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 261 through 264 No H-bonds generated for 'chain 'E' and resid 261 through 264' Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 276 through 286 Processing helix chain 'E' and resid 293 through 296 No H-bonds generated for 'chain 'E' and resid 293 through 296' Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 311 through 315 Processing helix chain 'E' and resid 319 through 322 No H-bonds generated for 'chain 'E' and resid 319 through 322' Processing helix chain 'E' and resid 340 through 350 Processing helix chain 'E' and resid 353 through 356 removed outlier: 3.748A pdb=" N GLN E 356 " --> pdb=" O THR E 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 353 through 356' Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 369 through 373 removed outlier: 4.281A pdb=" N VAL E 372 " --> pdb=" O PRO E 369 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS E 373 " --> pdb=" O SER E 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 369 through 373' Processing sheet with id= A, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.890A pdb=" N VAL A 105 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA A 137 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 107 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS A 12 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 33 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 54 through 56 removed outlier: 3.506A pdb=" N VAL A 37 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 39 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 299 through 302 removed outlier: 7.592A pdb=" N VAL A 300 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE A 153 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER A 302 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU A 155 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.891A pdb=" N VAL B 105 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA B 137 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 107 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 33 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 56 removed outlier: 3.506A pdb=" N VAL B 37 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 39 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 299 through 302 removed outlier: 7.592A pdb=" N VAL B 300 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 134 through 138 removed outlier: 6.890A pdb=" N VAL C 105 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA C 137 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 107 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE C 33 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.507A pdb=" N VAL C 37 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 39 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 299 through 302 removed outlier: 7.593A pdb=" N VAL C 300 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE C 153 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER C 302 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU C 155 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 134 through 138 removed outlier: 6.891A pdb=" N VAL D 105 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA D 137 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 107 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE D 33 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 54 through 56 removed outlier: 3.507A pdb=" N VAL D 37 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D 39 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 299 through 302 removed outlier: 7.593A pdb=" N VAL D 300 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE D 153 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER D 302 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU D 155 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 134 through 138 removed outlier: 6.890A pdb=" N VAL E 105 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA E 137 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU E 107 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 33 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 54 through 56 removed outlier: 3.506A pdb=" N VAL E 37 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG E 39 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 299 through 302 removed outlier: 7.592A pdb=" N VAL E 300 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE E 153 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER E 302 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU E 155 " --> pdb=" O SER E 302 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 6.