Starting phenix.real_space_refine on Sun May 25 08:47:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwm_29512/05_2025/8fwm_29512.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwm_29512/05_2025/8fwm_29512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fwm_29512/05_2025/8fwm_29512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwm_29512/05_2025/8fwm_29512.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwm_29512/05_2025/8fwm_29512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwm_29512/05_2025/8fwm_29512.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 155 5.16 5 C 16783 2.51 5 N 4494 2.21 5 O 5237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 227 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26669 Number of models: 1 Model: "" Number of chains: 15 Chain: "3" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1723 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "D" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1723 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1723 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1690 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain breaks: 1 Chain: "G" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1723 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "p" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2842 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 2 Chain: "q" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2871 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 20, 'TRANS': 352} Chain breaks: 2 Chain: "r" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2842 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 2 Chain: "s" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2863 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 20, 'TRANS': 351} Chain breaks: 2 Chain: "AV" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 119} Chain: "Aa" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 119} Chain: "Ae" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 119} Chain: "Ad" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 119} Chain: "AS" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1376 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 164} Chain: "AT" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1385 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 165} Time building chain proxies: 15.77, per 1000 atoms: 0.59 Number of scatterers: 26669 At special positions: 0 Unit cell: (185.76, 154.44, 156.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 155 16.00 O 5237 8.00 N 4494 7.00 C 16783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS 3 19 " - pdb=" SG CYS r 467 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 24 " - pdb=" SG CYS 3 221 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 229 " - pdb=" SG CYS G 23 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS q 244 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS s 467 " distance=2.14 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS F 229 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 221 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS G 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 221 " distance=2.02 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 221 " distance=2.03 Simple disulfide: pdb=" SG CYS p 14 " - pdb=" SG CYS s 244 " distance=2.03 Simple disulfide: pdb=" SG CYS p 26 " - pdb=" SG CYS p 303 " distance=2.03 Simple disulfide: pdb=" SG CYS p 73 " - pdb=" SG CYS p 320 " distance=2.00 Simple disulfide: pdb=" SG CYS p 75 " - pdb=" SG CYS p 300 " distance=2.04 Simple disulfide: pdb=" SG CYS p 217 " - pdb=" SG CYS p 249 " distance=2.02 Simple disulfide: pdb=" SG CYS p 327 " - pdb=" SG CYS r 216 " distance=2.03 Simple disulfide: pdb=" SG CYS q 26 " - pdb=" SG CYS q 303 " distance=2.04 Simple disulfide: pdb=" SG CYS q 73 " - pdb=" SG CYS q 320 " distance=2.03 Simple disulfide: pdb=" SG CYS q 75 " - pdb=" SG CYS q 300 " distance=2.03 Simple disulfide: pdb=" SG CYS q 217 " - pdb=" SG CYS q 249 " distance=2.03 Simple disulfide: pdb=" SG CYS r 26 " - pdb=" SG CYS r 303 " distance=2.02 Simple disulfide: pdb=" SG CYS r 73 " - pdb=" SG CYS r 320 " distance=2.04 Simple disulfide: pdb=" SG CYS r 75 " - pdb=" SG CYS r 300 " distance=2.03 Simple disulfide: pdb=" SG CYS r 217 " - pdb=" SG CYS r 249 " distance=2.02 Simple disulfide: pdb=" SG CYS s 26 " - pdb=" SG CYS s 303 " distance=2.03 Simple disulfide: pdb=" SG CYS s 73 " - pdb=" SG CYS s 320 " distance=2.04 Simple disulfide: pdb=" SG CYS s 75 " - pdb=" SG CYS s 300 " distance=2.03 Simple disulfide: pdb=" SG CYS s 217 " - pdb=" SG CYS s 249 " distance=2.03 Simple disulfide: pdb=" SG CYSAV 43 " - pdb=" SG CYSAa 82 " distance=2.03 Simple disulfide: pdb=" SG CYSAa 19 " - pdb=" SG CYSAe 3 " distance=2.03 Simple disulfide: pdb=" SG CYSAe 43 " - pdb=" SG CYSAd 82 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.91 Conformation dependent library (CDL) restraints added in 3.7 seconds 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6378 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 47 sheets defined 17.8% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain '3' and resid 41 through 46 Processing helix chain '3' and resid 105 through 109 removed outlier: 3.693A pdb=" N GLY 3 109 " --> pdb=" O GLU 3 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.976A pdb=" N GLY F 109 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 20 removed outlier: 3.770A pdb=" N CYS G 19 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 Processing helix chain 'G' and resid 106 through 109 Processing helix chain 'p' and resid 62 through 73 removed outlier: 3.702A pdb=" N GLU p 66 " --> pdb=" O SER p 62 " (cutoff:3.500A) Processing helix chain 'p' and resid 227 through 242 Processing helix chain 'p' and resid 260 through 267 Processing helix chain 'p' and resid 286 through 303 removed outlier: 4.136A pdb=" N THR p 290 " --> pdb=" O LEU p 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN p 291 " --> pdb=" O PRO p 287 " (cutoff:3.500A) Processing helix chain 'p' and resid 332 through 343 Processing helix chain 'p' and resid 379 through 383 Processing helix chain 'p' and resid 384 through 403 removed outlier: 3.897A pdb=" N GLN p 403 " --> pdb=" O ALA p 399 " (cutoff:3.500A) Processing helix chain 'p' and resid 404 through 406 No H-bonds generated for 'chain 'p' and resid 404 through 406' Processing helix chain 'p' and resid 425 through 438 Processing helix chain 'p' and resid 450 through 455 removed outlier: 3.777A pdb=" N ILE p 455 " --> pdb=" O ILE p 451 " (cutoff:3.500A) Processing helix chain 'p' and resid 460 through 464 Processing helix chain 'q' and resid 62 through 75 removed outlier: 3.658A pdb=" N CYS q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) Processing helix chain 'q' and resid 208 through 213 removed outlier: 3.538A pdb=" N VAL q 212 " --> pdb=" O ASP q 208 " (cutoff:3.500A) Processing helix chain 'q' and resid 227 through 243 Processing helix chain 'q' and resid 260 through 267 Processing helix chain 'q' and resid 286 through 302 removed outlier: 3.699A pdb=" N THR q 290 " --> pdb=" O LEU q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 332 through 342 removed outlier: 3.670A pdb=" N ALA q 341 " --> pdb=" O THR q 337 " (cutoff:3.500A) Processing helix chain 'q' and resid 384 through 403 Processing helix chain 'q' and resid 425 through 441 Processing helix chain 'q' and resid 450 through 455 removed outlier: 3.519A pdb=" N ILE q 455 " --> pdb=" O ILE q 451 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 removed outlier: 4.590A pdb=" N ILE r 55 " --> pdb=" O LEU r 52 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 75 removed outlier: 4.136A pdb=" N CYS r 75 " --> pdb=" O VAL r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 227 through 241 Processing helix chain 'r' and resid 260 through 267 Processing helix chain 'r' and resid 286 through 302 removed outlier: 4.227A pdb=" N THR r 290 " --> pdb=" O LEU r 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN r 291 " --> pdb=" O PRO r 287 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS r 300 " --> pdb=" O ALA r 296 " (cutoff:3.500A) Processing helix chain 'r' and resid 332 through 342 Processing helix chain 'r' and resid 378 through 383 Processing helix chain 'r' and resid 384 through 403 removed outlier: 3.521A pdb=" N ARG r 388 " --> pdb=" O ASP r 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN r 403 " --> pdb=" O ALA r 399 " (cutoff:3.500A) Processing helix chain 'r' and resid 404 through 406 No H-bonds generated for 'chain 'r' and resid 404 through 406' Processing helix chain 'r' and resid 425 through 441 Processing helix chain 'r' and resid 450 through 455 removed outlier: 3.620A pdb=" N ILE r 455 " --> pdb=" O ILE r 451 " (cutoff:3.500A) Processing helix chain 'r' and resid 460 through 464 Processing helix chain 's' and resid 62 through 75 Processing helix chain 's' and resid 227 through 239 Processing helix chain 's' and resid 260 through 267 Processing helix chain 's' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR s 290 " --> pdb=" O LEU s 286 " (cutoff:3.500A) Processing helix chain 's' and resid 332 through 342 Processing helix chain 's' and resid 379 through 383 removed outlier: 3.968A pdb=" N PHE s 382 " --> pdb=" O ASN s 379 " (cutoff:3.500A) Processing helix chain 's' and resid 384 through 402 Processing helix chain 's' and resid 425 through 441 removed outlier: 3.849A pdb=" N LYS s 432 " --> pdb=" O LEU s 428 " (cutoff:3.500A) Processing helix chain 's' and resid 450 through 455 removed outlier: 3.580A pdb=" N ASP s 454 " --> pdb=" O ASN s 450 " (cutoff:3.500A) Processing helix chain 's' and resid 459 through 463 removed outlier: 3.650A pdb=" N GLU s 462 " --> pdb=" O THR s 459 " (cutoff:3.500A) Processing helix chain 's' and resid 465 through 469 removed outlier: 4.155A pdb=" N GLY s 469 " --> pdb=" O LYS s 466 " (cutoff:3.500A) Processing helix chain 'AV' and resid 76 through 81 removed outlier: 3.508A pdb=" N GLYAV 81 " --> pdb=" O ALAAV 77 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 75 through 80 Processing helix chain 'Ae' and resid 75 through 79 Processing helix chain 'Ad' and resid 76 through 81 Processing helix chain 'AS' and resid 12 through 20 Processing helix chain 'AS' and resid 25 through 29 removed outlier: 3.961A pdb=" N ILEAS 28 " --> pdb=" O PHEAS 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLUAS 29 " --> pdb=" O HISAS 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'AS' and resid 25 through 29' Processing helix chain 'AS' and resid 107 through 126 Processing helix chain 'AT' and resid 12 through 21 Processing helix chain 'AT' and resid 107 through 126 Processing sheet with id=AA1, first strand: chain '3' and resid 2 through 5 removed outlier: 6.177A pdb=" N TYR 3 2 " --> pdb=" O MET 3 38 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER 3 40 " --> pdb=" O TYR 3 2 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE 3 4 " --> pdb=" O SER 3 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 2 through 5 removed outlier: 6.177A pdb=" N TYR 3 2 " --> pdb=" O MET 3 38 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER 3 40 " --> pdb=" O TYR 3 2 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE 3 4 " --> pdb=" O SER 3 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 25 through 29 removed outlier: 6.693A pdb=" N GLU 3 25 " --> pdb=" O ASP 3 223 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER 3 225 " --> pdb=" O GLU 3 25 