Starting phenix.real_space_refine on Mon Aug 10 06:58:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxj_47289/08_2026/9dxj_47289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxj_47289/08_2026/9dxj_47289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dxj_47289/08_2026/9dxj_47289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxj_47289/08_2026/9dxj_47289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dxj_47289/08_2026/9dxj_47289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxj_47289/08_2026/9dxj_47289.map" } resolution = 4.69 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 232 5.49 5 S 72 5.16 5 C 13268 2.51 5 N 3846 2.21 5 O 4760 1.98 5 H 20350 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42532 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "C" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "E" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1087 Classifications: {'DNA': 34} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1052 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "G" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 796 Classifications: {'DNA': 25} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 24} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 767 Classifications: {'DNA': 24} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 23} Chain: "I" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "K" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "M" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1087 Classifications: {'DNA': 34} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 33} Chain: "N" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1052 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "O" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 796 Classifications: {'DNA': 25} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 24} Chain: "P" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 767 Classifications: {'DNA': 24} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5206 SG CYS A 320 77.194 101.928 161.246 1.00416.19 S ATOM 5250 SG CYS A 323 75.402 99.901 158.669 1.00436.76 S ATOM 5738 SG CYS A 353 73.261 101.328 160.884 1.00426.67 S ATOM 5829 SG CYS A 358 75.781 98.793 162.519 1.00395.99 S ATOM 13987 SG CYS C 320 73.317 37.982 144.851 1.00478.80 S ATOM 14031 SG CYS C 323 73.950 37.874 141.192 1.00481.91 S ATOM 14519 SG CYS C 353 70.654 37.183 141.949 1.00434.83 S ATOM 14610 SG CYS C 358 73.205 34.650 143.427 1.00417.98 S ATOM 26470 SG CYS I 320 103.955 102.458 53.041 1.00416.19 S ATOM 26514 SG CYS I 323 100.659 101.273 54.342 1.00436.76 S ATOM 27002 SG CYS I 353 101.863 99.253 51.893 1.00426.67 S ATOM 27093 SG CYS I 358 101.162 102.937 50.713 1.00395.99 S ATOM 35251 SG CYS K 320 41.652 124.623 52.847 1.00478.80 S ATOM 35295 SG CYS K 323 40.538 124.427 56.385 1.00481.91 S ATOM 35783 SG CYS K 353 38.985 122.057 54.413 1.00434.83 S ATOM 35874 SG CYS K 358 38.244 125.732 53.389 1.00417.98 S Time building chain proxies: 7.16, per 1000 atoms: 0.17 Number of scatterers: 42532 At special positions: 0 Unit cell: (140.58, 150.165, 220.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 72 16.00 P 232 15.00 O 4760 8.00 N 3846 7.00 C 13268 6.00 H 20350 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 323 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 320 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 353 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 358 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 323 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 320 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 353 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 358 " pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 323 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 320 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 353 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 358 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 323 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 320 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 353 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 358 " Number of angles added : 24 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 24 sheets defined 55.9% alpha, 12.0% beta 110 base pairs and 184 stacking pairs defined. Time for finding SS restraints: 8.00 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.879A pdb=" N LEU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.919A pdb=" N ALA A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 164 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 285 through 299 Processing helix chain 'A' and resid 362 through 380 removed outlier: 3.610A pdb=" N ASN A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 405 through 433 Processing helix chain 'A' and resid 437 through 464 Processing helix chain 'A' and resid 473 through 491 Processing helix chain 'A' and resid 493 through 504 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 22 through 31 Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.555A pdb=" N GLU C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 129 through 164 Processing helix chain 'C' and resid 188 through 205 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 285 through 299 Processing helix chain 'C' and resid 363 through 380 removed outlier: 3.535A pdb=" N ASN C 378 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 379 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 395 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 405 through 433 Processing helix chain 'C' and resid 437 through 465 Processing helix chain 'C' and resid 473 through 491 Processing helix chain 'C' and resid 493 through 504 Processing helix chain 'C' and resid 531 through 537 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 22 through 33 Processing helix chain 'I' and resid 35 through 52 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 92 through 97 removed outlier: 3.880A pdb=" N LEU I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER I 97 " --> pdb=" O ILE I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 97' Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.919A pdb=" N ALA I 104 " --> pdb=" O SER I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 164 Processing helix chain 'I' and resid 188 through 205 Processing helix chain 'I' and resid 212 through 223 Processing helix chain 'I' and resid 235 through 245 Processing helix chain 'I' and resid 246 through 250 Processing helix chain 'I' and resid 285 through 299 Processing helix chain 'I' and resid 362 through 380 removed outlier: 3.609A pdb=" N ASN I 378 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP I 379 " --> pdb=" O SER I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 396 Processing helix chain 'I' and resid 405 through 433 Processing helix chain 'I' and resid 437 through 