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4713 1.34 - 1.46: 2975 1.46 - 1.58: 7027 1.58 - 1.69: 15 1.69 - 1.81: 180 Bond restraints: 14910 Sorted by residual: bond pdb=" CB ASP E 159 " pdb=" CG ASP E 159 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CB ASP A 159 " pdb=" CG ASP A 159 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" CB ASP B 159 " pdb=" CG ASP B 159 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.59e+00 bond pdb=" CB ASP D 159 " pdb=" CG ASP D 159 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.56e+00 bond pdb=" CB ASP C 159 " pdb=" CG ASP C 159 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.53e+00 ... (remaining 14905 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.95: 495 105.95 - 113.48: 8275 113.48 - 121.01: 7157 121.01 - 128.54: 4182 128.54 - 136.08: 126 Bond angle restraints: 20235 Sorted by residual: angle pdb=" C GLN A 51 " pdb=" N LYS A 52 " pdb=" CA LYS A 52 " ideal model delta sigma weight residual 122.32 129.04 -6.72 1.76e+00 3.23e-01 1.46e+01 angle pdb=" C GLN B 51 " pdb=" N LYS B 52 " pdb=" CA LYS B 52 " ideal model delta sigma weight residual 122.32 129.01 -6.69 1.76e+00 3.23e-01 1.45e+01 angle pdb=" C GLN D 51 " pdb=" N LYS D 52 " pdb=" CA LYS D 52 " ideal model delta sigma weight residual 122.32 129.00 -6.68 1.76e+00 3.23e-01 1.44e+01 angle pdb=" C GLN C 51 " pdb=" N LYS C 52 " pdb=" CA LYS C 52 " ideal model delta sigma weight residual 122.32 128.99 -6.67 1.76e+00 3.23e-01 1.44e+01 angle pdb=" C GLN E 51 " pdb=" N LYS E 52 " pdb=" CA LYS E 52 " ideal model delta sigma weight residual 122.32 128.99 -6.67 1.76e+00 3.23e-01 1.43e+01 ... (remaining 20230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 8770 23.28 - 46.56: 170 46.56 - 69.84: 10 69.84 - 93.11: 15 93.11 - 116.39: 5 Dihedral angle restraints: 8970 sinusoidal: 3620 harmonic: 5350 Sorted by residual: dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.39 -116.39 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.38 -116.38 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.35 -116.35 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 8967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1589 0.051 - 0.102: 525 0.102 - 0.154: 117 0.154 - 0.205: 9 0.205 - 0.256: 10 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE C 299 " pdb=" CA ILE C 299 " pdb=" CG1 ILE C 299 " pdb=" CG2 ILE C 299 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE E 299 " pdb=" CA ILE E 299 " pdb=" CG1 ILE E 299 " pdb=" CG2 ILE E 299 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE B 299 " pdb=" CA ILE B 299 " pdb=" CG1 ILE B 299 " pdb=" CG2 ILE B 299 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2247 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 244 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO E 245 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 245 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 245 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 244 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.94e+00 pdb=" N PRO C 245 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 245 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 245 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 244 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO D 245 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 245 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 245 " 0.031 5.00e-02 4.00e+02 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 299 2.66 - 3.22: 13440 3.22 - 3.78: 23431 3.78 - 4.34: 32079 4.34 - 4.90: 50553 Nonbonded interactions: 119802 Sorted by model distance: nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.106 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.106 2.170 ... (remaining 119797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.630 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 40.190 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.005 0.053 14910 Z= 0.333 Angle : 0.901 7.389 20235 Z= 0.494 Chirality : 0.055 0.256 2250 Planarity : 0.007 0.056 2580 Dihedral : 10.727 116.392 5550 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.96 % Allowed : 1.60 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.83 (0.16), residues: 1845 helix: -2.48 (0.13), residues: 765 sheet: -2.07 (0.29), residues: 275 loop : -2.64 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 342 HIS 0.013 0.002 HIS B 89 PHE 0.017 0.002 PHE E 264 TYR 0.028 0.002 TYR D 296 ARG 0.008 0.001 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 269 time to evaluate : 1.694 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: A 139 GLN cc_start: 0.7962 (mt0) cc_final: 0.7672 (mt0) REVERT: A 211 VAL cc_start: 0.9416 (t) cc_final: 0.8943 (t) REVERT: A 248 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8907 (mm110) REVERT: A 265 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8392 (mp10) REVERT: B 227 GLN cc_start: 0.8825 (mt0) cc_final: 0.8625 (tm-30) REVERT: B 265 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8347 (mp10) REVERT: B 327 MET cc_start: 0.6835 (tpp) cc_final: 0.6493 (tpt) REVERT: D 248 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8957 (mm110) REVERT: D 265 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8299 (mp10) REVERT: D 327 MET cc_start: 0.7040 (tpp) cc_final: 0.6676 (tpp) REVERT: E 123 GLN cc_start: 0.8717 (tt0) cc_final: 0.8383 (tm-30) REVERT: E 240 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8277 (ttpt) REVERT: E 248 GLN cc_start: 0.9336 (mm-40) cc_final: 0.9018 (mm-40) outliers start: 15 outliers final: 5 residues processed: 284 average time/residue: 0.2956 time to fit residues: 118.4713 Evaluate side-chains 164 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 240 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 47 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 145 optimal weight: 0.0000 chunk 56 optimal weight: 20.0000 chunk 88 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14910 Z= 0.189 Angle : 0.637 6.802 20235 Z= 0.310 Chirality : 0.045 0.176 2250 Planarity : 0.005 0.048 2580 Dihedral : 10.034 123.074 2089 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.24 % Allowed : 7.05 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.22 (0.18), residues: 1845 helix: -0.97 (0.17), residues: 775 sheet: -1.51 (0.30), residues: 275 loop : -1.86 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 358 HIS 0.007 0.001 HIS C 277 PHE 0.007 0.001 PHE D 264 TYR 0.025 0.001 TYR E 225 ARG 0.003 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.833 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: A 18 MET cc_start: 0.8136 (mtm) cc_final: 0.7599 (mmm) REVERT: A 139 GLN cc_start: 0.8089 (mt0) cc_final: 0.7765 (mt0) REVERT: A 227 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 265 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8428 (mp10) REVERT: A 356 GLN cc_start: 0.8781 (pt0) cc_final: 0.8491 (pm20) REVERT: B 265 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8409 (mp10) REVERT: B 356 GLN cc_start: 0.8667 (pt0) cc_final: 0.8446 (pm20) REVERT: C 328 LYS cc_start: 0.9099 (tttt) cc_final: 0.8805 (mmtm) REVERT: D 315 MET cc_start: 0.9283 (mmm) cc_final: 0.9054 (mmm) REVERT: E 214 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8110 (mtm) REVERT: E 224 ASP cc_start: 0.7389 (t0) cc_final: 0.6999 (t70) REVERT: E 230 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7337 (mm-30) outliers start: 35 outliers final: 26 residues processed: 215 average time/residue: 0.2500 time to fit residues: 81.4773 Evaluate side-chains 174 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 139 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 46 optimal weight: 0.0670 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** C 