Starting phenix.real_space_refine on Mon Aug 25 08:40:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwm_29512/08_2025/8fwm_29512.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwm_29512/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fwm_29512/08_2025/8fwm_29512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwm_29512/08_2025/8fwm_29512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fwm_29512/08_2025/8fwm_29512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwm_29512/08_2025/8fwm_29512.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.86, per 1000 atoms: 0.18 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: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.82 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: 4.09 Time building geometry restraints manager: 2.39 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.850 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 20.280 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- 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 : 13.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG p 372 TYR 0.038 0.002 TYR p 370 PHE 0.025 0.001 PHE r 250 TRP 0.013 0.001 TRP q 242 HIS 0.004 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00491 (27255) covalent geometry : angle 0.87777 (37145) SS BOND : bond 0.02059 ( 33) SS BOND : angle 7.00990 ( 66) hydrogen bonds : bond 0.16877 ( 780) hydrogen bonds : angle 7.09451 ( 2289) *********************** 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 : 0.785 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: 0.8395 (ttmt) cc_final: 0.8115 (ttpp) REVERT: 3 180 ARG cc_start: 0.7990 (mmp-170) cc_final: 0.7722 (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: 0.7511 (mtp) REVERT: D 135 ASP cc_start: 0.6047 (t0) cc_final: 0.3884 (p0) REVERT: D 148 TYR cc_start: 0.7641 (t80) cc_final: 0.6502 (t80) REVERT: D 150 ILE cc_start: 0.6984 (mt) cc_final: 0.6139 (mt) REVERT: D 185 LYS cc_start: 0.8605 (mttt) cc_final: 0.8237 (mttm) REVERT: D 198 ASP cc_start: 0.7492 (m-30) cc_final: 0.7233 (m-30) REVERT: E 14 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6638 (tmmt) REVERT: E 33 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7358 (pt0) REVERT: E 79 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7195 (mmtt) REVERT: E 103 GLU cc_start: 0.7372 (tt0) cc_final: 0.7081 (tt0) REVERT: E 106 GLU cc_start: 0.7627 (tt0) cc_final: 0.7079 (tm-30) REVERT: E 135 ASP cc_start: 0.6644 (t0) cc_final: 0.6188 (m-30) REVERT: E 178 ASP cc_start: 0.7518 (t70) cc_final: 0.7246 (t0) REVERT: F 25 GLU cc_start: 0.8315 (mp0) cc_final: 0.7611 (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: 0.2192 (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: 0.7591 (p90) REVERT: p 455 ILE cc_start: 0.9213 (mm) cc_final: 0.8998 (mm) REVERT: p 478 MET cc_start: 0.8221 (mtp) cc_final: 0.7969 (mtp) REVERT: q 16 ASP cc_start: 0.8976 (t0) cc_final: 0.8707 (t0) REVERT: q 457 LEU cc_start: 0.9294 (tt) cc_final: 0.9037 (tt) REVERT: q 473 ILE cc_start: 0.7779 (mm) cc_final: 0.7349 (mm) REVERT: r 258 LYS cc_start: 0.6159 (tttp) cc_final: 0.4685 (ptmt) REVERT: r 375 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6443 (tptm) REVERT: r 467 CYS cc_start: 0.4623 (OUTLIER) cc_final: 0.3520 (m) REVERT: r 480 TYR cc_start: 0.5769 (m-10) cc_final: 0.5026 (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: 0.6624 (pp) REVERT: s 72 PHE cc_start: 0.7652 (m-10) cc_final: 0.7112 (m-80) REVERT: s 208 ASP cc_start: 0.8756 (p0) cc_final: 0.8451 (p0) REVERT: s 311 GLN cc_start: 0.8342 (pt0) cc_final: 0.8044 (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: 0.8918 (mp) REVERT: s 379 ASN cc_start: 0.8000 (t0) cc_final: 0.7004 (t0) REVERT: s 414 ASN cc_start: 0.8461 (m-40) cc_final: 0.8086 (t0) REVERT: AV 52 ASN cc_start: 0.8719 (t0) cc_final: 0.7703 (t0) REVERT: AV 54 TYR cc_start: 0.8737 (m-80) cc_final: 0.8506 (m-80) REVERT: AV 97 MET cc_start: 0.8011 (mmt) cc_final: 0.7766 (mmt) REVERT: AV 109 GLU cc_start: 0.5846 (tp30) cc_final: 0.5383 (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: 0.6759 (tt0) REVERT: Ad 13 LEU cc_start: 0.9082 (mm) cc_final: 0.8807 (mp) REVERT: Ad 52 ASN cc_start: 0.8875 (t0) cc_final: 0.8608 (t0) REVERT: AS 10 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7509 (ttp80) REVERT: AS 112 ASP cc_start: 0.8137 (m-30) cc_final: 0.7769 (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: 0.5713 (m-80) REVERT: AT 108 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8472 (mt-10) REVERT: AT 112 ASP cc_start: 0.8414 (m-30) cc_final: 0.8145 (m-30) outliers start: 70 outliers final: 18 residues processed: 963 average time/residue: 0.1685 time to fit residues: 248.8367 Evaluate side-chains 604 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 583 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 0.0570 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 G 55 ASN G 161 GLN p 33 GLN ** p 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 365 ASN 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 r 452 ASN r 475 HIS r 490 ASN s 33 GLN ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 270 ASN s 369 ASN s 456 GLN AV 6 GLN AV 22 GLN AV 32 GLN Aa 32 GLN Ae 88 GLN AS 46 GLN AS 85 ASN AS 151 GLN AT 125 HIS AT 151 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.136796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108115 restraints weight = 61817.826| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.23 r_work: 0.3406 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 27288 Z= 0.146 Angle : 0.741 13.016 37211 Z= 0.379 Chirality : 0.048 0.233 4191 Planarity : 0.005 0.108 4931 Dihedral : 6.667 80.714 3783 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.50 % Favored : 88.27 % Rotamer: Outliers : 3.59 % Allowed : 15.30 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.13), residues: 3435 helix: -0.22 (0.22), residues: 522 sheet: -1.40 (0.15), residues: 1048 loop : -3.47 (0.12), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAS 92 TYR 0.019 0.002 TYR E 169 PHE 0.023 0.001 PHE s 58 TRP 0.028 0.001 TRP q 242 HIS 0.004 0.001 HISAT 125 Details of bonding type rmsd covalent geometry : bond 0.00323 (27255) covalent geometry : angle 0.73540 (37145) SS BOND : bond 0.00402 ( 33) SS BOND : angle 2.32482 ( 66) hydrogen bonds : bond 0.03835 ( 780) hydrogen bonds : angle 5.47743 ( 2289) *********************** 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 777 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 671 time to evaluate : 0.998 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: 3 180 ARG cc_start: 0.7962 (mmp-170) cc_final: 0.7695 (mtt90) REVERT: D 33 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7766 (mm-30) REVERT: D 159 LEU cc_start: 0.7408 (tp) cc_final: 0.7115 (mp) REVERT: D 185 LYS cc_start: 0.8747 (mttt) cc_final: 0.8449 (mttm) REVERT: E 14 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.6997 (tmmt) REVERT: E 33 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8058 (pt0) REVERT: E 79 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7246 (mmtt) REVERT: E 125 TYR cc_start: 0.7160 (t80) cc_final: 0.6838 (t80) REVERT: E 135 ASP cc_start: 0.7068 (t0) cc_final: 0.6490 (m-30) REVERT: E 215 GLU cc_start: 0.7848 (mp0) cc_final: 0.7642 (mp0) REVERT: F 1 MET cc_start: 0.8200 (ttt) cc_final: 0.7681 (ttt) REVERT: F 120 ASN cc_start: 0.6973 (t0) cc_final: 0.5991 (p0) REVERT: F 130 LEU cc_start: 0.7669 (mt) cc_final: 0.7310 (tt) REVERT: G 35 ASN cc_start: 0.9009 (t0) cc_final: 0.8806 (t0) REVERT: G 70 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8085 (tttt) REVERT: G 84 PHE cc_start: 0.6617 (t80) cc_final: 0.6315 (t80) REVERT: G 148 TYR cc_start: 0.7361 (t80) cc_final: 0.6788 (t80) REVERT: G 159 LEU cc_start: 0.6629 (mm) cc_final: 0.6071 (mp) REVERT: G 169 TYR cc_start: 0.8125 (p90) cc_final: 0.7792 (p90) REVERT: p 13 LEU cc_start: 0.8282 (pt) cc_final: 0.7948 (pt) REVERT: p 460 ASP cc_start: 