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE 3 27 " --> pdb=" O SER 3 225 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE 3 216 " --> pdb=" O ALA 3 208 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL 3 199 " --> pdb=" O VAL 3 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 74 through 78 removed outlier: 6.738A pdb=" N ALA 3 74 " --> pdb=" O VAL 3 149 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER 3 151 " --> pdb=" O ALA 3 74 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY 3 76 " --> pdb=" O SER 3 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 84 through 87 Processing sheet with id=AA6, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.265A pdb=" N TYR D 2 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER D 40 " --> pdb=" O TYR D 2 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE D 4 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.265A pdb=" N TYR D 2 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER D 40 " --> pdb=" O TYR D 2 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE D 4 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 25 through 29 removed outlier: 6.462A pdb=" N GLU D 25 " --> pdb=" O ASP D 223 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER D 225 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 27 " --> pdb=" O SER D 225 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 216 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 199 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 74 through 79 Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 87 Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AB4, first strand: chain 'E' and resid 25 through 29 Processing sheet with id=AB5, first strand: chain 'E' and resid 74 through 79 removed outlier: 6.451A pdb=" N ALA E 74 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N SER E 151 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY E 76 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASP E 153 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR E 78 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 87 Processing sheet with id=AB7, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.156A pdb=" N TYR F 2 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER F 40 " --> pdb=" O TYR F 2 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE F 4 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.156A pdb=" N TYR F 2 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER F 40 " --> pdb=" O TYR F 2 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE F 4 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 25 through 29 removed outlier: 6.573A pdb=" N GLU F 25 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER F 225 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE F 27 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL F 199 " --> pdb=" O VAL F 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 84 through 87 Processing sheet with id=AC2, first strand: chain 'F' and resid 133 through 141 Processing sheet with id=AC3, first strand: chain 'G' and resid 2 through 5 Processing sheet with id=AC4, first strand: chain 'G' and resid 2 through 5 Processing sheet with id=AC5, first strand: chain 'G' and resid 25 through 29 removed outlier: 6.484A pdb=" N GLU G 25 " --> pdb=" O ASP G 223 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER G 225 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE G 27 " --> pdb=" O SER G 225 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE G 216 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL G 199 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 74 through 75 removed outlier: 3.642A pdb=" N ALA G 74 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL G 149 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 84 through 87 Processing sheet with id=AC8, first strand: chain 'p' and resid 82 through 85 removed outlier: 6.673A pdb=" N VAL p 30 " --> pdb=" O LEU p 84 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE p 256 " --> pdb=" O LEU p 223 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU p 277 " --> pdb=" O GLY p 253 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL p 255 " --> pdb=" O LEU p 277 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'p' and resid 456 through 459 Processing sheet with id=AD1, first strand: chain 'p' and resid 489 through 491 removed outlier: 6.451A pdb=" N ASN p 490 " --> pdb=" O LEU r 476 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'q' and resid 46 through 47 removed outlier: 6.602A pdb=" N CYS q 26 " --> pdb=" O SER q 80 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR q 82 " --> pdb=" O CYS q 26 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE q 28 " --> pdb=" O TYR q 82 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU q 84 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL q 30 " --> pdb=" O LEU q 84 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG q 86 " --> pdb=" O VAL q 30 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY q 32 " --> pdb=" O ARG q 86 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL q 220 " --> pdb=" O GLY q 25 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS q 27 " --> pdb=" O VAL q 220 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL q 222 " --> pdb=" O LYS q 27 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU q 29 " --> pdb=" O VAL q 222 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR q 221 " --> pdb=" O TYR q 254 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N PHE q 256 " --> pdb=" O TYR q 221 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N LEU q 223 " --> pdb=" O PHE q 256 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N LYS q 258 " --> pdb=" O LEU q 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'q' and resid 492 through 494 Processing sheet with id=AD4, first strand: chain 'r' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'r' and resid 46 through 47 removed outlier: 3.543A pdb=" N ALA r 83 " --> pdb=" O THR r 46 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE r 28 " --> pdb=" O TYR r 82 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU r 84 " --> pdb=" O ILE r 28 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL r 30 " --> pdb=" O LEU r 84 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG r 86 " --> pdb=" O VAL r 30 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY r 32 " --> pdb=" O ARG r 86 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR r 221 " --> pdb=" O TYR r 254 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N PHE r 256 " --> pdb=" O TYR r 221 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU r 223 " --> pdb=" O PHE r 256 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LEU r 277 " --> pdb=" O GLY r 253 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL r 255 " --> pdb=" O LEU r 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 's' and resid 79 through 81 removed outlier: 7.105A pdb=" N GLY s 25 " --> pdb=" O SER s 80 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU s 84 " --> pdb=" O ILE s 28 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL s 30 " --> pdb=" O LEU s 84 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG s 86 " --> pdb=" O VAL s 30 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY s 32 " --> pdb=" O ARG s 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 's' and resid 79 through 81 removed outlier: 7.105A pdb=" N GLY s 25 " --> pdb=" O SER s 80 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR s 221 " --> pdb=" O TYR s 254 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N PHE s 256 " --> pdb=" O TYR s 221 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU s 223 " --> pdb=" O PHE s 256 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N LYS s 258 " --> pdb=" O LEU s 223 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY s 253 " --> pdb=" O SER s 275 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU s 277 " --> pdb=" O GLY s 253 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL s 255 " --> pdb=" O LEU s 277 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU s 279 " --> pdb=" O VAL s 255 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN s 257 " --> pdb=" O LEU s 279 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 's' and resid 346 through 347 removed outlier: 4.189A pdb=" N VAL s 346 " --> pdb=" O TYR s 364 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR s 364 " --> pdb=" O VAL s 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 's' and resid 409 through 410 removed outlier: 6.869A pdb=" N ALA s 409 " --> pdb=" O THR s 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'AV' and resid 24 through 29 removed outlier: 5.695A pdb=" N ILEAV 14 " --> pdb=" O PROAV 27 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SERAV 29 " --> pdb=" O ILEAV 12 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILEAV 12 " --> pdb=" O SERAV 29 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLUAV 90 " --> pdb=" O LYSAV 10 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILEAV 12 " --> pdb=" O GLNAV 88 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLNAV 88 " --> pdb=" O ILEAV 12 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILEAV 14 " --> pdb=" O ASPAV 86 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASPAV 86 " --> pdb=" O ILEAV 14 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHEAV 16 " --> pdb=" O GLNAV 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLNAV 84 " --> pdb=" O PHEAV 16 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VALAV 85 " --> pdb=" O GLUAV 101 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUAV 101 " --> pdb=" O VALAV 85 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'AV' and resid 47 through 49 Processing sheet with id=AE3, first strand: chain 'Aa' and resid 24 through 30 removed outlier: 5.693A pdb=" N ILEAa 14 " --> pdb=" O PROAa 27 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SERAa 29 " --> pdb=" O ILEAa 12 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILEAa 12 " --> pdb=" O SERAa 29 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VALAa 85 " --> pdb=" O GLUAa 101 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLUAa 101 " --> pdb=" O VALAa 85 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Aa' and resid 24 through 30 removed outlier: 5.693A pdb=" N ILEAa 14 " --> pdb=" O PROAa 27 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SERAa 29 " --> pdb=" O ILEAa 12 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILEAa 12 " --> pdb=" O SERAa 29 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VALAa 85 " --> pdb=" O GLUAa 101 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLUAa 101 " --> pdb=" O VALAa 85 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Aa' and resid 47 through 49 Processing sheet with id=AE6, first strand: chain 'Ae' and resid 24 through 29 removed outlier: 5.674A pdb=" N ILEAe 14 " --> pdb=" O PROAe 27 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SERAe 29 " --> pdb=" O ILEAe 12 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILEAe 12 " --> pdb=" O SERAe 29 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VALAe 85 " --> pdb=" O GLUAe 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLUAe 101 " --> pdb=" O VALAe 85 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Ae' and resid 45 through 46 Processing sheet with id=AE8, first strand: chain 'Ad' and resid 24 through 29 removed outlier: 5.643A pdb=" N ILEAd 14 " --> pdb=" O PROAd 27 