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14910 Z= 0.241 Angle : 0.663 10.279 20235 Z= 0.314 Chirality : 0.045 0.165 2250 Planarity : 0.004 0.039 2580 Dihedral : 9.937 131.638 2085 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.76 % Allowed : 8.53 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.20), residues: 1845 helix: -0.51 (0.18), residues: 815 sheet: -1.34 (0.35), residues: 200 loop : -1.69 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 358 HIS 0.009 0.001 HIS C 277 PHE 0.012 0.001 PHE A 264 TYR 0.022 0.001 TYR A 225 ARG 0.002 0.000 ARG E 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8102 (mtm) cc_final: 0.7685 (mmm) REVERT: A 227 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 265 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8431 (mp10) REVERT: B 121 MET cc_start: 0.8774 (ttp) cc_final: 0.8421 (tmm) REVERT: B 125 MET cc_start: 0.8873 (mmt) cc_final: 0.8452 (mmt) REVERT: B 227 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 230 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7721 (mm-30) REVERT: C 328 LYS cc_start: 0.9198 (tttt) cc_final: 0.8822 (mmtm) REVERT: D 49 MET cc_start: 0.4781 (mtt) cc_final: 0.3883 (mpp) outliers start: 43 outliers final: 23 residues processed: 186 average time/residue: 0.2363 time to fit residues: 67.9014 Evaluate side-chains 162 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 327 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14910 Z= 0.352 Angle : 0.747 10.963 20235 Z= 0.356 Chirality : 0.048 0.231 2250 Planarity : 0.004 0.036 2580 Dihedral : 9.813 132.836 2080 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.31 % Allowed : 10.00 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.20), residues: 1845 helix: -0.51 (0.18), residues: 815 sheet: -1.57 (0.32), residues: 230 loop : -1.76 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 81 HIS 0.010 0.002 HIS C 277 PHE 0.015 0.002 PHE A 264 TYR 0.024 0.002 TYR D 225 ARG 0.003 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8080 (mtm) cc_final: 0.7857 (mmm) REVERT: A 121 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8676 (tmm) REVERT: A 227 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8780 (tm-30) REVERT: A 265 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8313 (mp10) REVERT: B 18 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7701 (mmm) REVERT: B 121 MET cc_start: 0.8788 (ttp) cc_final: 0.8362 (tmm) REVERT: B 227 GLN cc_start: 0.8489 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 327 MET cc_start: 0.6625 (tpp) cc_final: 0.6278 (tpp) REVERT: C 328 LYS cc_start: 0.9117 (tttt) cc_final: 0.8870 (mmtm) REVERT: D 315 MET cc_start: 0.9295 (mmm) cc_final: 0.9025 (mmm) REVERT: E 123 GLN cc_start: 0.8614 (tt0) cc_final: 0.8066 (tm-30) REVERT: E 230 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7626 (mm-30) outliers start: 36 outliers final: 24 residues processed: 166 average time/residue: 0.2330 time to fit residues: 59.6754 Evaluate side-chains 156 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14910 Z= 0.337 Angle : 0.722 9.363 20235 Z= 0.343 Chirality : 0.047 0.250 2250 Planarity : 0.004 0.034 2580 Dihedral : 9.808 135.207 2080 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.44 % Allowed : 10.71 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.19), residues: 1845 helix: -0.41 (0.18), residues: 800 sheet: -1.33 (0.29), residues: 285 loop : -1.95 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 358 HIS 0.009 0.001 HIS C 277 PHE 0.014 0.002 PHE A 264 TYR 0.021 0.002 TYR D 225 ARG 0.004 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8675 (tmm) REVERT: A 227 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8779 (tm-30) REVERT: A 265 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8337 (mp10) REVERT: B 121 MET cc_start: 0.8774 (ttp) cc_final: 0.8370 (tmm) REVERT: B 227 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 265 GLN cc_start: 0.8522 (mp10) cc_final: 0.8116 (mp10) REVERT: B 307 MET cc_start: 0.8269 (mtt) cc_final: 0.7989 (mpp) REVERT: C 315 MET cc_start: 0.9255 (mmm) cc_final: 0.8962 (mmm) REVERT: C 327 MET cc_start: 0.6878 (tpp) cc_final: 0.6647 (tpp) REVERT: C 328 LYS cc_start: 0.9109 (tttt) cc_final: 0.8819 (mmtm) REVERT: D 18 MET cc_start: 0.8094 (mpp) cc_final: 0.7874 (mmm) REVERT: D 230 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7799 (mm-30) REVERT: E 18 MET cc_start: 0.8238 (mmm) cc_final: 0.8034 (mmt) REVERT: E 49 MET cc_start: 0.3448 (mpp) cc_final: 0.3100 (mpp) outliers start: 38 outliers final: 29 residues processed: 166 average time/residue: 0.2449 time to fit residues: 62.4471 Evaluate side-chains 163 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 chunk 148 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 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 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14910 Z= 0.262 Angle : 0.680 9.410 20235 Z= 0.320 Chirality : 0.046 0.246 2250 Planarity : 0.003 0.033 2580 Dihedral : 9.655 135.689 2080 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.18 % Allowed : 11.67 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.20), residues: 1845 helix: -0.22 (0.19), residues: 795 sheet: -1.32 (0.28), residues: 315 loop : -1.95 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 358 HIS 0.008 0.001 HIS C 277 PHE 0.012 0.001 PHE A 264 TYR 0.018 0.001 TYR D 225 ARG 0.001 0.000 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8018 (mmm) cc_final: 0.7788 (mmt) REVERT: A 121 MET cc_start: 0.9053 (ttp) cc_final: 0.8670 (tmm) REVERT: A 227 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8768 (tm-30) REVERT: A 265 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8359 (mp10) REVERT: B 121 MET cc_start: 0.8757 (ttp) cc_final: 0.8379 (tmm) REVERT: B 227 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 307 MET cc_start: 0.8227 (mtt) cc_final: 0.8015 (mtt) REVERT: B 357 MET cc_start: 0.8944 (mmm) cc_final: 0.8742 (mmm) REVERT: C 18 MET cc_start: 0.8163 (mmt) cc_final: 0.7931 (mmp) REVERT: C 315 MET cc_start: 0.9216 (mmm) cc_final: 0.8943 (mmm) REVERT: C 327 MET cc_start: 0.6884 (tpp) cc_final: 0.6600 (tpp) REVERT: C 328 LYS cc_start: 0.9122 (tttt) cc_final: 0.8843 (mmtm) REVERT: D 18 MET cc_start: 0.8065 (mpp) cc_final: 0.7865 (mmm) REVERT: D 230 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7877 (mm-30) REVERT: D 265 GLN cc_start: 0.8593 (mp10) cc_final: 0.8241 (mp10) REVERT: E 18 MET cc_start: 0.8314 (mmm) cc_final: 0.8110 (mmm) REVERT: E 49 MET cc_start: 0.3234 (mpp) cc_final: 0.2944 (mpp) REVERT: E 355 GLN cc_start: 0.8491 (mm-40) cc_final: 0.7962 (pp30) outliers start: 34 outliers final: 27 residues processed: 169 average time/residue: 0.2378 time to fit residues: 61.7091 Evaluate side-chains 164 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14910 Z= 0.149 Angle : 0.614 8.762 20235 Z= 0.284 Chirality : 0.045 0.208 2250 Planarity : 0.003 0.034 2580 Dihedral : 9.228 131.786 2080 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.99 % Allowed : 12.50 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.20), residues: 1845 helix: -0.08 (0.19), residues: 810 sheet: -0.68 (0.34), residues: 200 loop : -1.42 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 358 HIS 0.005 0.001 HIS C 277 PHE 0.009 0.001 PHE D 264 TYR 0.016 0.001 TYR C 225 ARG 0.003 0.000 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.808 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7917 (mmm) cc_final: 0.7702 (mmt) REVERT: A 83 ASP cc_start: 0.8281 (m-30) cc_final: 0.7823 (m-30) REVERT: A 121 MET cc_start: 0.9047 (ttp) cc_final: 0.8684 (tmm) REVERT: A 227 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8729 (tm-30) REVERT: A 230 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 265 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8366 (mp10) REVERT: A 357 MET cc_start: 0.9278 (mmm) cc_final: 0.8884 (mmm) REVERT: B 49 MET cc_start: 0.7240 (mmt) cc_final: 0.6850 (mmt) REVERT: B 121 MET cc_start: 0.8749 (ttp) cc_final: 0.8429 (tmm) REVERT: B 125 MET cc_start: 0.8660 (mmt) cc_final: 0.8381 (mmt) REVERT: B 227 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 265 GLN cc_start: 0.8477 (mp10) cc_final: 0.8079 (mp10) REVERT: B 307 MET cc_start: 0.8319 (mtt) cc_final: 0.8095 (mtt) REVERT: B 330 LYS