0.7956 (t0) cc_final: 0.7634 (t0) REVERT: q 22 PHE cc_start: 0.7934 (m-80) cc_final: 0.7713 (m-10) REVERT: q 250 PHE cc_start: 0.7074 (m-80) cc_final: 0.6833 (m-80) REVERT: r 82 TYR cc_start: 0.7828 (m-80) cc_final: 0.7456 (m-80) REVERT: r 258 LYS cc_start: 0.5856 (tttp) cc_final: 0.4827 (ptmt) REVERT: r 270 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6498 (t0) REVERT: r 375 LYS cc_start: 0.7719 (tptm) cc_final: 0.6539 (tmtt) REVERT: s 72 PHE cc_start: 0.7921 (m-10) cc_final: 0.7217 (m-80) REVERT: s 317 LEU cc_start: 0.7252 (tp) cc_final: 0.6713 (pt) REVERT: s 371 LEU cc_start: 0.9206 (mm) cc_final: 0.8945 (mp) REVERT: s 379 ASN cc_start: 0.7922 (t0) cc_final: 0.7563 (t0) REVERT: s 414 ASN cc_start: 0.8674 (m-40) cc_final: 0.8341 (t0) REVERT: s 462 GLU cc_start: 0.8471 (tt0) cc_final: 0.7604 (tp30) REVERT: AV 50 LEU cc_start: 0.9044 (mt) cc_final: 0.8725 (mt) REVERT: AV 54 TYR cc_start: 0.8901 (m-80) cc_final: 0.8581 (m-80) REVERT: AV 109 GLU cc_start: 0.6370 (tp30) cc_final: 0.5613 (mt-10) REVERT: Ae 18 ASP cc_start: 0.8462 (t0) cc_final: 0.8053 (t0) REVERT: Ae 70 ARG cc_start: 0.8862 (ttt90) cc_final: 0.8588 (ptm160) REVERT: Ae 109 GLU cc_start: 0.5632 (tm-30) cc_final: 0.5357 (tm-30) REVERT: Ad 22 GLN cc_start: 0.8652 (mp10) cc_final: 0.8431 (mp10) REVERT: Ad 52 ASN cc_start: 0.8933 (t0) cc_final: 0.8573 (t0) REVERT: Ad 117 MET cc_start: 0.9241 (mtp) cc_final: 0.8998 (mtp) REVERT: AS 10 ARG cc_start: 0.8543 (ttm110) cc_final: 0.7703 (ttp80) REVERT: AS 26 HIS cc_start: 0.7559 (p90) cc_final: 0.7346 (p90) REVERT: AT 18 LYS cc_start: 0.8554 (ptmt) cc_final: 0.8334 (ptmm) REVERT: AT 75 ASN cc_start: 0.9111 (m-40) cc_final: 0.8867 (m110) REVERT: AT 95 LYS cc_start: 0.8070 (mptt) cc_final: 0.7847 (mptt) REVERT: AT 104 TYR cc_start: 0.8811 (t80) cc_final: 0.5623 (m-80) outliers start: 106 outliers final: 63 residues processed: 738 average time/residue: 0.1630 time to fit residues: 189.3134 Evaluate side-chains 621 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 556 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 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 130 LEU Chi-restraints excluded: chain G residue 150 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 320 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 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 26 CYS Chi-restraints excluded: chain r residue 214 ASN Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 270 ASN 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 s residue 202 VAL 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 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 84 GLN Chi-restraints excluded: chain Ad residue 6 GLN 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 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 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 1 optimal weight: 6.9990 chunk 326 optimal weight: 2.9990 chunk 92 optimal weight: 30.0000 chunk 306 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 291 optimal weight: 2.9990 chunk 34 optimal weight: 30.0000 chunk 140 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN F 182 HIS ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 440 ASN ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 450 ASN r 270 ASN r 440 ASN ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 440 ASN s 475 HIS AV 6 GLN AV 22 GLN Aa 32 GLN Aa 42 ASN Ae 6 GLN Ae 42 ASN Ad 61 ASN Ad 88 GLN AT 71 ASN AT 151 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.127030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098834 restraints weight = 59928.982| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.97 r_work: 0.3268 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 27288 Z= 0.206 Angle : 0.726 12.300 37211 Z= 0.373 Chirality : 0.048 0.255 4191 Planarity : 0.005 0.116 4931 Dihedral : 6.011 82.956 3760 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.99 % Favored : 87.69 % Rotamer: Outliers : 5.08 % Allowed : 17.60 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.14), residues: 3435 helix: 0.60 (0.24), residues: 514 sheet: -1.06 (0.16), residues: 952 loop : -3.15 (0.12), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 174 TYR 0.023 0.002 TYR p 370 PHE 0.021 0.001 PHE G 131 TRP 0.040 0.002 TRP q 242 HIS 0.004 0.001 HIS s 252 Details of bonding type rmsd covalent geometry : bond 0.00465 (27255) covalent geometry : angle 0.72035 (37145) SS BOND : bond 0.00674 ( 33) SS BOND : angle 2.23199 ( 66) hydrogen bonds : bond 0.03720 ( 780) hydrogen bonds : angle 5.13144 ( 2289) *********************** 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 693 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 543 time to evaluate : 0.855 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: 0.7785 (mp0) cc_final: 0.7501 (mp0) REVERT: 3 30 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8251 (ttm-80) REVERT: 3 180 ARG cc_start: 0.7982 (mmp-170) cc_final: 0.7724 (mtt90) REVERT: D 33 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7853 (mm-30) REVERT: D 159 LEU cc_start: 0.7552 (tp) cc_final: 0.7153 (mp) REVERT: D 185 LYS cc_start: 0.8786 (mttt) cc_final: 0.8511 (mttm) REVERT: E 14 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6548 (tmmt) REVERT: E 33 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8064 (pt0) REVERT: E 215 GLU cc_start: 0.8014 (mp0) cc_final: 0.7777 (mp0) REVERT: F 1 MET cc_start: 0.8470 (ttt) cc_final: 0.8099 (ttt) REVERT: F 120 ASN cc_start: 0.7400 (t0) cc_final: 0.6116 (p0) REVERT: F 130 LEU cc_start: 0.7470 (mt) cc_final: 0.7188 (tt) REVERT: G 70 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8195 (tttt) REVERT: G 148 TYR cc_start: 0.7352 (t80) cc_final: 0.6879 (t80) REVERT: G 159 LEU cc_start: 0.6519 (mm) cc_final: 0.6054 (mp) REVERT: p 58 PHE cc_start: 0.3958 (p90) cc_final: 0.3666 (p90) REVERT: q 372 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7824 (ttp80) REVERT: q 460 ASP cc_start: 0.8600 (p0) cc_final: 0.8232 (p0) REVERT: r 82 TYR cc_start: 0.7804 (m-80) cc_final: 0.7399 (m-80) REVERT: r 248 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: r 258 LYS cc_start: 0.6106 (tttp) cc_final: 0.4658 (ptmt) REVERT: r 375 LYS cc_start: 0.7754 (tptm) cc_final: 0.6488 (tttt) REVERT: r 400 GLU cc_start: 0.8038 (pt0) cc_final: 0.7686 (tm-30) REVERT: s 19 LEU cc_start: 0.7050 (tp) cc_final: 0.6826 (pt) REVERT: s 72 PHE cc_start: 0.8154 (m-10) cc_final: 0.7366 (m-80) REVERT: s 317 LEU cc_start: 0.7463 (tp) cc_final: 0.6928 (pt) REVERT: s 379 ASN cc_start: 0.8142 (t0) cc_final: 0.7526 (t0) REVERT: s 414 ASN cc_start: 0.8697 (m-40) cc_final: 0.8396 (t0) REVERT: s 462 GLU cc_start: 0.8551 (tt0) cc_final: 0.7671 (tp30) REVERT: AV 54 TYR cc_start: 0.8959 (m-80) cc_final: 0.8594 (m-80) REVERT: Ae 18 ASP cc_start: 0.8593 (t0) cc_final: 0.8166 (t0) REVERT: Ae 84 GLN cc_start: 0.8102 (tt0) cc_final: 0.7521 (tt0) REVERT: Ae 97 MET cc_start: 0.8839 (mmt) cc_final: 0.8321 (mmt) REVERT: Ae 101 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8072 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9347 (mm) cc_final: 0.8997 (mp) REVERT: Ad 22 GLN cc_start: 0.8768 (mp10) cc_final: 0.8534 (mp10) REVERT: Ad 52 ASN cc_start: 0.9065 (t0) cc_final: 0.8730 (t0) REVERT: AS 108 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7408 (mm-30) REVERT: AT 18 LYS cc_start: 0.8763 (ptmt) cc_final: 0.8485 (ptmm) REVERT: AT 71 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7802 (p0) REVERT: AT 104 TYR cc_start: 0.8765 (t80) cc_final: 0.5879 (m-10) outliers start: 150 outliers final: 94 residues processed: 646 average time/residue: 0.1590 time to fit residues: 163.3712 Evaluate side-chains 602 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 504 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 183 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 E residue 168 VAL Chi-restraints excluded: chain E residue 177 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 