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SERAd 29 " --> pdb=" O ILEAd 12 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILEAd 12 " --> pdb=" O SERAd 29 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLUAd 90 " --> pdb=" O LYSAd 10 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILEAd 12 " --> pdb=" O GLNAd 88 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLNAd 88 " --> pdb=" O ILEAd 12 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILEAd 14 " --> pdb=" O ASPAd 86 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASPAd 86 " --> pdb=" O ILEAd 14 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHEAd 16 " --> pdb=" O GLNAd 84 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLNAd 84 " --> pdb=" O PHEAd 16 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VALAd 87 " --> pdb=" O THRAd 100 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THRAd 100 " --> pdb=" O VALAd 87 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VALAd 89 " --> pdb=" O THRAd 98 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THRAd 98 " --> pdb=" O VALAd 89 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYSAd 91 " --> pdb=" O VALAd 96 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VALAd 96 " --> pdb=" O LYSAd 91 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VALAd 120 " --> pdb=" O ALAAd 103 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Ad' and resid 47 through 49 Processing sheet with id=AF1, first strand: chain 'AS' and resid 32 through 35 removed outlier: 4.148A pdb=" N LEUAS 57 " --> pdb=" O VALAS 35 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VALAS 53 " --> pdb=" O ASNAS 85 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASNAS 85 " --> pdb=" O VALAS 53 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VALAS 55 " --> pdb=" O GLUAS 83 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLUAS 83 " --> pdb=" O VALAS 55 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEUAS 57 " --> pdb=" O ILEAS 81 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILEAS 81 " --> pdb=" O LEUAS 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERAS 133 " --> pdb=" O ARGAS 148 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARGAS 150 " --> pdb=" O PHEAS 131 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHEAS 131 " --> pdb=" O ARGAS 150 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASNAS 152 " --> pdb=" O PHEAS 129 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHEAS 129 " --> pdb=" O ASNAS 152 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHEAS 129 " --> pdb=" O ILEAT 68 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'AT' and resid 32 through 35 removed outlier: 4.250A pdb=" N LEUAT 57 " --> pdb=" O VALAT 35 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VALAT 53 " --> pdb=" O ASNAT 85 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASNAT 85 " --> pdb=" O VALAT 53 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VALAT 55 " --> pdb=" O GLUAT 83 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLUAT 83 " --> pdb=" O VALAT 55 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEUAT 57 " --> pdb=" O ILEAT 81 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILEAT 81 " --> pdb=" O LEUAT 57 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SERAT 133 " --> pdb=" O ARGAT 148 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARGAT 150 " --> pdb=" O PHEAT 131 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHEAT 131 " --> pdb=" O ARGAT 150 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2289 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: 8.78 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7745 1.33 - 1.46: 6919 1.46 - 1.59: 12390 1.59 - 1.71: 0 1.71 - 1.84: 201 Bond restraints: 27255 Sorted by residual: bond pdb=" CA ASN 3 10 " pdb=" C ASN 3 10 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.28e-02 6.10e+03 1.66e+01 bond pdb=" CA LEUAd 127 " pdb=" C LEUAd 127 " ideal model delta sigma weight residual 1.527 1.480 0.048 1.20e-02 6.94e+03 1.58e+01 bond pdb=" CA CYS r 303 " pdb=" C CYS r 303 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.29e-02 6.01e+03 1.14e+01 bond pdb=" CA GLNAV 6 " pdb=" C GLNAV 6 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.23e-02 6.61e+03 1.14e+01 bond pdb=" CA TRPAS 155 " pdb=" C TRPAS 155 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.28e-02 6.10e+03 1.06e+01 ... (remaining 27250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 36288 2.52 - 5.04: 752 5.04 - 7.56: 81 7.56 - 10.08: 19 10.08 - 12.61: 5 Bond angle restraints: 37145 Sorted by residual: angle pdb=" N CYS r 303 " pdb=" CA CYS r 303 " pdb=" C CYS r 303 " ideal model delta sigma weight residual 111.36 99.08 12.28 1.09e+00 8.42e-01 1.27e+02 angle pdb=" N GLY 3 11 " pdb=" CA GLY 3 11 " pdb=" C GLY 3 11 " ideal model delta sigma weight residual 114.61 105.37 9.24 1.49e+00 4.50e-01 3.84e+01 angle pdb=" N LYSAS 95 " pdb=" CA LYSAS 95 " pdb=" C LYSAS 95 " ideal model delta sigma weight residual 110.80 98.19 12.61 2.13e+00 2.20e-01 3.50e+01 angle pdb=" N GLNAV 6 " pdb=" CA GLNAV 6 " pdb=" C GLNAV 6 " ideal model delta sigma weight residual 110.42 118.84 -8.42 1.46e+00 4.69e-01 3.33e+01 angle pdb=" N PHE s 250 " pdb=" CA PHE s 250 " pdb=" C PHE s 250 " ideal model delta sigma weight residual 110.80 122.97 -12.17 2.13e+00 2.20e-01 3.26e+01 ... (remaining 37140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14692 17.98 - 35.97: 1207 35.97 - 53.95: 276 53.95 - 71.93: 66 71.93 - 89.92: 35 Dihedral angle restraints: 16276 sinusoidal: 6329 harmonic: 9947 Sorted by residual: dihedral pdb=" CB CYS p 327 " pdb=" SG CYS p 327 " pdb=" SG CYS r 216 " pdb=" CB CYS r 216 " ideal model delta sinusoidal sigma weight residual -86.00 -175.79 89.79 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS r 73 " pdb=" SG CYS r 73 " pdb=" SG CYS r 320 " pdb=" CB CYS r 320 " ideal model delta sinusoidal sigma weight residual -86.00 -172.29 86.29 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS 3 19 " pdb=" SG CYS 3 19 " pdb=" SG CYS r 467 " pdb=" CB CYS r 467 " ideal model delta sinusoidal sigma weight residual 93.00 177.38 -84.38 1 1.00e+01 1.00e-02 8.66e+01 ... (remaining 16273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3499 0.068 - 0.136: 664 0.136 - 0.204: 26 0.204 - 0.272: 1 0.272 - 0.340: 1 Chirality restraints: 4191 Sorted by residual: chirality pdb=" CB ILE p 54 " pdb=" CA ILE p 54 " pdb=" CG1 ILE p 54 " pdb=" CG2 ILE p 54 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA PHE s 250 " pdb=" N PHE s 250 " pdb=" C PHE s 250 " pdb=" CB PHE s 250 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA CYS r 467 " pdb=" N CYS r 467 " pdb=" C CYS r 467 " pdb=" CB CYS r 467 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 4188 not shown) Planarity restraints: 4931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THRAS 165 " 0.023 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" C THRAS 165 " -0.077 2.00e-02 2.50e+03 pdb=" O THRAS 165 " 0.029 2.00e-02 2.50e+03 pdb=" N ILEAS 166 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS q 246 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO q 247 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO q 247 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO q 247 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO s 465 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C PRO s 465 " -0.067 2.00e-02 2.50e+03 pdb=" O PRO s 465 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS s 466 " 0.023 2.00e-02 2.50e+03 ... (remaining 4928 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3003 2.74 - 3.28: 27581 3.28 - 3.82: 43060 3.82 - 4.36: 49354 4.36 - 4.90: 84830 Nonbonded interactions: 207828 Sorted by model distance: nonbonded pdb=" OG1 THR q 328 " pdb=" OD1 ASN s 214 " model vdw 2.205 3.040 nonbonded pdb=" O GLY r 59 " pdb=" OG1 THR r 65 " model vdw 2.205 3.040 nonbonded pdb=" ND2 ASN r 257 " pdb=" OD2 ASP r 267 " model vdw 2.216 3.120 nonbonded pdb=" NH1 ARGAS 31 " pdb=" O PROAS 51 " model vdw 2.223 3.120 nonbonded pdb=" O ASPAS 41 " pdb=" OG1 THRAS 45 " model vdw 2.228 3.040 ... (remaining 207823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '3' and (resid 1 through 12 or resid 18 through 230)) selection = (chain 'D' and (resid 1 through 12 or resid 18 through 230)) selection = (chain 'E' and (resid 1 through 12 or resid 18 through 230)) selection = chain 'F' selection = (chain 'G' and (resid 1 through 12 or resid 18 through 230)) } ncs_group { reference = chain 'AS' selection = (chain 'AT' and resid 5 through 175) } ncs_group { reference = chain 'AV' selection = chain 'Aa' selection = chain 'Ad' selection = chain 'Ae' } ncs_group { reference = (chain 'p' and resid 5 through 498) selection = (chain 'q' and (resid 5 through 347 or resid 363 through 498)) selection = (chain 'r' and resid 5 through 498) selection = (chain 's' and (resid 5 through 347 or resid 363 through 498)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.640 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: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 58.380 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.130 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 0.110 27288 Z= 0.270 Angle : 0.925 47.157 37211 Z= 0.546 Chirality : 0.049 0.340 4191 Planarity : 0.005 0.109 4931 Dihedral : 14.583 89.917 9799 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 1.16 % Allowed : 13.77 % Favored : 85.07 % Rotamer: Outliers : 2.37 % Allowed : 7.07 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.12), residues: 3435 helix: -2.42 (0.18), residues: 487 sheet: -1.95 (0.15), residues: 1025 loop : -4.08 (0.11), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 242 HIS 0.004 0.001 HIS E 218 PHE 0.025 0.001 PHE r 250 TYR 0.038 0.002 TYR p 370 ARG 0.007 0.001 ARG p 372 Details of bonding type rmsd hydrogen bonds : bond 0.16877 ( 780) hydrogen bonds : angle 7.09451 ( 2289) SS BOND : bond 0.02059 ( 33) SS BOND : angle 7.00990 ( 66) covalent geometry : bond 0.00491 (27255) covalent geometry : angle 0.87777 (37145) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 921 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 56 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8114 (ttpp) REVERT: 3 180 ARG cc_start: 0.7990 (mmp-170) cc_final: 0.7723 (mtt90) REVERT: D 33 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7513 (mm-30) REVERT: D 38 MET cc_start: 0.8148 (mtp) cc_final: 0.7502 (mtp) REVERT: D 135 ASP cc_start: 0.6047 (t0) cc_final: 0.3898 (p0) REVERT: D 148 TYR cc_start: 0.7641 (t80) cc_final: 0.6503 (t80) REVERT: D 150 ILE cc_start: 0.6984 (mt) cc_final: 0.5979 (mt) REVERT: D 185 LYS cc_start: 0.8605 (mttt) cc_final: 0.8246 (mttm) REVERT: D 198 ASP cc_start: 0.7492 (m-30) cc_final: 0.7230 (m-30) REVERT: E 14 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6633 (tmmt) REVERT: E 33 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7382 (pt0) REVERT: E 79 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7194 (mmtt) REVERT: E 103 GLU cc_start: 0.7372 (tt0) cc_final: 0.7086 (tt0) REVERT: E 106 GLU cc_start: 0.7627 (tt0) cc_final: 0.7075 (tm-30) REVERT: E 135 ASP cc_start: 0.6644 (t0) cc_final: 0.6186 (m-30) REVERT: E 178 ASP cc_start: 0.7518 (t70) cc_final: 0.7249 (t0) REVERT: F 25 GLU cc_start: 0.8315 (mp0) cc_final: 0.7613 (mp0) REVERT: F 120 ASN cc_start: 0.7262 (t0) cc_final: 0.6127 (p0) REVERT: F 130 LEU cc_start: 0.7589 (mt) cc_final: 0.7357 (tt) REVERT: G 62 ASP cc_start: 0.7293 (m-30) cc_final: 0.6775 (m-30) REVERT: G 70 