cc_start: 0.8387 (tttt) cc_final: 0.8137 (pttp) REVERT: C 18 MET cc_start: 0.8026 (mmt) cc_final: 0.7821 (mmp) REVERT: C 230 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 327 MET cc_start: 0.6993 (tpp) cc_final: 0.6690 (tpp) REVERT: C 328 LYS cc_start: 0.9121 (tttt) cc_final: 0.8784 (mmtm) REVERT: D 313 ASP cc_start: 0.8524 (t0) cc_final: 0.8272 (t70) REVERT: D 358 TRP cc_start: 0.8510 (m100) cc_final: 0.8287 (m100) REVERT: E 18 MET cc_start: 0.8237 (mmm) cc_final: 0.7976 (mmm) REVERT: E 49 MET cc_start: 0.4147 (mpp) cc_final: 0.3648 (mpp) REVERT: E 230 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7508 (mm-30) REVERT: E 355 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8016 (pp30) REVERT: E 358 TRP cc_start: 0.8572 (m100) cc_final: 0.7869 (m100) outliers start: 31 outliers final: 24 residues processed: 182 average time/residue: 0.2497 time to fit residues: 68.6892 Evaluate side-chains 166 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14910 Z= 0.294 Angle : 0.697 8.793 20235 Z= 0.327 Chirality : 0.047 0.220 2250 Planarity : 0.003 0.035 2580 Dihedral : 9.588 140.922 2080 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.05 % Allowed : 13.14 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.20), residues: 1845 helix: -0.05 (0.19), residues: 780 sheet: -0.81 (0.31), residues: 260 loop : -1.37 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 358 HIS 0.008 0.002 HIS C 277 PHE 0.012 0.001 PHE A 264 TYR 0.035 0.002 TYR C 225 ARG 0.002 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8063 (mmm) cc_final: 0.7822 (mmt) REVERT: A 121 MET cc_start: 0.9089 (ttp) cc_final: 0.8704 (tmm) REVERT: A 227 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8799 (tm-30) REVERT: A 265 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8302 (mp10) REVERT: A 271 MET cc_start: 0.8668 (tpp) cc_final: 0.8412 (tpp) REVERT: B 121 MET cc_start: 0.8779 (ttp) cc_final: 0.8432 (tmm) REVERT: B 125 MET cc_start: 0.8783 (mmt) cc_final: 0.8525 (mmt) REVERT: B 227 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 265 GLN cc_start: 0.8456 (mp10) cc_final: 0.8020 (mp10) REVERT: B 307 MET cc_start: 0.8291 (mtt) cc_final: 0.8043 (mtt) REVERT: C 18 MET cc_start: 0.8133 (mmt) cc_final: 0.7884 (mmp) REVERT: C 315 MET cc_start: 0.9258 (mmm) cc_final: 0.9038 (mmm) REVERT: C 327 MET cc_start: 0.6886 (tpp) cc_final: 0.6583 (tpp) REVERT: C 328 LYS cc_start: 0.9121 (tttt) cc_final: 0.8852 (mmtm) REVERT: D 49 MET cc_start: 0.3337 (mpp) cc_final: 0.3017 (mpp) REVERT: D 84 MET cc_start: 0.9100 (mmm) cc_final: 0.8864 (tpp) REVERT: E 230 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7541 (mm-30) REVERT: E 355 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7943 (pp30) outliers start: 32 outliers final: 23 residues processed: 164 average time/residue: 0.2243 time to fit residues: 57.3422 Evaluate side-chains 159 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14910 Z= 0.275 Angle : 0.701 10.046 20235 Z= 0.328 Chirality : 0.047 0.206 2250 Planarity : 0.003 0.034 2580 Dihedral : 9.577 141.746 2080 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 1.79 % Allowed : 13.53 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.20), residues: 1845 helix: 0.01 (0.19), residues: 765 sheet: -1.14 (0.28), residues: 315 loop : -1.47 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 358 HIS 0.009 0.001 HIS C 277 PHE 0.011 0.001 PHE D 264 TYR 0.036 0.001 TYR C 225 ARG 0.002 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 2.050 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8092 (mmm) cc_final: 0.7810 (mmt) REVERT: A 121 MET cc_start: 0.9036 (ttp) cc_final: 0.8681 (tmm) REVERT: A 227 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8813 (tm-30) REVERT: A 265 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8276 (mp10) REVERT: A 271 MET cc_start: 0.8687 (tpp) cc_final: 0.8388 (tpp) REVERT: B 49 MET cc_start: 0.7535 (mmt) cc_final: 0.7090 (mmt) REVERT: B 121 MET cc_start: 0.8756 (ttp) cc_final: 0.8431 (tmm) REVERT: B 125 MET cc_start: 0.8766 (mmt) cc_final: 0.8519 (mmt) REVERT: B 227 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 265 GLN