91 LEU Chi-restraints excluded: chain F residue 126 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 53 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 260 THR 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 400 GLU 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 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 345 VAL Chi-restraints excluded: chain q residue 372 ARG Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 497 LEU Chi-restraints excluded: chain r residue 11 VAL 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 248 GLN Chi-restraints excluded: chain r residue 282 THR 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 s residue 11 VAL 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 440 ASN 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 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU 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 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 142 VAL Chi-restraints excluded: chain AS residue 156 CYS 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 71 ASN 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 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 72 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN G 10 ASN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 365 ASN ** r 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 263 GLN ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 231 GLN ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN AV 22 GLN Ad 61 ASN AS 46 GLN AT 71 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.132659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104016 restraints weight = 61835.988| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.17 r_work: 0.3343 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27288 Z= 0.138 Angle : 0.680 13.890 37211 Z= 0.343 Chirality : 0.047 0.225 4191 Planarity : 0.005 0.117 4931 Dihedral : 5.847 83.200 3758 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.06 % Favored : 88.68 % Rotamer: Outliers : 4.53 % Allowed : 19.73 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.14), residues: 3435 helix: 0.91 (0.24), residues: 514 sheet: -0.92 (0.16), residues: 1005 loop : -2.95 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 174 TYR 0.023 0.001 TYR p 480 PHE 0.018 0.001 PHE G 131 TRP 0.014 0.001 TRP q 242 HIS 0.003 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00316 (27255) covalent geometry : angle 0.67622 (37145) SS BOND : bond 0.00370 ( 33) SS BOND : angle 1.75434 ( 66) hydrogen bonds : bond 0.03356 ( 780) hydrogen bonds : angle 4.90768 ( 2289) *********************** 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 683 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 549 time to evaluate : 1.098 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: 3 25 GLU cc_start: 0.7802 (mp0) cc_final: 0.7593 (mp0) REVERT: 3 30 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8268 (ttm-80) REVERT: 3 180 ARG cc_start: 0.7940 (mmp-170) cc_final: 0.7720 (mtt90) REVERT: D 33 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7885 (mm-30) REVERT: D 159 LEU cc_start: 0.7641 (tp) cc_final: 0.7172 (mp) REVERT: D 185 LYS cc_start: 0.8764 (mttt) cc_final: 0.8472 (mttm) REVERT: D 201 ARG cc_start: 0.8552 (ttm110) cc_final: 0.8125 (mtp85) REVERT: E 1 MET cc_start: 0.8267 (ttp) cc_final: 0.8061 (ttp) REVERT: E 14 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6480 (tmmt) REVERT: E 33 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8046 (pt0) REVERT: E 79 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7360 (mmtm) REVERT: E 215 GLU cc_start: 0.8088 (mp0) cc_final: 0.7814 (mp0) REVERT: F 1 MET cc_start: 0.8461 (ttt) cc_final: 0.8205 (ttt) REVERT: F 120 ASN cc_start: 0.7412 (t0) cc_final: 0.6080 (p0) REVERT: F 130 LEU cc_start: 0.7543 (mt) cc_final: 0.7289 (tt) REVERT: G 30 ARG cc_start: 0.8448 (ttt-90) cc_final: 0.7935 (mtt-85) REVERT: G 70 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8148 (tttt) REVERT: G 136 ARG cc_start: 0.8138 (ptp-110) cc_final: 0.7872 (ptp-110) REVERT: G 148 TYR cc_start: 0.7378 (t80) cc_final: 0.6911 (t80) REVERT: G 159 LEU cc_start: 0.6403 (mm) cc_final: 0.5930 (mp) REVERT: p 58 PHE cc_start: 0.3904 (p90) cc_final: 0.3519 (p90) REVERT: q 377 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.7966 (mmm160) REVERT: r 22 PHE cc_start: 0.6043 (p90) cc_final: 0.5707 (p90) REVERT: r 82 TYR cc_start: 0.7772 (m-80) cc_final: 0.7408 (m-80) REVERT: r 258 LYS cc_start: 0.5926 (tttp) cc_final: 0.4721 (ptmt) REVERT: r 375 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6387 (tttt) REVERT: r 400 GLU cc_start: 0.8025 (pt0) cc_final: 0.7714 (tm-30) REVERT: r 432 LYS cc_start: 0.9293 (tppt) cc_final: 0.8994 (ttpt) REVERT: r 467 CYS cc_start: 0.5115 (OUTLIER) cc_final: 0.4450 (m) REVERT: s 19 LEU cc_start: 0.7123 (tp) cc_final: 0.6849 (pt) REVERT: s 66 GLU cc_start: 0.8362 (tp30) cc_final: 0.8114 (tp30) REVERT: s 72 PHE cc_start: 0.8220 (m-10) cc_final: 0.7395 (m-80) REVERT: s 317 LEU cc_start: 0.7371 (tp) cc_final: 0.7010 (pt) REVERT: s 379 ASN cc_start: 0.7887 (t0) cc_final: 0.7486 (t0) REVERT: s 414 ASN cc_start: 0.8667 (m-40) cc_final: 0.8381 (t0) REVERT: s 462 GLU cc_start: 0.8507 (tt0) cc_final: 0.7661 (tp30) REVERT: AV 54 TYR cc_start: 0.8875 (m-80) cc_final: 0.8533 (m-80) REVERT: Ae 18 ASP cc_start: 0.8615 (t0) cc_final: 0.8211 (t70) REVERT: Ae 35 ASP cc_start: 0.8945 (p0) cc_final: 0.8731 (p0) REVERT: Ae 97 MET cc_start: 0.8937 (mmt) cc_final: 0.8477 (mmt) REVERT: Ae 101 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8334 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9348 (mm) cc_final: 0.9014 (mp) REVERT: Ad 22 GLN cc_start: 0.8817 (mp10) cc_final: 0.8571 (mp10) REVERT: Ad 52 ASN cc_start: 0.9099 (t0) cc_final: 0.8807 (t0) REVERT: AS 26 HIS cc_start: 0.7530 (p90) cc_final: 0.7286 (p90) REVERT: AT 18 LYS cc_start: 0.8783 (ptmt) cc_final: 0.8524 (ptmm) REVERT: AT 104 TYR cc_start: 0.8733 (t80) cc_final: 0.5807 (m-10) outliers start: 134 outliers final: 86 residues processed: 635 average time/residue: 0.1636 time to fit residues: 163.7892 Evaluate side-chains 596 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 507 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 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 39 VAL 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 G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 260 THR Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 300 CYS 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 453 GLU 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 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 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 497 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 344 PHE Chi-restraints excluded: chain r residue 375 LYS 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 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 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 Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU 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 13 LEU 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 43 SER Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 321 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 299 optimal weight: 2.9990 chunk 2 optimal weight: 40.0000 chunk 145 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 339 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 51 HIS G 10 ASN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 490 ASN ** r 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 342 ASN AV 6 GLN AV 22 GLN Ad 61 ASN AS 152 ASN AT 71 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099851 restraints weight = 62023.700| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.17 r_work: 0.3264 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27288 Z= 0.253 Angle : 0.734 10.874 37211 Z= 0.375 Chirality : 0.049 0.206 