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7976 (tttt) REVERT: G 131 PHE cc_start: 0.3329 (t80) cc_final: 0.2202 (t80) REVERT: G 148 TYR cc_start: 0.6957 (t80) cc_final: 0.6657 (t80) REVERT: G 169 TYR cc_start: 0.7879 (p90) cc_final: 0.7592 (p90) REVERT: p 345 VAL cc_start: 0.8145 (t) cc_final: 0.7884 (p) REVERT: p 455 ILE cc_start: 0.9213 (mm) cc_final: 0.8997 (mm) REVERT: p 478 MET cc_start: 0.8221 (mtp) cc_final: 0.7970 (mtp) REVERT: q 16 ASP cc_start: 0.8976 (t0) cc_final: 0.8705 (t0) REVERT: q 457 LEU cc_start: 0.9294 (tt) cc_final: 0.9033 (tt) REVERT: q 473 ILE cc_start: 0.7779 (mm) cc_final: 0.7325 (mm) REVERT: r 258 LYS cc_start: 0.6159 (tttp) cc_final: 0.4686 (ptmt) REVERT: r 375 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6366 (tptm) REVERT: r 467 CYS cc_start: 0.4623 (OUTLIER) cc_final: 0.3518 (m) REVERT: r 480 TYR cc_start: 0.5769 (m-10) cc_final: 0.5021 (m-10) REVERT: r 495 PRO cc_start: 0.8122 (Cg_endo) cc_final: 0.7878 (Cg_exo) REVERT: s 64 LEU cc_start: 0.6838 (pp) cc_final: 0.6625 (pp) REVERT: s 72 PHE cc_start: 0.7652 (m-10) cc_final: 0.7111 (m-80) REVERT: s 311 GLN cc_start: 0.8342 (pt0) cc_final: 0.8043 (pt0) REVERT: s 317 LEU cc_start: 0.7343 (tp) cc_final: 0.6775 (pt) REVERT: s 371 LEU cc_start: 0.9186 (mm) cc_final: 0.8908 (mp) REVERT: s 379 ASN cc_start: 0.8000 (t0) cc_final: 0.7015 (t0) REVERT: s 414 ASN cc_start: 0.8461 (m-40) cc_final: 0.8084 (t0) REVERT: AV 52 ASN cc_start: 0.8719 (t0) cc_final: 0.7702 (t0) REVERT: AV 54 TYR cc_start: 0.8737 (m-80) cc_final: 0.8507 (m-80) REVERT: AV 97 MET cc_start: 0.8011 (mmt) cc_final: 0.7757 (mmt) REVERT: AV 109 GLU cc_start: 0.5846 (tp30) cc_final: 0.5381 (mt-10) REVERT: Aa 93 ASP cc_start: 0.8887 (p0) cc_final: 0.8637 (p0) REVERT: Ae 18 ASP cc_start: 0.8150 (t0) cc_final: 0.7721 (t70) REVERT: Ae 126 GLU cc_start: 0.7067 (tt0) cc_final: 0.6756 (tt0) REVERT: Ad 13 LEU cc_start: 0.9082 (mm) cc_final: 0.8806 (mp) REVERT: Ad 52 ASN cc_start: 0.8875 (t0) cc_final: 0.8609 (t0) REVERT: AS 10 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7665 (ttp80) REVERT: AS 112 ASP cc_start: 0.8137 (m-30) cc_final: 0.7763 (m-30) REVERT: AT 18 LYS cc_start: 0.8625 (ptmt) cc_final: 0.8318 (ptmm) REVERT: AT 104 TYR cc_start: 0.8691 (t80) cc_final: 0.5712 (m-80) REVERT: AT 108 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8474 (mt-10) REVERT: AT 112 ASP cc_start: 0.8414 (m-30) cc_final: 0.8144 (m-30) outliers start: 70 outliers final: 19 residues processed: 963 average time/residue: 0.3946 time to fit residues: 576.8576 Evaluate side-chains 605 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 583 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 221 CYS Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 320 CYS Chi-restraints excluded: chain r residue 301 SER Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain s residue 217 CYS Chi-restraints excluded: chain s residue 250 PHE Chi-restraints excluded: chain AS residue 156 CYS Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 167 GLU Chi-restraints excluded: chain AS residue 170 ARG Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 158 THR Chi-restraints excluded: chain AT residue 167 GLU Chi-restraints excluded: chain AT residue 170 ARG Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 5.9990 chunk 259 optimal weight: 0.0060 chunk 143 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 162 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN F 182 HIS G 55 ASN p 33 GLN p 452 ASN p 470 GLN q 60 GLN q 263 GLN ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 369 ASN r 33 GLN r 214 ASN r 252 HIS r 270 ASN ** r 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 452 ASN r 475 HIS r 490 ASN s 33 GLN ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 369 ASN s 456 GLN AV 6 GLN AV 22 GLN AV 32 GLN Aa 32 GLN Ae 88 GLN AS 46 GLN AT 125 HIS AT 151 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105408 restraints weight = 61902.012| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.20 r_work: 0.3364 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27288 Z= 0.167 Angle : 0.742 10.320 37211 Z= 0.380 Chirality : 0.048 0.218 4191 Planarity : 0.005 0.104 4931 Dihedral : 6.835 80.185 3786 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.99 % Favored : 87.74 % Rotamer: Outliers : 4.20 % Allowed : 15.84 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -3.35 (0.13), residues: 3435 helix: -0.20 (0.22), residues: 523 sheet: -1.45 (0.15), residues: 1048 loop : -3.46 (0.12), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP q 242 HIS 0.004 0.001 HIS E 218 PHE 0.022 0.001 PHE s 58 TYR 0.019 0.002 TYR E 169 ARG 0.007 0.001 ARGAS 92 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 780) hydrogen bonds : angle 5.43873 ( 2289) SS BOND : bond 0.01399 ( 33) SS BOND : angle 2.51119 ( 66) covalent geometry : bond 0.00380 (27255) covalent geometry : angle 0.73489 (37145) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 638 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 56 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8372 (ttmm) REVERT: 3 180 ARG cc_start: 0.7951 (mmp-170) cc_final: 0.7734 (mtt90) REVERT: D 33 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7888 (mm-30) REVERT: D 159 LEU cc_start: 0.7604 (tp) cc_final: 0.7019 (mp) REVERT: D 185 LYS cc_start: 0.8785 (mttt) cc_final: 0.8481 (mttm) REVERT: E 2 TYR cc_start: 0.8381 (m-80) cc_final: 0.7989 (m-80) REVERT: E 14 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7004 (tmmt) REVERT: E 33 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8076 (pt0) REVERT: E 38 MET cc_start: 0.8931 (mtp) cc_final: 0.8284 (mtp) REVERT: E 135 ASP cc_start: 0.7148 (t0) cc_final: 0.6532 (m-30) REVERT: E 215 GLU cc_start: 0.7977 (mp0) cc_final: 0.7760 (mp0) REVERT: F 1 MET cc_start: 0.8273 (ttt) cc_final: 0.7815 (ttt) REVERT: F 120 ASN cc_start: 0.7242 (t0) cc_final: 0.6145 (p0) REVERT: F 130 LEU cc_start: 0.7686 (mt) cc_final: 0.7342 (tt) REVERT: G 30 ARG cc_start: 0.8528 (ttt-90) cc_final: 0.7884 (mtt-85) REVERT: G 70 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8124 (tttt) REVERT: G 84 PHE cc_start: 0.6616 (t80) cc_final: 0.6298 (t80) REVERT: G 148 TYR cc_start: 0.7376 (t80) cc_final: 0.6815 (t80) REVERT: G 159 LEU cc_start: 0.6709 (mm) cc_final: 0.5705 (mp) REVERT: p 460 ASP cc_start: 0.8001 (t0) cc_final: 0.7692 (t0) REVERT: r 82 TYR cc_start: 0.7752 (m-80) cc_final: 0.7384 (m-80) REVERT: r 258 LYS cc_start: 0.5978 (tttp) cc_final: 0.4805 (ptmt) REVERT: r 310 ILE cc_start: 0.8557 (mt) cc_final: 0.8138 (mm) REVERT: r 367 VAL cc_start: 0.8675 (m) cc_final: 0.8383 (m) REVERT: r 375 LYS cc_start: 0.7574 (tptm) cc_final: 0.6421 (tmtt) REVERT: r 390 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7954 (tp) REVERT: s 27 LYS cc_start: 0.7741 (tppt) cc_final: 0.7317 (mmtp) REVERT: s 29 LEU cc_start: 0.8845 (tp) cc_final: 0.8627 (tp) REVERT: s 72 PHE cc_start: 0.8107 (m-10) cc_final: 0.7403 (m-80) REVERT: s 82 TYR cc_start: 0.7887 (m-10) cc_final: 0.7673 (m-10) REVERT: s 317 LEU cc_start: 0.7483 (tp) cc_final: 0.6938 (pt) REVERT: s 379 ASN cc_start: 0.8072 (t0) cc_final: 0.7520 (t0) REVERT: s 414 ASN cc_start: 0.8662 (m-40) cc_final: 0.8355 (t0) REVERT: s 462 GLU cc_start: 0.8462 (tt0) cc_final: 0.7637 (tp30) REVERT: AV 54 TYR cc_start: 0.8935 (m-80) cc_final: 0.8624 (m-80) REVERT: AV 109 GLU cc_start: 0.6198 (tp30) cc_final: 0.5144 (mt-10) REVERT: Ae 18 ASP cc_start: 0.8537 (t0) cc_final: 0.8130 (t0) REVERT: Ae 70 ARG cc_start: 0.8894 (ttt90) cc_final: 0.8556 (ptm160) REVERT: Ae 109 GLU cc_start: 0.5329 (tm-30) cc_final: 0.5099 (tm-30) REVERT: Ad 13 LEU cc_start: 0.9342 (mm) cc_final: 0.8990 (mp) REVERT: Ad 22 GLN cc_start: 0.8737 (mp10) cc_final: 0.8515 (mp10) REVERT: Ad 52 ASN cc_start: 0.9023 (t0) cc_final: 0.8651 (t0) REVERT: Ad 117 MET cc_start: 0.9251 (mtp) cc_final: 0.9026 (mtp) REVERT: AS 10 ARG cc_start: 0.8592 (ttm110) cc_final: 0.7913 (ttp80) REVERT: AS 26 HIS cc_start: 0.7595 (p90) cc_final: 0.7338 (p90) REVERT: AT 75 ASN cc_start: 0.9147 (m-40) cc_final: 0.8931 (m110) REVERT: AT 104 TYR cc_start: 0.8832 (t80) cc_final: 0.5831 (m-80) outliers start: 124 outliers final: 78 residues processed: 717 average time/residue: 0.3714 time to fit residues: 415.0144 Evaluate side-chains 597 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 517 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 401 PHE Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 453 GLU Chi-restraints excluded: chain q residue 28 ILE Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 301 SER Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 476 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 248 GLN Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 38 VAL Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 156 CYS Chi-restraints excluded: chain AS residue 167 GLU Chi-restraints excluded: chain AT residue 5 LEU Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 158 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 233 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 214 ASN D 55 ASN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN D 182 HIS D 214 ASN F 51 HIS G 10 ASN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 365 ASN q 490 ASN r 214 ASN r 263 GLN r 305 ASN ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 342 ASN s 440 ASN AV 6 GLN AV 22 GLN Aa 32 GLN Ae 6 GLN Ae 22 GLN Ae 42 ASN Ae 88 GLN Ad 61 ASN Ad 88 GLN AT 151 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.121180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.093015 restraints weight = 60754.243| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.17 r_work: 0.3148 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 27288 Z= 0.348 Angle : 0.849 11.995 37211 Z= 0.440 Chirality : 0.053 0.222 4191 Planarity : 0.007 0.117 4931 Dihedral : 6.696 87.708 3761 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.97 % Favored : 85.68 % Rotamer: Outliers : 6.73 % Allowed : 19.53 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -3.06 (0.13), residues: 3435 helix: 0.17 (0.23), residues: 517 sheet: -1.31 (0.16), residues: 957 loop : -3.20 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP q 242 HIS 0.010 0.002 HIS F 182 PHE 0.027 0.002 PHE G 131 TYR 0.026 0.002 TYR s 480 ARG 0.012 0.001 ARG r 86 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 780) hydrogen bonds : angle 5.49618 ( 2289) SS BOND : bond 0.00880 ( 33) SS BOND : angle 2.30152 ( 66) covalent geometry : bond 0.00821 (27255) covalent geometry : angle 0.84459 (37145) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 483 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 25 GLU cc_start: 0.7859 (mp0) cc_final: 0.7580 (mp0) REVERT: 3 30 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8275 (ttt90) REVERT: 3 56 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8526 (ttmm) REVERT: 3 180 ARG cc_start: 0.8020 (mmp-170) cc_final: 0.7553 (mpp80) REVERT: D 33 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8002 (mm-30) REVERT: D 185 LYS cc_start: 0.8777 (mttt) cc_final: 0.8452 (mttm) REVERT: D 201 ARG cc_start: 0.8681 (ttm110) cc_final: 0.8289 (mtp-110) REVERT: E 2 TYR cc_start: 0.8534 (m-80) cc_final: 0.8182 (m-80) REVERT: E 14 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6400 (tmmt) REVERT: E 33 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8197 (pt0) REVERT: E 38 MET cc_start: 0.8929 (mtp) cc_final: 0.8340 (mtp) REVERT: E 206 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8435 (tm-30) REVERT: F 130 LEU cc_start: 0.7769 (mt) cc_final: 0.7537 (tt) REVERT: F 226 ILE