cc_start: 0.8452 (mp10) cc_final: 0.8022 (mp10) REVERT: B 307 MET cc_start: 0.8285 (mtt) cc_final: 0.8027 (mtt) REVERT: C 327 MET cc_start: 0.6920 (tpp) cc_final: 0.6609 (tpp) REVERT: C 328 LYS cc_start: 0.9092 (tttt) cc_final: 0.8835 (mmtm) REVERT: D 49 MET cc_start: 0.3577 (mpp) cc_final: 0.3317 (mpp) REVERT: D 84 MET cc_start: 0.9162 (mmm) cc_final: 0.8684 (mmm) REVERT: D 307 MET cc_start: 0.8613 (mtt) cc_final: 0.8206 (mtm) REVERT: E 230 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7569 (mm-30) REVERT: E 355 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7948 (pp30) outliers start: 28 outliers final: 24 residues processed: 163 average time/residue: 0.2379 time to fit residues: 60.6729 Evaluate side-chains 163 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14910 Z= 0.212 Angle : 0.680 12.147 20235 Z= 0.314 Chirality : 0.046 0.203 2250 Planarity : 0.003 0.035 2580 Dihedral : 9.511 141.487 2080 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.86 % Allowed : 13.59 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.20), residues: 1845 helix: 0.15 (0.20), residues: 765 sheet: -1.05 (0.28), residues: 315 loop : -1.33 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 358 HIS 0.007 0.001 HIS C 277 PHE 0.009 0.001 PHE D 264 TYR 0.030 0.001 TYR C 225 ARG 0.002 0.000 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7992 (mmm) cc_final: 0.7692 (mmt) REVERT: A 52 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7950 (mmtp) REVERT: A 121 MET cc_start: 0.9031 (ttp) cc_final: 0.8701 (tmm) REVERT: A 227 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8813 (tm-30) REVERT: A 265 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8322 (mt0) REVERT: A 271 MET cc_start: 0.8678 (tpp) cc_final: 0.8380 (tpp) REVERT: B 121 MET cc_start: 0.8755 (ttp) cc_final: 0.8436 (tmm) REVERT: B 125 MET cc_start: 0.8729 (mmt) cc_final: 0.8492 (mmt) REVERT: B 227 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 265 GLN cc_start: 0.8324 (mp10) cc_final: 0.7878 (mp10) REVERT: B 307 MET cc_start: 0.8267 (mtt) cc_final: 0.7715 (mtt) REVERT: C 18 MET cc_start: 0.8279 (mmt) cc_final: 0.8010 (mmp) REVERT: C 230 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7654 (mm-30) REVERT: C 327 MET cc_start: 0.6803 (tpp) cc_final: 0.6482 (tpp) REVERT: C 328 LYS cc_start: 0.9065 (tttt) cc_final: 0.8798 (mmtm) REVERT: D 18 MET cc_start: 0.8455 (mmm) cc_final: 0.8226 (mmm) REVERT: D 49 MET cc_start: 0.3822 (mpp) cc_final: 0.3526 (mpp) REVERT: D 84 MET cc_start: 0.9170 (mmm) cc_final: 0.8935 (mmm) REVERT: D 307 MET cc_start: 0.8477 (mtt) cc_final: 0.8057 (mtm) REVERT: D 355 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7948 (tm-30) REVERT: D 358 TRP cc_start: 0.8514 (m100) cc_final: 0.8098 (m-90) REVERT: E 123 GLN cc_start: 0.8668 (tt0) cc_final: 0.8063 (tm-30) REVERT: E 230 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7557 (mm-30) REVERT: E 355 GLN cc_start: 0.8491 (mm-40) cc_final: 0.7951 (pp30) outliers start: 29 outliers final: 25 residues processed: 164 average time/residue: 0.2341 time to fit residues: 59.6714 Evaluate side-chains 163 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.045138 restraints weight = 83607.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046399 restraints weight = 43114.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.047237 restraints weight = 26390.654| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14910 Z= 0.196 Angle : 0.675 12.202 20235 Z= 0.310 Chirality : 0.046 0.288 2250 Planarity : 0.003 0.035 2580 Dihedral : 9.443 140.742 2080 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.73 % Allowed : 14.04 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.21), residues: 1845 helix: 0.20 (0.20), residues: 765 sheet: -0.95 (0.28), residues: 315 loop : -1.27 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 358 HIS 0.006 0.001 HIS C 277 PHE 0.009 0.001 PHE D 264 TYR 0.028 0.001 TYR C 225 ARG 0.004 0.000 ARG C 337 =============================================================================== Job complete usr+sys time: 2316.52 seconds wall clock time: 43 minutes 29.45 seconds (2609.45 seconds total)