4191 Planarity : 0.005 0.120 4931 Dihedral : 5.827 85.627 3752 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.29 % Favored : 87.42 % Rotamer: Outliers : 5.38 % Allowed : 21.05 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.14), residues: 3435 helix: 0.71 (0.24), residues: 525 sheet: -0.88 (0.16), residues: 967 loop : -2.85 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG q 427 TYR 0.032 0.002 TYRAT 7 PHE 0.016 0.002 PHE r 250 TRP 0.019 0.002 TRP r 331 HIS 0.006 0.001 HIS F 182 Details of bonding type rmsd covalent geometry : bond 0.00592 (27255) covalent geometry : angle 0.73109 (37145) SS BOND : bond 0.00497 ( 33) SS BOND : angle 1.77901 ( 66) hydrogen bonds : bond 0.03841 ( 780) hydrogen bonds : angle 4.93958 ( 2289) *********************** 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 637 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 478 time to evaluate : 0.958 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: 3 19 CYS cc_start: 0.4969 (OUTLIER) cc_final: 0.4285 (p) REVERT: 3 30 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8135 (ttt90) REVERT: D 33 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7908 (mm-30) REVERT: D 60 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7255 (tm-30) REVERT: D 185 LYS cc_start: 0.8699 (mttt) cc_final: 0.8407 (mttm) REVERT: D 201 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8326 (mtp-110) REVERT: E 14 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6308 (tmmt) REVERT: E 33 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8160 (pt0) REVERT: E 79 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7457 (mmtt) REVERT: F 120 ASN cc_start: 0.7732 (t0) cc_final: 0.6223 (p0) REVERT: G 38 MET cc_start: 0.8324 (mtt) cc_final: 0.8005 (mtt) REVERT: G 70 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8145 (tttt) REVERT: G 136 ARG cc_start: 0.8138 (ptp-110) cc_final: 0.7874 (ptp-110) REVERT: G 159 LEU cc_start: 0.6404 (mm) cc_final: 0.5996 (mt) REVERT: p 58 PHE cc_start: 0.3967 (p90) cc_final: 0.3576 (p90) REVERT: p 265 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8375 (tt) REVERT: p 403 GLN cc_start: 0.8606 (mm-40) cc_final: 0.7964 (mm-40) REVERT: q 22 PHE cc_start: 0.7705 (m-10) cc_final: 0.7446 (m-10) REVERT: r 22 PHE cc_start: 0.6082 (p90) cc_final: 0.5770 (p90) REVERT: r 82 TYR cc_start: 0.7923 (m-80) cc_final: 0.7588 (m-80) REVERT: r 258 LYS cc_start: 0.5857 (tttp) cc_final: 0.4727 (ptmt) REVERT: r 331 TRP cc_start: 0.6077 (OUTLIER) cc_final: 0.5805 (p90) REVERT: r 375 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.6193 (tttt) REVERT: s 19 LEU cc_start: 0.7502 (tp) cc_final: 0.7090 (pt) REVERT: s 27 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7543 (ttmm) REVERT: s 66 GLU cc_start: 0.8469 (tp30) cc_final: 0.8246 (tp30) REVERT: s 317 LEU cc_start: 0.7314 (tp) cc_final: 0.6900 (pt) REVERT: s 379 ASN cc_start: 0.8186 (t0) cc_final: 0.7503 (t0) REVERT: s 414 ASN cc_start: 0.8668 (m-40) cc_final: 0.8426 (t0) REVERT: s 458 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8878 (mt) REVERT: AV 54 TYR cc_start: 0.8955 (m-80) cc_final: 0.8649 (m-80) REVERT: Ae 18 ASP cc_start: 0.8725 (t0) cc_final: 0.8321 (t70) REVERT: Ae 84 GLN cc_start: 0.8018 (tt0) cc_final: 0.7527 (tt0) REVERT: Ad 13 LEU cc_start: 0.9386 (mm) cc_final: 0.9021 (mp) REVERT: Ad 52 ASN cc_start: 0.9196 (t0) cc_final: 0.8925 (t0) REVERT: Ad 120 VAL cc_start: 0.9624 (OUTLIER) cc_final: 0.9387 (p) REVERT: AT 94 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8363 (mpp80) REVERT: AT 104 TYR cc_start: 0.8781 (t80) cc_final: 0.5857 (m-10) REVERT: AT 166 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8595 (pt) outliers start: 159 outliers final: 114 residues processed: 595 average time/residue: 0.1623 time to fit residues: 151.4159 Evaluate side-chains 569 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 447 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 D residue 6 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 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 152 VAL Chi-restraints excluded: chain E residue 168 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 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 150 ILE 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 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 p residue 29 LEU Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 260 THR Chi-restraints excluded: chain p residue 265 LEU 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 400 GLU 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 497 LEU 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 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE 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 497 LEU 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 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 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 390 LEU Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain AV residue 4 ASN 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 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 99 LEU Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 13 LEU 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 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 135 ASP Chi-restraints excluded: chain AT residue 137 SER 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 166 ILE 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 55 optimal weight: 0.0270 chunk 278 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 287 optimal weight: 0.0770 chunk 274 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 51 HIS 3 120 ASN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** p 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 365 ASN ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 263 GLN s 338 GLN s 342 ASN s 379 ASN AV 6 GLN Ad 61 ASN ** Ad 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 71 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.131041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102619 restraints weight = 61643.478| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.29 r_work: 0.3335 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27288 Z= 0.134 Angle : 0.678 11.427 37211 Z= 0.341 Chirality : 0.047 0.208 4191 Planarity : 0.005 0.120 4931 Dihedral : 5.624 85.808 3752 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.95 % Favored : 88.85 % Rotamer: Outliers : 5.01 % Allowed : 22.00 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.14), residues: 3435 helix: 0.94 (0.24), residues: 519 sheet: -0.70 (0.17), residues: 953 loop : -2.70 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAS 92 TYR 0.020 0.002 TYRAT 7 PHE 0.017 0.001 PHEAT 171 TRP 0.020 0.001 TRP r 331 HIS 0.003 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00310 (27255) covalent geometry : angle 0.67587 (37145) SS BOND : bond 0.00318 ( 33) SS BOND : angle 1.53268 ( 66) hydrogen bonds : bond 0.03296 ( 780) hydrogen bonds : angle 4.77230 ( 2289) *********************** 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: 148 poor density : 504 time to evaluate : 0.863 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 19 CYS cc_start: 0.4885 (OUTLIER) cc_final: 0.4242 (p) REVERT: 3 30 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8216 (ttt90) REVERT: D 33 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7842 (mm-30) REVERT: D 60 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7365 (tm-30) REVERT: D 136 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7248 (mtt90) REVERT: D 185 LYS cc_start: 0.8687 (mttt) cc_final: 0.8403 (mttm) REVERT: E 14 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6416 (tmmt) REVERT: E 33 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7997 (pt0) REVERT: F 120 ASN cc_start: 0.7628 (t0) cc_final: 0.6135 (p0) REVERT: G 38 MET cc_start: 0.8247 (mtt) cc_final: 0.7954 (mtt) REVERT: G 70 