cc_start: 0.9430 (mm) cc_final: 0.9046 (mt) REVERT: G 30 ARG cc_start: 0.8778 (ttt-90) cc_final: 0.8480 (ttt-90) REVERT: G 60 GLU cc_start: 0.7471 (pt0) cc_final: 0.7202 (pt0) REVERT: G 159 LEU cc_start: 0.6501 (mm) cc_final: 0.6251 (mm) REVERT: p 58 PHE cc_start: 0.4045 (p90) cc_final: 0.3811 (p90) REVERT: p 460 ASP cc_start: 0.8216 (t0) cc_final: 0.7948 (p0) REVERT: q 450 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8088 (t0) REVERT: r 82 TYR cc_start: 0.7992 (m-80) cc_final: 0.7491 (m-80) REVERT: r 258 LYS cc_start: 0.6001 (tttp) cc_final: 0.4825 (ptmt) REVERT: r 375 LYS cc_start: 0.7763 (tptm) cc_final: 0.6494 (tttt) REVERT: r 400 GLU cc_start: 0.8517 (pt0) cc_final: 0.8141 (tm-30) REVERT: r 467 CYS cc_start: 0.4920 (OUTLIER) cc_final: 0.4516 (m) REVERT: s 29 LEU cc_start: 0.8866 (tp) cc_final: 0.8664 (tp) REVERT: s 315 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7447 (p90) REVERT: s 317 LEU cc_start: 0.7474 (tp) cc_final: 0.6889 (pt) REVERT: s 379 ASN cc_start: 0.8159 (t0) cc_final: 0.7667 (t0) REVERT: s 414 ASN cc_start: 0.8731 (m-40) cc_final: 0.8439 (t0) REVERT: AV 54 TYR cc_start: 0.9121 (m-80) cc_final: 0.8777 (m-80) REVERT: Aa 126 GLU cc_start: 0.8046 (tt0) cc_final: 0.7829 (tt0) REVERT: Ae 18 ASP cc_start: 0.8709 (t0) cc_final: 0.8192 (t70) REVERT: Ae 70 ARG cc_start: 0.9101 (ttt90) cc_final: 0.8893 (ttt90) REVERT: Ae 97 MET cc_start: 0.9085 (mmt) cc_final: 0.8773 (mmt) REVERT: Ad 52 ASN cc_start: 0.9110 (t0) cc_final: 0.8704 (t0) REVERT: AS 19 TYR cc_start: 0.9288 (m-10) cc_final: 0.9054 (m-10) REVERT: AS 112 ASP cc_start: 0.8960 (m-30) cc_final: 0.8724 (m-30) REVERT: AS 157 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7965 (tm-30) REVERT: AT 94 ARG cc_start: 0.8815 (mmm-85) cc_final: 0.8372 (mpp80) REVERT: AT 104 TYR cc_start: 0.8888 (t80) cc_final: 0.6008 (m-10) outliers start: 199 outliers final: 123 residues processed: 628 average time/residue: 0.3689 time to fit residues: 363.1354 Evaluate side-chains 567 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 440 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 290 THR Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 400 GLU Chi-restraints excluded: chain p residue 401 PHE Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 476 LEU Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 28 ILE Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 260 THR Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 228 THR Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 440 ASN Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain AV residue 14 ILE Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 20 ILE Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 35 VAL Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 167 GLU Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 158 THR Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 33 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 273 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 51 HIS ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN G 10 ASN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 365 ASN ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN r 233 ASN ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 248 GLN ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 342 ASN AV 6 GLN AV 88 GLN Ad 61 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.128266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.100106 restraints weight = 62350.737| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.24 r_work: 0.3297 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27288 Z= 0.183 Angle : 0.700 13.218 37211 Z= 0.357 Chirality : 0.048 0.185 4191 Planarity : 0.005 0.117 4931 Dihedral : 6.259 86.163 3758 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.03 % Favored : 88.76 % Rotamer: Outliers : 5.55 % Allowed : 21.15 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -2.64 (0.14), residues: 3435 helix: 0.64 (0.24), residues: 519 sheet: -1.08 (0.16), residues: 998 loop : -2.96 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP q 242 HIS 0.004 0.001 HIS r 475 PHE 0.018 0.001 PHE G 131 TYR 0.024 0.002 TYR p 480 ARG 0.006 0.001 ARGAS 92 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 780) hydrogen bonds : angle 5.05148 ( 2289) SS BOND : bond 0.00395 ( 33) SS BOND : angle 1.81165 ( 66) covalent geometry : bond 0.00427 (27255) covalent geometry : angle 0.69673 (37145) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 505 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 9 ARG cc_start: 0.8749 (mtp85) cc_final: 0.7566 (ttt180) REVERT: 3 25 GLU cc_start: 0.7821 (mp0) cc_final: 0.7598 (mp0) REVERT: 3 30 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8182 (ttt90) REVERT: 3 56 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8505 (ttmm) REVERT: 3 180 ARG cc_start: 0.7919 (mmp-170) cc_final: 0.7557 (mpp80) REVERT: D 33 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7950 (mm-30) REVERT: D 38 MET cc_start: 0.8801 (mtp) cc_final: 0.8165 (ttm) REVERT: D 201 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8295 (mtp-110) REVERT: E 2 TYR cc_start: 0.8458 (m-80) cc_final: 0.8147 (m-80) REVERT: E 14 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6268 (tmmt) REVERT: E 33 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8128 (pt0) REVERT: E 38 MET cc_start: 0.8944 (mtp) cc_final: 0.8309 (mtp) REVERT: G 30 ARG cc_start: 0.8800 (ttt-90) cc_final: 0.8167 (mtt-85) REVERT: G 62 ASP cc_start: 0.8347 (m-30) cc_final: 0.8083 (m-30) REVERT: G 136 ARG cc_start: 0.8021 (ptp-110) cc_final: 0.7764 (ptp-110) REVERT: G 137 PHE cc_start: 0.8187 (p90) cc_final: 0.7782 (p90) REVERT: G 148 TYR cc_start: 0.7429 (t80) cc_final: 0.6927 (t80) REVERT: G 159 LEU cc_start: 0.6299 (mm) cc_final: 0.6067 (mm) REVERT: p 265 LEU cc_start: 0.8777 (mt) cc_final: 0.8564 (tt) REVERT: p 403 GLN cc_start: 0.8616 (mm-40) cc_final: 0.7926 (mm-40) REVERT: p 466 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8091 (pttp) REVERT: q 450 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7911 (t0) REVERT: r 22 PHE cc_start: 0.6262 (p90) cc_final: 0.5921 (p90) REVERT: r 82 TYR cc_start: 0.7850 (m-80) cc_final: 0.7435 (m-80) REVERT: r 258 LYS cc_start: 0.5638 (tttp) cc_final: 0.4437 (ptmt) REVERT: r 331 TRP cc_start: 0.6016 (OUTLIER) cc_final: 0.5757 (p90) REVERT: r 375 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6468 (tttt) REVERT: r 467 CYS cc_start: 0.4914 (OUTLIER) cc_final: 0.4516 (m) REVERT: s 19 LEU cc_start: 0.7656 (tp) cc_final: 0.7148 (pt) REVERT: s 27 LYS cc_start: 0.8045 (tppt) cc_final: 0.7740 (mmmt) REVERT: s 29 LEU cc_start: 0.8859 (tp) cc_final: 0.8565 (tp) REVERT: s 317 LEU cc_start: 0.7322 (tp) cc_final: 0.7018 (pt) REVERT: s 379 ASN cc_start: 0.7981 (t0) cc_final: 0.7521 (t0) REVERT: s 414 ASN cc_start: 0.8644 (m-40) cc_final: 0.8409 (t0) REVERT: s 457 LEU cc_start: 0.9334 (tt) cc_final: 0.9126 (tt) REVERT: s 458 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8784 (mt) REVERT: AV 54 TYR cc_start: 0.8921 (m-80) cc_final: 0.8596 (m-80) REVERT: AV 109 GLU cc_start: 0.3842 (tp30) cc_final: 0.3597 (tp30) REVERT: Ae 18 ASP cc_start: 0.8736 (t0) cc_final: 0.8268 (t70) REVERT: Ae 35 ASP cc_start: 0.9138 (p0) cc_final: 0.8860 (p0) REVERT: Ae 97 MET cc_start: 0.9063 (mmt) cc_final: 0.8824 (mmt) REVERT: Ad 13 LEU cc_start: 0.9393 (mm) cc_final: 0.9049 (mp) REVERT: Ad 52 ASN cc_start: 0.9267 (t0) cc_final: 0.8888 (t0) REVERT: AS 112 ASP cc_start: 0.8838 (m-30) cc_final: 0.8532 (m-30) REVERT: AT 94 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8500 (mpp80) REVERT: AT 104 TYR cc_start: 0.8864 (t80) cc_final: 0.5949 (m-10) outliers start: 164 outliers final: 109 residues processed: 625 average time/residue: 0.3719 time to fit residues: 363.2435 Evaluate side-chains 579 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 463 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 320 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 368 THR Chi-restraints excluded: chain p residue 400 GLU Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 466 LYS Chi-restraints excluded: chain p residue 476 LEU Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 285 VAL Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 342 ASN Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 127 LEU Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 167 GLU Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 142 VAL Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 122 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 32 optimal weight: 0.1980 chunk 244 optimal weight: 4.9990 chunk 76 optimal weight: 30.0000 chunk 1 optimal weight: 0.0060 chunk 263 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 overall best weight: 3.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 GLN ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 342 ASN AV 6 GLN AV 88 GLN Ae 88 GLN Ad 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100030 restraints weight = 62059.025| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.23 r_work: 0.3257 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27288 Z= 0.185 Angle : 0.698 13.879 37211 Z= 0.354 Chirality : 0.047 0.250 4191 Planarity : 0.005 0.119 4931 Dihedral : 6.117 87.027 3757 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.76 % Favored : 88.03 % Rotamer: Outliers : 5.58 % Allowed : 22.54 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -2.42 (0.14), residues: 3435 helix: 0.78 (0.24), residues: 519 sheet: -0.91 (0.16), residues: 994 loop : -2.81 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP r 331 HIS 0.004 0.001 HIS E 218 PHE 0.015 0.001 PHE D 137 TYR 0.020 0.001 TYR p 370 ARG 0.007 0.001 ARG q 372 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 780) hydrogen bonds : angle 4.92745 ( 2289) SS BOND : bond 0.00381 ( 33) SS BOND : angle 1.67078 ( 66) covalent geometry : bond 0.00436 (27255) covalent geometry : angle 0.69505 (37145) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 473 time to evaluate : 3.147 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: 3 9 ARG cc_start: 0.8748 (mtp85) cc_final: 0.7539 (ttt180) REVERT: 3 19 CYS cc_start: 0.4824 (OUTLIER) cc_final: 0.4122 (p) REVERT: 3 30 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8152 (ttt90) REVERT: 3 162 PRO cc_start: 0.7983 (Cg_exo) cc_final: 0.7658 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7897 (mmp-170) cc_final: 0.7543 (mpp80) REVERT: D 33 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7922 (mm-30) REVERT: D 38 MET cc_start: 0.8872 (mtp) cc_final: 0.8550 (mtp) REVERT: D 60 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7291 (tm-30) REVERT: D 138 TRP cc_start: 0.8171 (m100) cc_final: 0.7878 (m100) REVERT: D 185 LYS cc_start: 0.8661 (mttt) cc_final: 0.8323 (mttp) REVERT: D 201 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8256 (mtp-110) REVERT: E 2 TYR cc_start: 0.8448 (m-80) cc_final: 0.8126 (m-80) REVERT: E 14 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6244 (tmmt) REVERT: E 33 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8143 (pt0) REVERT: E 174 ARG cc_start: 0.8650 (mtp180) cc_final: 0.8431 (mtp85) REVERT: F 1 MET cc_start: 0.7649 (ttt) cc_final: 0.7090 (ttt) REVERT: F 120 ASN cc_start: 0.7646 (t0) cc_final: 0.6318 (p0) REVERT: G 30 ARG cc_start: 0.8754 (ttt-90) cc_final: 0.8497 (ttt-90) REVERT: G 148 TYR cc_start: 0.7458 (t80) cc_final: 0.6992 (t80) REVERT: G 159 LEU cc_start: 0.6255 (mm) cc_final: 0.6054 (mm) REVERT: p 403 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8021 (mm-40) REVERT: p 466 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8079 (pttp) REVERT: q 450 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7947 (t0) REVERT: r 22 PHE cc_start: 0.6664 (p90) cc_final: 0.6329 (p90) REVERT: r 82 TYR cc_start: 0.7960 (m-80) cc_final: 0.7461 (m-80) REVERT: r 258 LYS cc_start: 0.5755 (tttp) cc_final: 0.4616 (ptmt) REVERT: r 331 TRP cc_start: 0.5996 (OUTLIER) cc_final: 0.5742 (p90) REVERT: r 375 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6212 (tttt) REVERT: s 19 LEU cc_start: 0.7632 (tp) cc_final: 0.7136 (pt) REVERT: s 29 LEU cc_start: 0.8841 (tp) cc_final: 0.8555 (tp) REVERT: s 317 LEU cc_start: 0.7337 (tp) cc_final: 0.7071 (pt) REVERT: s 379 ASN cc_start: 0.7982 (t0) cc_final: 0.7508 (t0) REVERT: s 414 ASN cc_start: 0.8658 (m-40) cc_final: 0.8422 (t0) REVERT: AV 54 TYR cc_start: 0.8960 (m-80) cc_final: 0.8643 (m-80) REVERT: Ae 18 ASP cc_start: 0.8710 (t0) cc_final: 0.8301 (t70) REVERT: Ae 97 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8649 (mmt) REVERT: Ad 13 LEU cc_start: 0.9370 (mm) cc_final: 0.9048 (mp) REVERT: Ad 52 ASN cc_start: 0.9225 (t0) cc_final: 0.8869 (t0) REVERT: AS 94 ARG cc_start: 0.8816 (ptt90) cc_final: 0.8424 (mmt-90) REVERT: AS 108 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7554 (mm-30) REVERT: AS 112 ASP cc_start: 0.8857 (m-30) cc_final: 0.8539 (m-30) REVERT: AS 137 SER cc_start: 0.9099 (t) cc_final: 0.8683 (p) REVERT: AT 94 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8591 (mpp80) REVERT: AT 104 TYR cc_start: 0.8835 (t80) cc_final: 0.5949 (m-10) outliers start: 165 outliers final: 131 residues processed: 595 average time/residue: 0.4005 time to fit residues: 377.9946 Evaluate side-chains 594 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 456 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 368 THR Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 466 LYS Chi-restraints excluded: chain p residue 476 LEU Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 22 PHE Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain AV residue 40 TYR Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 43 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 127 LEU Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 97 MET Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 142 VAL Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 chunk 327 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 281 optimal weight: 0.0570 chunk 221 optimal weight: 0.8980 overall best weight: 3.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN G 10 ASN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 342 ASN AV 6 GLN AV 88 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099614 restraints weight = 61701.376| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.24 r_work: 0.3284 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 27288 Z= 0.197 Angle : 0.699 12.911 37211 Z= 0.355 Chirality : 0.047 0.213 4191 Planarity : 0.005 0.119 4931 Dihedral : 5.837 86.889 3752 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.53 % Favored : 88.27 % Rotamer: Outliers : 6.23 % Allowed : 22.81 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -2.29 (0.14), residues: 3435 helix: 0.87 (0.24), residues: 517 sheet: -0.85 (0.16), residues: 1001 loop : -2.71 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP r 331 HIS 0.004 0.001 HIS F 182 PHE 0.015 0.001 PHE D 137 TYR 0.021 0.002 TYR s 480 ARG 0.008 0.001 ARG 3 77 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 780) hydrogen bonds : angle 4.89495 ( 2289) SS BOND : bond 0.00359 ( 33) SS BOND : angle 1.55739 ( 66) covalent geometry : bond 0.00463 (27255) covalent geometry : angle 0.69612 (37145) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 468 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 9 ARG cc_start: 0.8739 (mtp85) cc_final: 0.7562 (ttt180) REVERT: 3 19 CYS cc_start: 0.4942 (OUTLIER) cc_final: 0.4211 (p) REVERT: 3 30 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8238 (ttt90) REVERT: 3 162 PRO cc_start: 0.8060 (Cg_exo) cc_final: 0.7750 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7875 (mmp-170) cc_final: 0.7547 (mpp80) REVERT: D 33 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7955 (mm-30) REVERT: D 60 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7234 (tm-30) REVERT: D 185 LYS cc_start: 0.8695 (mttt) cc_final: 0.8362 (mttp) REVERT: D 201 ARG cc_start: 0.8734 (ttm110) cc_final: 0.8284 (mtp-110) REVERT: E 1 MET cc_start: 0.8279 (ttp) cc_final: 0.8007 (ttm) REVERT: E 2 TYR cc_start: 0.8432 (m-80) cc_final: 0.8105 (m-80) REVERT: E 14 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6315 (tmmt) REVERT: E 33 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8117 (pt0) REVERT: F 1 MET cc_start: 0.7822 (ttt) cc_final: 0.7301 (ttt) REVERT: G 148 TYR cc_start: 0.7469 (t80) cc_final: 0.7005 (t80) REVERT: G 159 LEU cc_start: 0.6252 (mm) cc_final: 0.6037 (mm) REVERT: p 58 PHE cc_start: 0.3808 (p90) cc_final: 0.3557 (p90) REVERT: p 403 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8125 (mm-40) REVERT: p 466 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8123 (pttp) REVERT: q 450 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7956 (t0) REVERT: r 22 PHE cc_start: 0.6675 (p90) cc_final: 0.6388 (p90) REVERT: r 82 TYR cc_start: 0.7889 (m-80) cc_final: 0.7437 (m-80) REVERT: r 258 LYS cc_start: 0.5898 (tttp) cc_final: 0.4543 (ptmt) REVERT: r 331 TRP cc_start: 0.6082 (OUTLIER) cc_final: 0.5817 (p90) REVERT: r 375 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.5966 (tttt) REVERT: s 19 LEU cc_start: 0.7806 (tp) cc_final: 0.7233 (pt) REVERT: s 29 LEU cc_start: 0.8867 (tp) cc_final: 0.8585 (tp) REVERT: s 317 LEU cc_start: 0.7308 (tp) cc_final: 0.7068 (pt) REVERT: s 379 ASN cc_start: 0.7967 (t0) cc_final: 0.7494 (t0) REVERT: s 414 ASN cc_start: 0.8637 (m-40) cc_final: 0.8425 (t0) REVERT: s 480 TYR cc_start: 0.8165 (m-80) cc_final: 0.7953 (m-80) REVERT: AV 54 TYR cc_start: 0.8952 (m-80) cc_final: 0.8614 (m-80) REVERT: Ae 18 ASP cc_start: 0.8713 (t0) cc_final: 0.8318 (t70) REVERT: Ae 97 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8824 (mmt) REVERT: Ae 126 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7762 (mt-10) REVERT: Ad 13 LEU cc_start: 0.9385 (mm) cc_final: 0.9051 (mp) REVERT: Ad 52 ASN cc_start: 0.9212 (t0) cc_final: 0.8829 (t0) REVERT: AS 94 ARG cc_start: 0.8775 (ptt90) cc_final: 0.8454 (mmt-90) REVERT: AS 108 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7574 (mm-30) REVERT: AS 112 ASP cc_start: 0.8853 (m-30) cc_final: 0.8555 (m-30) REVERT: AS 137 SER cc_start: 0.9099 (t) cc_final: 0.8681 (p) REVERT: AT 104 TYR cc_start: 0.8855 (t80) cc_final: 0.5936 (m-10) REVERT: AT 167 GLU cc_start: 0.8139 (tp30) cc_final: 0.7723 (tp30) outliers start: 184 outliers final: 144 residues processed: 610 average time/residue: 0.3570 time to fit residues: 346.3166 Evaluate side-chains 603 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 452 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 320 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 368 THR Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 466 LYS Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 22 PHE Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 79 VAL Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 213 VAL Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 346 VAL Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain AV residue 24 VAL Chi-restraints excluded: chain AV residue 40 TYR Chi-restraints excluded: chain AV residue 84 GLN Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 21 THR Chi-restraints excluded: chain Aa residue 43 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 127 LEU Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 72 LEU Chi-restraints excluded: chain Ae residue 97 MET Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 142 VAL Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 333 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 204 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 365 ASN ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 369 ASN r 214 ASN ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 379 ASN AV 6 GLN AV 88 GLN Ae 22 GLN AT 151 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100369 restraints weight = 61754.641| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.29 r_work: 0.3298 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27288 Z= 0.166 Angle : 0.692 13.058 37211 Z= 0.349 Chirality : 0.047 0.218 4191 Planarity : 0.005 0.119 4931 Dihedral : 5.707 84.823 3752 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.24 % Favored : 88.56 % Rotamer: Outliers : 5.48 % Allowed : 24.53 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -2.19 (0.14), residues: 3435 helix: 0.97 (0.24), residues: 513 sheet: -0.73 (0.16), residues: 1020 loop : -2.70 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP r 331 HIS 0.003 0.001 HIS E 218 PHE 0.026 0.001 PHE p 250 TYR 0.023 0.001 TYR p 480 ARG 0.007 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 780) hydrogen bonds : angle 4.81558 ( 2289) SS BOND : bond 0.00382 ( 33) SS BOND : angle 1.72851 ( 66) covalent geometry : bond 0.00388 (27255) covalent geometry : angle 0.68922 (37145) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 488 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 9 ARG cc_start: 0.8675 (mtp85) cc_final: 0.7542 (ttt180) REVERT: 3 19 CYS cc_start: 0.4968 (OUTLIER) cc_final: 0.4277 (p) REVERT: 3 30 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8333 (ttt90) REVERT: 3 162 PRO cc_start: 0.8036 (Cg_exo) cc_final: 0.7728 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7869 (mmp-170) cc_final: 0.7550 (mpp80) REVERT: 3 202 LEU cc_start: 0.9269 (tt) cc_final: 0.9064 (tp) REVERT: D 33 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7884 (mm-30) REVERT: D 60 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7256 (tm-30) REVERT: D 136 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7395 (mtt90) REVERT: D 185 LYS cc_start: 0.8642 (mttt) cc_final: 0.8385 (mttm) REVERT: E 2 TYR cc_start: 0.8378 (m-80) cc_final: 0.8083 (m-80) REVERT: E 14 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6316 (tmmt) REVERT: E 33 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8086 (pt0) REVERT: E 79 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7623 (mmtt) REVERT: F 1 MET cc_start: 0.7756 (ttt) cc_final: 0.7281 (ttt) REVERT: F 120 ASN cc_start: 0.7647 (t0) cc_final: 0.6413 (m110) REVERT: G 38 MET cc_start: 0.7811 (mtp) cc_final: 0.7342 (mtm) REVERT: G 70 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8300 (tttt) REVERT: G 148 TYR cc_start: 0.7434 (t80) cc_final: 0.7057 (t80) REVERT: G 159 LEU cc_start: 0.6286 (mm) cc_final: 0.6067 (mm) REVERT: p 58 PHE cc_start: 0.3753 (p90) cc_final: 0.3507 (p90) REVERT: p 403 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8112 (mm-40) REVERT: p 466 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8008 (pttp) REVERT: r 22 PHE cc_start: 0.6616 (p90) cc_final: 0.6363 (p90) REVERT: r 82 TYR cc_start: 0.7881 (m-80) cc_final: 0.7252 (m-80) REVERT: r 207 ASN cc_start: 0.8289 (p0) cc_final: 0.7701 (p0) REVERT: r 258 LYS cc_start: 0.5843 (tttp) cc_final: 0.4464 (ptmt) REVERT: r 331 TRP cc_start: 0.5980 (OUTLIER) cc_final: 0.5739 (p90) REVERT: r 375 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.5740 (tttt) REVERT: r 462 GLU cc_start: 0.7839 (tt0) cc_final: 0.7398 (tm-30) REVERT: s 19 LEU cc_start: 0.7765 (tp) cc_final: 0.7199 (pt) REVERT: s 27 LYS