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8096 (tttt) REVERT: G 91 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6149 (mm) REVERT: G 148 TYR cc_start: 0.7309 (t80) cc_final: 0.6927 (t80) REVERT: G 159 LEU cc_start: 0.6366 (mm) cc_final: 0.5950 (mt) REVERT: p 58 PHE cc_start: 0.3819 (p90) cc_final: 0.3353 (p90) REVERT: p 265 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8321 (tt) REVERT: p 403 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8008 (mm-40) REVERT: q 400 GLU cc_start: 0.8503 (mp0) cc_final: 0.8206 (mp0) REVERT: r 22 PHE cc_start: 0.6533 (p90) cc_final: 0.6312 (p90) REVERT: r 82 TYR cc_start: 0.7904 (m-80) cc_final: 0.7602 (m-80) REVERT: r 258 LYS cc_start: 0.5768 (tttp) cc_final: 0.4609 (ptmt) REVERT: r 331 TRP cc_start: 0.6067 (OUTLIER) cc_final: 0.5820 (p90) REVERT: r 365 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6557 (p0) REVERT: r 375 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6099 (tttt) REVERT: r 432 LYS cc_start: 0.9344 (tppt) cc_final: 0.9020 (ttpt) REVERT: s 19 LEU cc_start: 0.7410 (tp) cc_final: 0.7029 (pt) REVERT: s 66 GLU cc_start: 0.8382 (tp30) cc_final: 0.8146 (tp30) REVERT: s 375 LYS cc_start: 0.7149 (tmtt) cc_final: 0.6239 (pptt) REVERT: s 379 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7489 (t0) REVERT: s 414 ASN cc_start: 0.8645 (m-40) cc_final: 0.8387 (t0) REVERT: s 462 GLU cc_start: 0.8485 (tt0) cc_final: 0.7655 (tp30) REVERT: AV 54 TYR cc_start: 0.8890 (m-80) cc_final: 0.8522 (m-80) REVERT: AV 109 GLU cc_start: 0.3964 (tp30) cc_final: 0.3760 (tp30) REVERT: Ae 18 ASP cc_start: 0.8721 (t0) cc_final: 0.8307 (t70) REVERT: Ae 35 ASP cc_start: 0.9095 (p0) cc_final: 0.8841 (p0) REVERT: Ae 97 MET cc_start: 0.9000 (mmt) cc_final: 0.8596 (mmt) REVERT: Ae 101 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8411 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9353 (mm) cc_final: 0.9062 (mp) REVERT: Ad 52 ASN cc_start: 0.9186 (t0) cc_final: 0.8919 (t0) REVERT: AT 94 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8525 (mpp80) REVERT: AT 104 TYR cc_start: 0.8732 (t80) cc_final: 0.5757 (m-10) REVERT: AT 166 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8577 (pt) outliers start: 148 outliers final: 101 residues processed: 605 average time/residue: 0.1523 time to fit residues: 145.5160 Evaluate side-chains 588 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 477 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 30 ARG 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 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 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 F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 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 p residue 29 LEU Chi-restraints excluded: chain p residue 79 VAL 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 260 THR Chi-restraints excluded: chain p residue 265 LEU 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 400 GLU Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 497 LEU 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 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 497 LEU Chi-restraints excluded: chain r residue 11 VAL 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 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 365 ASN 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 28 ILE 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 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 379 ASN Chi-restraints excluded: chain s residue 390 LEU Chi-restraints excluded: chain AV residue 4 ASN 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 Ae residue 40 TYR Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain AS residue 13 LEU 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 43 SER Chi-restraints excluded: chain AT residue 128 THR 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 166 ILE 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 338 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 273 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 317 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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** ** p 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 GLN ** s 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN AV 88 GLN Ad 61 ASN AT 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099405 restraints weight = 61606.530| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.20 r_work: 0.3284 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27288 Z= 0.235 Angle : 0.746 13.218 37211 Z= 0.376 Chirality : 0.049 0.257 4191 Planarity : 0.006 0.121 4931 Dihedral : 5.775 87.012 3752 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.08 % Favored : 87.66 % Rotamer: Outliers : 5.18 % Allowed : 23.15 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.14), residues: 3435 helix: 0.79 (0.24), residues: 531 sheet: -0.72 (0.17), residues: 963 loop : -2.69 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG r 377 TYR 0.024 0.002 TYR F 222 PHE 0.017 0.002 PHEAT 171 TRP 0.018 0.001 TRP r 331 HIS 0.006 0.001 HIS F 182 Details of bonding type rmsd covalent geometry : bond 0.00557 (27255) covalent geometry : angle 0.74321 (37145) SS BOND : bond 0.00464 ( 33) SS BOND : angle 1.78791 ( 66) hydrogen bonds : bond 0.03695 ( 780) hydrogen bonds : angle 4.85797 ( 2289) *********************** 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 608 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 455 time to evaluate : 0.889 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 1 MET cc_start: 0.8880 (tmm) cc_final: 0.8014 (tpp) REVERT: 3 19 CYS cc_start: 0.4850 (OUTLIER) cc_final: 0.4253 (p) REVERT: 3 30 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8033 (ttt90) REVERT: 3 38 MET cc_start: 0.8061 (mtt) cc_final: 0.7267 (mtm) REVERT: D 1 MET cc_start: 0.8085 (ttp) cc_final: 0.7873 (ttt) REVERT: D 33 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7877 (mm-30) REVERT: D 60 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7290 (tm-30) REVERT: D 136 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7288 (mtt90) REVERT: D 138 TRP cc_start: 0.8209 (m100) cc_final: 0.7963 (m100) REVERT: D 185 LYS cc_start: 0.8739 (mttt) cc_final: 0.8472 (mttm) REVERT: D 201 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8271 (mtp-110) REVERT: E 1 MET cc_start: 0.8037 (ttp) cc_final: 0.7521 (tmm) REVERT: E 14 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6398 (tmmt) REVERT: E 33 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8033 (pt0) REVERT: F 1 MET cc_start: 0.7874 (ttt) cc_final: 0.7333 (ttt) REVERT: G 148 TYR cc_start: 0.7272 (t80) cc_final: 0.6911 (t80) REVERT: G 159 LEU cc_start: 0.6494 (mm) cc_final: 0.6129 (mt) REVERT: p 54 ILE cc_start: 0.8365 (tp) cc_final: 0.8029 (tp) REVERT: p 58 PHE cc_start: 0.3857 (p90) cc_final: 0.3353 (p90) REVERT: p 265 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8320 (tt) REVERT: p 403 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8095 (mm-40) REVERT: q 400 GLU cc_start: 0.8469 (mp0) cc_final: 0.8200 (mp0) REVERT: r 22 PHE cc_start: 0.6658 (p90) cc_final: 0.6382 (p90) REVERT: r 82 TYR cc_start: 0.7921 (m-80) cc_final: 0.7573 (m-80) REVERT: r 258 LYS cc_start: 0.5906 (tttp) cc_final: 0.4704 (ptmt) REVERT: r 331 TRP cc_start: 0.6224 (OUTLIER) cc_final: 0.6003 (p90) REVERT: r 375 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.5357 (tttt) REVERT: s 19 LEU cc_start: 0.7651 (tp) cc_final: 0.7173 (pt) REVERT: s 27 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7346 (ttmm) REVERT: s 66 GLU cc_start: 0.8432 (tp30) cc_final: 0.8216 (tp30) REVERT: s 379 ASN cc_start: 0.7878 (t0) cc_final: 0.7094 (t0) REVERT: s 414 ASN cc_start: 0.8674 (m-40) cc_final: 0.8425 (t0) REVERT: s 458 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8858 (mt) REVERT: AV 54 TYR cc_start: 0.8935 (m-80) cc_final: 0.8624 (m-80) REVERT: AV 109 GLU cc_start: 0.4151 (tp30) cc_final: 