cc_start: 0.8161 (tppt) cc_final: 0.7745 (mmmt) REVERT: s 29 LEU cc_start: 0.8897 (tp) cc_final: 0.8636 (tp) REVERT: s 364 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7752 (p90) REVERT: s 375 LYS cc_start: 0.7253 (tmtt) cc_final: 0.6177 (pptt) REVERT: s 379 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7526 (t0) REVERT: s 414 ASN cc_start: 0.8643 (m-40) cc_final: 0.8400 (t0) REVERT: s 458 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8786 (mt) REVERT: s 480 TYR cc_start: 0.8061 (m-80) cc_final: 0.7701 (m-80) REVERT: AV 54 TYR cc_start: 0.8919 (m-80) cc_final: 0.8567 (m-80) REVERT: Ae 18 ASP cc_start: 0.8710 (t0) cc_final: 0.8315 (t70) REVERT: Ae 97 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8776 (mmt) REVERT: Ae 126 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7667 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9370 (mm) cc_final: 0.9061 (mp) REVERT: Ad 52 ASN cc_start: 0.9218 (t0) cc_final: 0.8867 (t0) REVERT: Ad 106 GLU cc_start: 0.8970 (tp30) cc_final: 0.8728 (mm-30) REVERT: Ad 117 MET cc_start: 0.9077 (mtp) cc_final: 0.8759 (mtt) REVERT: AS 108 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7545 (mm-30) REVERT: AS 112 ASP cc_start: 0.8807 (m-30) cc_final: 0.8491 (m-30) REVERT: AS 137 SER cc_start: 0.9118 (t) cc_final: 0.8722 (p) REVERT: AT 104 TYR cc_start: 0.8830 (t80) cc_final: 0.5960 (m-10) outliers start: 162 outliers final: 130 residues processed: 613 average time/residue: 0.3571 time to fit residues: 346.4200 Evaluate side-chains 610 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 470 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 368 THR Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 466 LYS Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 214 ASN Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 338 GLN Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain s residue 6 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 79 VAL Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 213 VAL Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 345 VAL Chi-restraints excluded: chain s residue 346 VAL Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 379 ASN Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain AV residue 40 TYR Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 127 LEU Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 72 LEU Chi-restraints excluded: chain Ae residue 97 MET Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 247 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 338 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 214 ASN ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN AV 88 GLN Ae 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.127638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099482 restraints weight = 62069.885| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.25 r_work: 0.3284 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27288 Z= 0.196 Angle : 0.719 24.273 37211 Z= 0.357 Chirality : 0.048 0.272 4191 Planarity : 0.006 0.195 4931 Dihedral : 5.686 81.099 3751 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.41 % Favored : 88.38 % Rotamer: Outliers : 5.75 % Allowed : 24.77 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.16 (0.14), residues: 3435 helix: 0.92 (0.24), residues: 519 sheet: -0.73 (0.16), residues: 1032 loop : -2.65 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP r 331 HIS 0.004 0.001 HIS F 182 PHE 0.019 0.001 PHE p 250 TYR 0.020 0.002 TYR p 370 ARG 0.006 0.001 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 780) hydrogen bonds : angle 4.81524 ( 2289) SS BOND : bond 0.00470 ( 33) SS BOND : angle 1.75331 ( 66) covalent geometry : bond 0.00464 (27255) covalent geometry : angle 0.71576 (37145) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 462 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 9 ARG cc_start: 0.8705 (mtp85) cc_final: 0.7578 (ttt180) REVERT: 3 19 CYS cc_start: 0.4726 (OUTLIER) cc_final: 0.4148 (p) REVERT: 3 30 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8261 (ttt90) REVERT: 3 162 PRO cc_start: 0.8085 (Cg_exo) cc_final: 0.7788 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7850 (mmp-170) cc_final: 0.7545 (mpp80) REVERT: 3 215 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7578 (mt-10) REVERT: D 33 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7880 (mm-30) REVERT: D 60 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7241 (tm-30) REVERT: D 136 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7376 (mtt-85) REVERT: D 185 LYS cc_start: 0.8662 (mttt) cc_final: 0.8361 (mttm) REVERT: D 201 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8353 (mtp-110) REVERT: E 1 MET cc_start: 0.8254 (ttp) cc_final: 0.8021 (ttm) REVERT: E 2 TYR cc_start: 0.8312 (m-80) cc_final: 0.7972 (m-80) REVERT: E 14 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6320 (tmmt) REVERT: E 33 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8088 (pt0) REVERT: E 79 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7690 (mmtt) REVERT: F 1 MET cc_start: 0.7939 (ttt) cc_final: 0.7340 (ttt) REVERT: G 148 TYR cc_start: 0.7367 (t80) cc_final: 0.7028 (t80) REVERT: G 159 LEU cc_start: 0.6395 (mm) cc_final: 0.6110 (mm) REVERT: p 58 PHE cc_start: 0.3677 (p90) cc_final: 0.3404 (p90) REVERT: p 265 LEU cc_start: 0.8639 (mm) cc_final: 0.8243 (tt) REVERT: p 403 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8180 (mm-40) REVERT: p 466 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8238 (pttp) REVERT: q 450 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7689 (t0) REVERT: q 454 ASP cc_start: 0.8769 (m-30) cc_final: 0.8460 (m-30) REVERT: r 82 TYR cc_start: 0.7900 (m-80) cc_final: 0.7276 (m-80) REVERT: r 207 ASN cc_start: 0.8306 (p0) cc_final: 0.7710 (p0) REVERT: r 258 LYS cc_start: 0.5851 (tttp) cc_final: 0.4439 (ptmt) REVERT: r 331 TRP cc_start: 0.6023 (OUTLIER) cc_final: 0.5814 (p90) REVERT: r 375 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.5746 (tttt) REVERT: r 462 GLU cc_start: 0.7931 (tt0) cc_final: 0.7602 (tm-30) REVERT: s 19 LEU cc_start: 0.7795 (tp) cc_final: 0.7169 (pt) REVERT: s 29 LEU cc_start: 0.8905 (tp) cc_final: 0.8643 (tp) REVERT: s 364 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7741 (p90) REVERT: s 375 LYS cc_start: 0.7251 (tmtt) cc_final: 0.6162 (pptt) REVERT: s 379 ASN cc_start: 0.7744 (t0) cc_final: 0.7082 (t0) REVERT: s 414 ASN cc_start: 0.8637 (m-40) cc_final: 0.8408 (t0) REVERT: s 458 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8803 (mt) REVERT: s 461 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8211 (p90) REVERT: AV 54 TYR cc_start: 0.8934 (m-80) cc_final: 0.8574 (m-80) REVERT: AV 109 GLU cc_start: 0.4296 (tp30) cc_final: 0.3990 (tp30) REVERT: Ae 18 ASP cc_start: 0.8717 (t0) cc_final: 0.8450 (t70) REVERT: Ae 97 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8839 (mmt) REVERT: Ae 108 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8348 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9399 (mm) cc_final: 0.9072 (mp) REVERT: Ad 18 ASP cc_start: 0.8976 (t0) cc_final: 0.8668 (t0) REVERT: Ad 52 ASN cc_start: 0.9223 (t0) cc_final: 0.8883 (t0) REVERT: Ad 106 GLU cc_start: 0.8984 (tp30) cc_final: 0.8741 (mm-30) REVERT: Ad 117 MET cc_start: 0.9144 (mtp) cc_final: 0.8861 (mtt) REVERT: AS 108 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7625 (mm-30) REVERT: AS 112 ASP cc_start: 0.8814 (m-30) cc_final: 0.8479 (m-30) REVERT: AS 137 SER cc_start: 0.9108 (t) cc_final: 0.8699 (p) REVERT: AT 104 TYR cc_start: 0.8885 (t80) cc_final: 0.6054 (m-10) outliers start: 170 outliers final: 144 residues processed: 588 average time/residue: 0.3542 time to fit residues: 328.3408 Evaluate side-chains 604 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 449 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 368 THR Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 466 LYS Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 39 SER Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 338 GLN Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 6 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 79 VAL Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 213 VAL Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 285 VAL Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 345 VAL Chi-restraints excluded: chain s residue 346 VAL Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain s residue 461 PHE Chi-restraints excluded: chain AV residue 24 VAL Chi-restraints excluded: chain AV residue 40 TYR Chi-restraints excluded: chain AV residue 84 GLN Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 21 THR Chi-restraints excluded: chain Aa residue 43 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 127 LEU Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 72 LEU Chi-restraints excluded: chain Ae residue 97 MET Chi-restraints excluded: chain Ae residue 108 GLU Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ae residue 128 LEU Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 110 SER Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 106 ASP Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 136 ILE Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 292 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 365 ASN r 214 ASN r 291 ASN ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 338 GLN AV 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094172 restraints weight = 62446.342| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.11 r_work: 0.3215 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 27288 Z= 0.250 Angle : 0.750 22.733 37211 Z= 0.376 Chirality : 0.049 0.252 4191 Planarity : 0.006 0.189 4931 Dihedral : 5.806 78.463 3749 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.58 % Favored : 87.25 % Rotamer: Outliers : 5.75 % Allowed : 25.11 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.21 (0.14), residues: 3435 helix: 0.84 (0.23), residues: 519 sheet: -0.76 (0.16), residues: 1024 loop : -2.67 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP r 331 HIS 0.005 0.001 HIS F 182 PHE 0.023 0.002 PHE p 250 TYR 0.024 0.002 TYR r 254 ARG 0.019 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 780) hydrogen bonds : angle 4.93954 ( 2289) SS BOND : bond 0.00493 ( 33) SS BOND : angle 1.76658 ( 66) covalent geometry : bond 0.00589 (27255) covalent geometry : angle 0.74662 (37145) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 442 time to evaluate : 3.295 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: 3 9 ARG cc_start: 0.8692 (mtp85) cc_final: 0.7634 (ttt180) REVERT: 3 19 CYS cc_start: 0.4642 (OUTLIER) cc_final: 0.4127 (p) REVERT: 3 30 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8241 (ttt90) REVERT: 3 162 PRO cc_start: 0.8227 (Cg_exo) cc_final: 0.7960 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7924 (mmp-170) cc_final: 0.7596 (mpp80) REVERT: D 33 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7949 (mm-30) REVERT: D 38 MET cc_start: 0.8063 (ptp) cc_final: 0.7586 (ptp) REVERT: D 60 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7229 (tm-30) REVERT: D 136 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7657 (mtt90) REVERT: D 138 TRP cc_start: 0.8215 (m100) cc_final: 0.7876 (m100) REVERT: D 185 LYS cc_start: 0.8761 (mttt) cc_final: 0.8407 (mttm) REVERT: D 201 ARG cc_start: 0.8806 (ttm110) cc_final: 0.8446 (mtp-110) REVERT: E 14 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6277 (tmmt) REVERT: E 33 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8076 (pt0) REVERT: E 79 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7791 (mmtt) REVERT: F 1 MET cc_start: 0.8107 (ttt) cc_final: 0.7502 (ttt) REVERT: G 1 MET cc_start: 0.5631 (tpp) cc_final: 0.5423 (tpt) REVERT: G 2 TYR cc_start: 0.8211 (m-10) cc_final: 0.8008 (m-10) REVERT: G 148 TYR cc_start: 0.7376 (t80) cc_final: 0.7050 (t80) REVERT: G 157 SER cc_start: 0.8507 (p) cc_final: 0.8215 (t) REVERT: p 52 LEU cc_start: 0.8054 (tp) cc_final: 0.7728 (tp) REVERT: p 58 PHE cc_start: 0.3599 (p90) cc_final: 0.3219 (p90) REVERT: p 265 LEU cc_start: 0.8651 (mm) cc_final: 0.8246 (tt) REVERT: q 16 ASP cc_start: 0.9191 (t0) cc_final: 0.8761 (p0) REVERT: q 450 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7644 (t0) REVERT: q 454 ASP cc_start: 0.8799 (m-30) cc_final: 0.8526 (m-30) REVERT: r 82 TYR cc_start: 0.8011 (m-80) cc_final: 0.7523 (m-80) REVERT: r 207 ASN cc_start: 0.8285 (p0) cc_final: 0.7629 (p0) REVERT: r 258 LYS cc_start: 0.5964 (tttp) cc_final: 0.4477 (ptmt) REVERT: r 331 TRP cc_start: 0.6114 (OUTLIER) cc_final: 0.5859 (p90) REVERT: r 375 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.5908 (tttt) REVERT: r 462 GLU cc_start: 0.8026 (tt0) cc_final: 0.7751 (tm-30) REVERT: s 19 LEU cc_start: 0.7904 (tp) cc_final: 0.7202 (pt) REVERT: s 29 LEU cc_start: 0.8925 (tp) cc_final: 0.8649 (tp) REVERT: s 364 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7653 (p90) REVERT: s 375 LYS cc_start: 0.7133 (tmtt) cc_final: 0.6060 (pptt) REVERT: s 379 ASN cc_start: 0.8091 (t0) cc_final: 0.7735 (t0) REVERT: s 458 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8821 (mt) REVERT: s 461 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8261 (p90) REVERT: AV 54 TYR cc_start: 0.8928 (m-80) cc_final: 0.8577 (m-80) REVERT: Ae 18 ASP cc_start: 0.8884 (t0) cc_final: 0.8473 (t70) REVERT: Ae 97 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8498 (mmt) REVERT: Ae 126 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7484 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9384 (mm) cc_final: 0.9050 (mp) REVERT: Ad 18 ASP cc_start: 0.9053 (t0) cc_final: 0.8657 (t0) REVERT: Ad 117 MET cc_start: 0.9176 (mtp) cc_final: 0.8751 (mtm) REVERT: AS 95 LYS cc_start: 0.9097 (mttp) cc_final: 0.8846 (mmtt) REVERT: AS 108 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7682 (mm-30) REVERT: AS 112 ASP cc_start: 0.8846 (m-30) cc_final: 0.8505 (m-30) REVERT: AT 104 TYR cc_start: 0.8937 (t80) cc_final: 0.6028 (m-10) outliers start: 170 outliers final: 151 residues processed: 570 average time/residue: 0.3552 time to fit residues: 320.6111 Evaluate side-chains 593 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 433 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 368 THR Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 463 VAL Chi-restraints excluded: chain p residue 466 LYS Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 39 SER Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 338 GLN Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 447 GLU Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 6 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 58 PHE Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 79 VAL Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 213 VAL Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 285 VAL Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain s residue 461 PHE Chi-restraints excluded: chain AV residue 24 VAL Chi-restraints excluded: chain AV residue 40 TYR Chi-restraints excluded: chain AV residue 84 GLN Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 98 THR Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 21 THR Chi-restraints excluded: chain Aa residue 43 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 127 LEU Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 17 THR Chi-restraints excluded: chain Ae residue 72 LEU Chi-restraints excluded: chain Ae residue 97 MET Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ae residue 128 LEU Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 110 SER Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 11 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 106 ASP Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 135 ASP Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 177 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 10 optimal weight: 0.0770 chunk 56 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN Ad 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096486 restraints weight = 61725.414| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.19 r_work: 0.3221 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27288 Z= 0.170 Angle : 0.709 12.179 37211 Z= 0.357 Chirality : 0.048 0.229 4191 Planarity : 0.005 0.101 4931 Dihedral : 5.668 77.630 3749 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.09 % Favored : 88.79 % Rotamer: Outliers : 5.25 % Allowed : 25.62 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.13 (0.14), residues: 3435 helix: 0.81 (0.23), residues: 528 sheet: -0.72 (0.16), residues: 1031 loop : -2.61 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP r 331 HIS 0.003 0.001 HIS F 182 PHE 0.019 0.001 PHE p 250 TYR 0.023 0.001 TYR r 254 ARG 0.009 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 780) hydrogen bonds : angle 4.84361 ( 2289) SS BOND : bond 0.00410 ( 33) SS BOND : angle 1.61485 ( 66) covalent geometry : bond 0.00401 (27255) covalent geometry : angle 0.70659 (37145) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 474 time to evaluate : 2.856 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: 3 9 ARG cc_start: 0.8674 (mtp85) cc_final: 0.7596 (ttt180) REVERT: 3 19 CYS cc_start: 0.4599 (OUTLIER) cc_final: 0.4249 (p) REVERT: 3 30 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8189 (ttt90) REVERT: 3 162 PRO cc_start: 0.8175 (Cg_exo) cc_final: 0.7911 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7902 (mmp-170) cc_final: 0.7572 (mpp80) REVERT: D 33 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7993 (mm-30) REVERT: D 60 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 136 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7550 (mtt90) REVERT: D 201 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8407 (mtp-110) REVERT: E 14 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6182 (tmmt) REVERT: E 33 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8044 (pt0) REVERT: E 79 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7710 (mmtt) REVERT: F 1 MET cc_start: 0.7941 (ttt) cc_final: 0.7366 (ttt) REVERT: G 2 TYR cc_start: 0.8223 (m-10) cc_final: 0.7905 (m-10) REVERT: G 38 MET cc_start: 0.7857 (mtp) cc_final: 0.7653 (mtm) REVERT: G 148 TYR cc_start: 0.7341 (t80) cc_final: 0.7054 (t80) REVERT: G 157 SER cc_start: 0.8516 (p) cc_final: 0.8220 (t) REVERT: p 52 LEU cc_start: 0.8069 (tp) cc_final: 0.7718 (tp) REVERT: p 58 PHE cc_start: 0.3778 (p90) cc_final: 0.3193 (p90) REVERT: p 265 LEU cc_start: 0.8625 (mm) cc_final: 0.8226 (tt) REVERT: p 274 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8443 (mp) REVERT: q 16 ASP cc_start: 0.9171 (t0) cc_final: 0.8889 (p0) REVERT: q 450 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7622 (t0) REVERT: q 454 ASP cc_start: 0.8754 (m-30) cc_final: 0.8514 (m-30) REVERT: r 82 TYR cc_start: 0.7985 (m-80) cc_final: 0.7350 (m-80) REVERT: r 207 ASN cc_start: 0.8325 (p0) cc_final: 0.7717 (p0) REVERT: r 258 LYS cc_start: 0.5900 (tttp) cc_final: 0.4427 (ptmt) REVERT: r 331 TRP cc_start: 0.6095 (OUTLIER) cc_final: 0.5824 (p90) REVERT: r 375 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.5851 (tttt) REVERT: r 462 GLU cc_start: 0.8083 (tt0) cc_final: 0.7874 (tm-30) REVERT: s 19 LEU cc_start: 0.7975 (tp) cc_final: 0.7199 (pt) REVERT: s 29 LEU cc_start: 0.8885 (tp) cc_final: 0.8618 (tp) REVERT: s 364 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.8210 (p90) REVERT: s 375 LYS cc_start: 0.7018 (tmtt) cc_final: 0.6018 (pptt) REVERT: s 379 ASN cc_start: 0.8039 (t0) cc_final: 0.7540 (t0) REVERT: s 458 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8806 (mt) REVERT: AV 54 TYR cc_start: 0.8879 (m-80) cc_final: 0.8533 (m-80) REVERT: AV 109 GLU cc_start: 0.4114 (tp30) cc_final: 0.3786 (tp30) REVERT: Ae 18 ASP cc_start: 0.8862 (t0) cc_final: 0.8471 (t70) REVERT: Ae 126 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7814 (mt-10) REVERT: Ad 13 LEU cc_start: 0.9367 (mm) cc_final: 0.9055 (mp) REVERT: Ad 18 ASP cc_start: 0.9061 (t0) cc_final: 0.8727 (t0) REVERT: Ad 52 ASN cc_start: 0.9189 (t0) cc_final: 0.8884 (t0) REVERT: AS 112 ASP cc_start: 0.8821 (m-30) cc_final: 0.8524 (m-30) REVERT: AS 137 SER cc_start: 0.9106 (t) cc_final: 0.8700 (p) REVERT: AT 104 TYR cc_start: 0.8910 (t80) cc_final: 0.6058 (m-10) outliers start: 155 outliers final: 133 residues processed: 596 average time/residue: 0.3594 time to fit residues: 339.9062 Evaluate side-chains 592 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 451 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 368 THR Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 466 LYS Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 338 GLN Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 6 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 79 VAL Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 213 VAL Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 285 VAL Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain AV residue 24 VAL Chi-restraints excluded: chain AV residue 40 TYR Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 21 THR Chi-restraints excluded: chain Aa residue 43 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 127 LEU Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 17 THR Chi-restraints excluded: chain Ae residue 72 LEU Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ad residue 4 ASN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 110 SER Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 11 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 333 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 77 optimal weight: 0.2980 chunk 254 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 231 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 257 ASN ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 342 ASN AV 6 GLN AV 88 GLN Ad 4 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.125466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097300 restraints weight = 62014.191| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.23 r_work: 0.3235 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27288 Z= 0.149 Angle : 0.710 11.695 37211 Z= 0.356 Chirality : 0.048 0.221 4191 Planarity : 0.005 0.112 4931 Dihedral : 5.584 76.431 3749 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.06 % Favored : 88.82 % Rotamer: Outliers : 4.91 % Allowed : 25.99 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.03 % 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: -2.09 (0.14), residues: 3435 helix: 0.87 (0.24), residues: 528 sheet: -0.65 (0.16), residues: 1023 loop : -2.61 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP r 331 HIS 0.003 0.001 HIS 3 218 PHE 0.020 0.001 PHE p 250 TYR 0.038 0.001 TYR r 254 ARG 0.009 0.000 ARG E 174 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 780) hydrogen bonds : angle 4.77979 ( 2289) SS BOND : bond 0.00393 ( 33) SS BOND : angle 1.66327 ( 66) covalent geometry : bond 0.00349 (27255) covalent geometry : angle 0.70713 (37145) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13903.30 seconds wall clock time: 241 minutes 19.12 seconds (14479.12 seconds total)