0.3907 (tp30) REVERT: Ae 18 ASP cc_start: 0.8727 (t0) cc_final: 0.8343 (t70) REVERT: Ae 97 MET cc_start: 0.9075 (mmt) cc_final: 0.8745 (mmt) REVERT: Ae 101 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8423 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9432 (mm) cc_final: 0.9084 (mp) REVERT: Ad 52 ASN cc_start: 0.9181 (t0) cc_final: 0.8808 (t0) REVERT: AT 18 LYS cc_start: 0.9169 (ptpt) cc_final: 0.8901 (ttpt) REVERT: AT 71 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7784 (p0) REVERT: AT 94 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8626 (mpp80) REVERT: AT 104 TYR cc_start: 0.8813 (t80) cc_final: 0.5956 (m-10) outliers start: 153 outliers final: 113 residues processed: 570 average time/residue: 0.1559 time to fit residues: 140.8366 Evaluate side-chains 559 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 438 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 30 ARG 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 85 GLU 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 F residue 18 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL 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 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 260 THR Chi-restraints excluded: chain p residue 265 LEU 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 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 368 THR Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 497 LEU 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 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 497 LEU Chi-restraints excluded: chain r residue 11 VAL 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 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 297 LEU 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 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 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 390 LEU Chi-restraints excluded: chain s residue 458 LEU 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 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 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 AS residue 13 LEU 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 81 ILE Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 128 THR 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 43 SER Chi-restraints excluded: chain AT residue 71 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 284 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 61 optimal weight: 0.0770 chunk 92 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- 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** ** p 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 365 ASN ** s 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN Ad 61 ASN AT 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100441 restraints weight = 61960.539| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.25 r_work: 0.3314 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27288 Z= 0.188 Angle : 0.706 11.503 37211 Z= 0.356 Chirality : 0.048 0.237 4191 Planarity : 0.005 0.121 4931 Dihedral : 5.604 81.270 3749 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.27 % Favored : 88.50 % Rotamer: Outliers : 4.97 % Allowed : 23.65 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.14), residues: 3435 helix: 0.89 (0.24), residues: 525 sheet: -0.71 (0.16), residues: 1015 loop : -2.65 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 9 TYR 0.020 0.002 TYR F 222 PHE 0.018 0.001 PHEAT 171 TRP 0.022 0.001 TRP r 331 HIS 0.004 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00445 (27255) covalent geometry : angle 0.70343 (37145) SS BOND : bond 0.00377 ( 33) SS BOND : angle 1.63802 ( 66) hydrogen bonds : bond 0.03437 ( 780) hydrogen bonds : angle 4.78835 ( 2289) *********************** 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 606 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 459 time to evaluate : 0.899 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: 3 19 CYS cc_start: 0.4852 (OUTLIER) cc_final: 0.4260 (p) REVERT: 3 30 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8072 (ttt90) REVERT: 3 38 MET cc_start: 0.8361 (mtt) cc_final: 0.8106 (mtt) REVERT: D 33 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7875 (mm-30) REVERT: D 60 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7303 (tm-30) REVERT: D 136 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7233 (mtt90) REVERT: D 185 LYS cc_start: 0.8722 (mttt) cc_final: 0.8443 (mttm) REVERT: D 201 ARG cc_start: 0.8778 (ttm110) cc_final: 0.8317 (mtp-110) REVERT: E 1 MET cc_start: 0.7960 (ttp) cc_final: 0.7485 (tmm) REVERT: E 14 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6468 (tmmt) REVERT: E 33 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7989 (pt0) REVERT: F 120 ASN cc_start: 0.7561 (t0) cc_final: 0.6372 (m110) REVERT: G 38 MET cc_start: 0.8065 (mtt) cc_final: 0.7656 (mtm) REVERT: G 148 TYR cc_start: 0.7291 (t80) cc_final: 0.6979 (t80) REVERT: G 159 LEU cc_start: 0.6499 (mm) cc_final: 0.6124 (mt) REVERT: p 54 ILE cc_start: 0.8257 (tp) cc_final: 0.7918 (tp) REVERT: p 58 PHE cc_start: 0.3656 (p90) cc_final: 0.3105 (p90) REVERT: p 265 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8327 (tt) REVERT: p 403 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8186 (mm-40) REVERT: q 372 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7202 (ttp80) REVERT: q 400 GLU cc_start: 0.8483 (mp0) cc_final: 0.8254 (mp0) REVERT: r 22 PHE cc_start: 0.6681 (p90) cc_final: 0.6425 (p90) REVERT: r 82 TYR cc_start: 0.7948 (m-80) cc_final: 0.7391 (m-80) REVERT: r 258 LYS cc_start: 0.5908 (tttp) cc_final: 0.4703 (ptmt) REVERT: r 331 TRP cc_start: 0.6230 (OUTLIER) cc_final: 0.5985 (p90) REVERT: r 375 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.5308 (tttt) REVERT: s 19 LEU cc_start: 0.7682 (tp) cc_final: 0.7212 (pt) REVERT: s 27 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7248 (ttmm) REVERT: s 364 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7754 (p90) REVERT: s 375 LYS cc_start: 0.7343 (tmtt) cc_final: 0.6278 (pptt) REVERT: s 379 ASN cc_start: 0.8008 (t0) cc_final: 0.7545 (t0) REVERT: s 414 ASN cc_start: 0.8637 (m-40) cc_final: 0.8406 (t0) REVERT: s 458 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8788 (mt) REVERT: AV 54 TYR cc_start: 0.8892 (m-80) cc_final: 0.8573 (m-80) REVERT: Ae 18 ASP cc_start: 0.8710 (t0) cc_final: 0.8348 (t70) REVERT: Ae 35 ASP cc_start: 0.9092 (p0) cc_final: 0.8825 (p0) REVERT: Ae 97 MET cc_start: 0.9064 (mmt) cc_final: 0.8777 (mmt) REVERT: Ad 13 LEU cc_start: 0.9381 (mm) cc_final: 0.9067 (mp) REVERT: Ad 52 ASN cc_start: 0.9197 (t0) cc_final: 0.8920 (t0) REVERT: AS 112 ASP cc_start: 0.8705 (m-30) cc_final: 0.8477 (m-30) REVERT: AT 71 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7847 (p0) REVERT: AT 94 ARG cc_start: 0.8865 (mmm-85) cc_final: 0.8612 (mpp80) REVERT: AT 104 TYR cc_start: 0.8781 (t80) cc_final: 0.5958 (m-10) REVERT: AT 135 ASP cc_start: 0.8325 (m-30) cc_final: 0.8056 (m-30) outliers start: 147 outliers final: 117 residues processed: 574 average time/residue: 0.1541 time to fit residues: 140.5530 Evaluate side-chains 575 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 448 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 30 ARG Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 185 LYS Chi-restraints excluded: chain D residue 6 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 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 F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL 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 p residue 29 LEU Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 260 THR Chi-restraints excluded: chain p residue 265 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 419 THR Chi-restraints excluded: chain p residue 476 LEU Chi-restraints excluded: chain p residue 497 LEU 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 213 VAL Chi-restraints excluded: chain q residue 260 THR 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 345 VAL Chi-restraints excluded: chain q residue 372 ARG Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 497 LEU Chi-restraints excluded: chain r residue 11 VAL 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 297 LEU 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 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 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 390 LEU Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain AV residue 4 ASN 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 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 87 VAL 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 81 ILE Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 128 THR 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 43 SER Chi-restraints excluded: chain AT residue 71 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 323 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 309 optimal weight: 8.9990 chunk 339 optimal weight: 0.8980 chunk 275 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 317 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN AV 88 GLN Ae 88 GLN Ad 4 ASN ** Ad 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098948 restraints weight = 62149.536| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.26 r_work: 0.3262 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 27288 Z= 0.138 Angle : 0.697 12.677 37211 Z= 0.348 Chirality : 0.047 0.241 4191 Planarity : 0.005 0.120 4931 Dihedral : 5.433 77.979 3749 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.18 % Favored : 88.62 % Rotamer: Outliers : 4.91 % Allowed : 24.16 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.14), residues: 3435 helix: 0.88 (0.24), residues: 528 sheet: -0.59 (0.16), residues: 1007 loop : -2.60 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 9 TYR 0.018 0.001 TYR p 480 PHE 0.022 0.001 PHE p 250 TRP 0.023 0.001 TRP r 331 HIS 0.003 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00322 (27255) covalent geometry : angle 0.69464 (37145) SS BOND : bond 0.00351 ( 33) SS BOND : angle 1.48790 ( 66) hydrogen bonds : bond 0.03201 ( 780) hydrogen bonds : angle 4.69089 ( 2289) *********************** 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 638 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 493 time to evaluate : 1.049 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 19 CYS cc_start: 0.4621 (OUTLIER) cc_final: 0.4106 (p) REVERT: 3 30 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8141 (ttt90) REVERT: D 33 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7779 (mm-30) REVERT: D 60 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7220 (tm-30) REVERT: D 66 VAL cc_start: 0.7194 (m) cc_final: 0.6994 (t) REVERT: D 136 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7208 (mtt90) REVERT: D 185 LYS cc_start: 0.8791 (mttt) cc_final: 0.8405 (mttm) REVERT: D 201 ARG cc_start: 0.8718 (ttm110) cc_final: 0.8334 (mtp-110) REVERT: E 1 MET cc_start: 0.7917 (ttp) cc_final: 0.7336 (tmm) REVERT: E 14 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6307 (tmmt) REVERT: E 33 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7865 (pt0) REVERT: E 79 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7617 (tppt) REVERT: F 1 MET cc_start: 0.7787 (ttt) cc_final: 0.7140 (ttt) REVERT: F 120 ASN cc_start: 0.7497 (t0) cc_final: 0.6261 (m110) REVERT: G 38 MET cc_start: 0.8228 (mtt) cc_final: 0.7944 (mtp) REVERT: G 148 TYR cc_start: 0.7255 (t80) cc_final: 0.6987 (t80) REVERT: G 159 LEU cc_start: 0.6547 (mm) cc_final: 0.6140 (mt) REVERT: p 54 ILE cc_start: 0.8143 (tp) cc_final: 0.7798 (tp) REVERT: p 58 PHE cc_start: 0.3678 (p90) cc_final: 0.2854 (p90) REVERT: p 265 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8297 (tt) REVERT: p 416 ASN cc_start: 0.9174 (t0) cc_final: 0.8956 (t0) REVERT: p 447 GLU cc_start: 0.8511 (tp30) cc_final: 0.8070 (pm20) REVERT: q 372 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6919 (ttp80) REVERT: q 377 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7620 (mmp80) REVERT: q 400 GLU cc_start: 0.8528 (mp0) cc_final: 0.8302 (mp0) REVERT: r 82 TYR cc_start: 0.7952 (m-80) cc_final: 0.7379 (m-80) REVERT: r 258 LYS cc_start: 0.5939 (tttp) cc_final: 0.4673 (ptmt) REVERT: r 331 TRP cc_start: 0.6187 (OUTLIER) cc_final: 0.5926 (p90) REVERT: r 375 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.5067 (tttt) REVERT: s 19 LEU cc_start: 0.7716 (tp) cc_final: 0.7212 (pt) REVERT: s 27 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7095 (ttmm) REVERT: s 364 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7771 (p90) REVERT: s 375 LYS cc_start: 0.7113 (tmtt) cc_final: 0.6133 (pptt) REVERT: s 379 ASN cc_start: 0.7848 (t0) cc_final: 0.7427 (t0) REVERT: s 414 ASN cc_start: 0.8628 (m-40) cc_final: 0.8401 (t0) REVERT: s 458 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8791 (mt) REVERT: s 462 GLU cc_start: 0.8608 (tt0) cc_final: 0.7729 (tp30) REVERT: AV 54 TYR cc_start: 0.8881 (m-80) cc_final: 0.8513 (m-80) REVERT: Ae 18 ASP cc_start: 0.8714 (t0) cc_final: 0.8324 (t70) REVERT: Ae 35 ASP cc_start: 0.9147 (p0) cc_final: 0.8865 (p0) REVERT: Ae 97 MET cc_start: 0.9023 (mmt) cc_final: 0.8753 (mmt) REVERT: Ae 108 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8334 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9330 (mm) cc_final: 0.9064 (mp) REVERT: Ad 52 ASN cc_start: 0.9237 (t0) cc_final: 0.8981 (t0) REVERT: AS 112 ASP cc_start: 0.8689 (m-30) cc_final: 0.8387 (m-30) REVERT: AT 94 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8594 (mpp80) REVERT: AT 104 TYR cc_start: 0.8724 (t80) cc_final: 0.5807 (m-10) REVERT: AT 135 ASP cc_start: 0.8416 (m-30) cc_final: 0.8137 (m-30) outliers start: 145 outliers final: 111 residues processed: 600 average time/residue: 0.1601 time to fit residues: 152.4315 Evaluate side-chains 591 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 470 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 30 ARG 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 85 GLU 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 207 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 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 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 260 THR Chi-restraints excluded: chain p residue 265 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 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 476 LEU Chi-restraints excluded: chain p residue 497 LEU Chi-restraints excluded: chain q residue 28 ILE Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 260 THR 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 345 VAL Chi-restraints excluded: chain q residue 372 ARG Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 497 LEU Chi-restraints excluded: chain r residue 11 VAL 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 297 LEU 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 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 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 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 390 LEU 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 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 Ae residue 108 GLU Chi-restraints excluded: chain Ad residue 4 ASN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 50 LEU 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 81 ILE Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 128 THR 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 128 THR Chi-restraints excluded: chain AT residue 137 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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** ** p 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN Ad 4 ASN AS 116 ASN AT 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.125134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096808 restraints weight = 62215.326| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.28 r_work: 0.3223 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27288 Z= 0.211 Angle : 0.759 29.802 37211 Z= 0.374 Chirality : 0.049 0.286 4191 Planarity : 0.006 0.211 4931 Dihedral : 5.527 70.126 3749 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.59 % Favored : 88.21 % Rotamer: Outliers : 4.43 % Allowed : 24.91 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.14), residues: 3435 helix: 0.75 (0.23), residues: 541 sheet: -0.59 (0.17), residues: 975 loop : -2.59 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG r 377 TYR 0.020 0.002 TYR F 222 PHE 0.020 0.001 PHE p 250 TRP 0.022 0.001 TRP r 331 HIS 0.004 0.001 HIS F 182 Details of bonding type rmsd covalent geometry : bond 0.00500 (27255) covalent geometry : angle 0.75616 (37145) SS BOND : bond 0.00412 ( 33) SS BOND : angle 1.60427 ( 66) hydrogen bonds : bond 0.03491 ( 780) hydrogen bonds : angle 4.77338 ( 2289) ********************** 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 591 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 460 time to evaluate : 0.870 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 1 MET cc_start: 0.8626 (tmm) cc_final: 0.8249 (tpp) REVERT: 3 19 CYS cc_start: 0.4089 (OUTLIER) cc_final: 0.3668 (p) REVERT: 3 30 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8165 (ttt90) REVERT: 3 38 MET cc_start: 0.7969 (mtt) cc_final: 0.7518 (ptp) REVERT: D 33 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7782 (mm-30) REVERT: D 60 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7234 (tm-30) REVERT: D 136 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7229 (mtt90) REVERT: D 185 LYS cc_start: 0.8746 (mttt) cc_final: 0.8450 (mttm) REVERT: D 201 ARG cc_start: 0.8758 (ttm110) cc_final: 0.8367 (mtp-110) REVERT: E 1 MET cc_start: 0.8110 (ttp) cc_final: 0.7618 (tmm) REVERT: E 14 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6347 (tmmt) REVERT: E 33 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7989 (pt0) REVERT: E 79 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7629 (tppt) REVERT: F 1 MET cc_start: 0.8038 (ttt) cc_final: 0.7344 (ttt) REVERT: G 38 MET cc_start: 0.8197 (mtt) cc_final: 0.7922 (mtp) REVERT: G 148 TYR cc_start: 0.7141 (t80) cc_final: 0.6905 (t80) REVERT: G 159 LEU cc_start: 0.6527 (mm) cc_final: 0.6085 (mt) REVERT: p 54 ILE cc_start: 0.8162 (tp) cc_final: 0.7843 (tp) REVERT: p 58 PHE cc_start: 0.3781 (p90) cc_final: 0.3015 (p90) REVERT: p 265 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8291 (tt) REVERT: p 375 LYS cc_start: 0.7456 (mmmt) cc_final: 0.6795 (mttt) REVERT: p 403 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8244 (mm-40) REVERT: q 372 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6981 (ttp80) REVERT: q 400 GLU cc_start: 0.8572 (mp0) cc_final: 0.8331 (mp0) REVERT: r 82 TYR cc_start: 0.8003 (m-80) cc_final: 0.7317 (m-80) REVERT: r 258 LYS cc_start: 0.5944 (tttp) cc_final: 0.4646 (ptmt) REVERT: r 331 TRP cc_start: 0.6117 (OUTLIER) cc_final: 0.5859 (p90) REVERT: r 375 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.5375 (tttt) REVERT: s 19 LEU cc_start: 0.7893 (tp) cc_final: 0.7325 (pt) REVERT: s 27 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7228 (ttmm) REVERT: s 364 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7863 (p90) REVERT: s 375 LYS cc_start: 0.7183 (tmtt) cc_final: 0.6218 (pptt) REVERT: s 379 ASN cc_start: 0.8090 (t0) cc_final: 0.7516 (t0) REVERT: s 414 ASN cc_start: 0.8660 (m-40) cc_final: 0.8437 (t0) REVERT: s 458 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8823 (mt) REVERT: AV 54 TYR cc_start: 0.8934 (m-80) cc_final: 0.8582 (m-80) REVERT: Ae 18 ASP cc_start: 0.8742 (t0) cc_final: 0.8335 (t70) REVERT: Ae 35 ASP cc_start: 0.9156 (p0) cc_final: 0.8864 (p0) REVERT: Ae 108 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8409 (mm-30) REVERT: Ae 126 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7699 (mt-10) REVERT: Ad 13 LEU cc_start: 0.9357 (mm) cc_final: 0.9060 (mp) REVERT: Ad 52 ASN cc_start: 0.9221 (t0) cc_final: 0.8907 (t0) REVERT: AS 95 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8898 (mmtt) REVERT: AS 112 ASP cc_start: 0.8751 (m-30) cc_final: 0.8525 (m-30) REVERT: AT 94 ARG cc_start: 0.8959 (mmm-85) cc_final: 0.8613 (mpp80) REVERT: AT 104 TYR cc_start: 0.8813 (t80) cc_final: 0.5963 (m-10) REVERT: AT 135 ASP cc_start: 0.8393 (m-30) cc_final: 0.8112 (m-30) REVERT: AT 144 TYR cc_start: 0.9173 (m-80) cc_final: 0.8746 (m-80) outliers start: 131 outliers final: 115 residues processed: 562 average time/residue: 0.1566 time to fit residues: 139.0816 Evaluate side-chains 569 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 444 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 30 ARG Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 185 LYS Chi-restraints excluded: chain D residue 6 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 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 19 CYS 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 207 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL 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 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 260 THR Chi-restraints excluded: chain p residue 265 LEU 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 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 476 LEU Chi-restraints excluded: chain p residue 497 LEU Chi-restraints excluded: chain q residue 28 ILE 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 345 VAL Chi-restraints excluded: chain q residue 372 ARG Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 497 LEU Chi-restraints excluded: chain r residue 11 VAL 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 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 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 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 390 LEU Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain AV residue 4 ASN 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 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 Ae residue 108 GLU 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 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 81 ILE Chi-restraints excluded: chain AS residue 106 ASP Chi-restraints excluded: chain AS residue 122 SER Chi-restraints excluded: chain AS residue 128 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 265 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** ** p 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 369 ASN ** r 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN Ad 4 ASN ** Ad 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 88 GLN AT 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.128433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099876 restraints weight = 61647.181| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.17 r_work: 0.3295 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27288 Z= 0.127 Angle : 0.719 22.389 37211 Z= 0.353 Chirality : 0.047 0.250 4191 Planarity : 0.006 0.187 4931 Dihedral : 5.352 68.229 3749 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.42 % Favored : 89.40 % Rotamer: Outliers : 3.59 % Allowed : 25.69 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.14), residues: 3435 helix: 0.92 (0.24), residues: 530 sheet: -0.46 (0.16), residues: 1013 loop : -2.52 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG r 377 TYR 0.022 0.001 TYR r 254 PHE 0.019 0.001 PHEAT 171 TRP 0.024 0.001 TRP r 331 HIS 0.003 0.000 HIS 3 218 Details of bonding type rmsd covalent geometry : bond 0.00286 (27255) covalent geometry : angle 0.71716 (37145) SS BOND : bond 0.00346 ( 33) SS BOND : angle 1.38392 ( 66) hydrogen bonds : bond 0.03008 ( 780) hydrogen bonds : angle 4.63625 ( 2289) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5870.26 seconds wall clock time: 101 minutes 19.42 seconds (6079.42 seconds total)