464 Processing helix chain 'I' and resid 473 through 491 Processing helix chain 'I' and resid 493 through 504 Processing helix chain 'I' and resid 531 through 537 Processing helix chain 'K' and resid 4 through 9 Processing helix chain 'K' and resid 22 through 31 Processing helix chain 'K' and resid 35 through 52 removed outlier: 3.555A pdb=" N GLU K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 Processing helix chain 'K' and resid 92 through 96 Processing helix chain 'K' and resid 101 through 115 Processing helix chain 'K' and resid 129 through 164 Processing helix chain 'K' and resid 188 through 205 Processing helix chain 'K' and resid 212 through 223 Processing helix chain 'K' and resid 235 through 245 Processing helix chain 'K' and resid 246 through 250 Processing helix chain 'K' and resid 285 through 299 Processing helix chain 'K' and resid 363 through 380 removed outlier: 3.535A pdb=" N ASN K 378 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP K 379 " --> pdb=" O SER K 375 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 395 Processing helix chain 'K' and resid 396 through 401 Processing helix chain 'K' and resid 405 through 433 Processing helix chain 'K' and resid 437 through 465 Processing helix chain 'K' and resid 473 through 491 Processing helix chain 'K' and resid 493 through 504 Processing helix chain 'K' and resid 531 through 537 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.022A pdb=" N ILE A 15 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS A 58 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY A 17 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 16 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 88 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 259 Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.303A pdb=" N THR A 319 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET A 512 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN A 523 " --> pdb=" O THR A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 328 through 337 Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.482A pdb=" N ILE C 15 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS C 58 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY C 17 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 88 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AA9, first strand: chain 'C' and resid 252 through 254 Processing sheet with id=AB1, first strand: chain 'C' and resid 257 through 259 Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.063A pdb=" N THR C 319 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET C 512 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN C 523 " --> pdb=" O THR C 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 328 through 337 Processing sheet with id=AB4, first strand: chain 'I' and resid 55 through 59 removed outlier: 6.022A pdb=" N ILE I 15 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS I 58 " --> pdb=" O ILE I 15 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY I 17 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU I 16 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE I 88 " --> pdb=" O ILE I 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 176 through 179 Processing sheet with id=AB6, first strand: chain 'I' and resid 252 through 254 Processing sheet with id=AB7, first strand: chain 'I' and resid 257 through 259 Processing sheet with id=AB8, first strand: chain 'I' and resid 318 through 320 removed outlier: 6.304A pdb=" N THR I 319 " --> pdb=" O VAL I 510 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET I 512 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN I 523 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 328 through 337 Processing sheet with id=AC1, first strand: chain 'K' and resid 55 through 59 removed outlier: 6.481A pdb=" N ILE K 15 " --> pdb=" O GLU K 56 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LYS K 58 " --> pdb=" O ILE K 15 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY K 17 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE K 88 " --> pdb=" O ILE K 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 176 through 179 Processing sheet with id=AC3, first strand: chain 'K' and resid 252 through 254 Processing sheet with id=AC4, first strand: chain 'K' and resid 257 through 259 Processing sheet with id=AC5, first strand: chain 'K' and resid 318 through 320 removed outlier: 6.063A pdb=" N THR K 319 " --> pdb=" O VAL K 510 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET K 512 " --> pdb=" O THR K 319 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN K 523 " --> pdb=" O THR K 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 328 through 337 1001 hydrogen bonds defined for protein. 2919 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 248 hydrogen bonds 496 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 184 stacking parallelities Total time for adding SS restraints: 11.91 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19067 1.03 - 1.22: 1427 1.22 - 1.42: 9862 1.42 - 1.62: 12888 1.62 - 1.81: 122 Bond restraints: 43366 Sorted by residual: bond pdb=" C6 DA O -3 " pdb=" N6 DA O -3 " ideal model delta sigma weight residual 1.335 1.237 0.098 8.00e-03 1.56e+04 1.51e+02 bond pdb=" C6 DA G -3 " pdb=" N6 DA G -3 " ideal model delta sigma weight residual 1.335 1.237 0.098 8.00e-03 1.56e+04 1.51e+02 bond pdb=" C6 DA G -5 " pdb=" N6 DA G -5 " ideal model delta sigma weight residual 1.335 1.237 0.098 8.00e-03 1.56e+04 1.49e+02 bond pdb=" C6 DA O -5 " pdb=" N6 DA O -5 " ideal model delta sigma weight residual 1.335 1.238 0.097 8.00e-03 1.56e+04 1.48e+02 bond pdb=" C4 DC P 4 " pdb=" N4 DC P 4 " ideal model delta sigma weight residual 1.335 1.237 0.098 9.00e-03 1.23e+04 1.19e+02 ... (remaining 43361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.14: 78135 7.14 - 14.28: 507 14.28 - 21.42: 2 21.42 - 28.56: 0 28.56 - 35.71: 60 Bond angle restraints: 78704 Sorted by residual: angle pdb=" CB ALA I 217 " pdb=" CA ALA I 217 " pdb=" HA ALA I 217 " ideal model delta sigma weight residual 109.00 73.29 35.71 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB ALA A 217 " pdb=" CA ALA A 217 " pdb=" HA ALA A 217 " ideal model delta sigma weight residual 109.00 73.32 35.68 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C ASP A 379 " pdb=" CA ASP A 379 " pdb=" HA ASP A 379 " ideal model delta sigma weight residual 109.00 73.52 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C ASP I 379 " pdb=" CA ASP I 379 " pdb=" HA ASP I 379 " ideal model delta sigma weight residual 109.00 73.52 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C ASN A 402 " pdb=" CA ASN A 402 " pdb=" HA ASN A 402 " ideal model delta sigma weight residual 109.00 73.57 35.43 3.00e+00 1.11e-01 1.39e+02 ... (remaining 78699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 17954 35.10 - 70.20: 1488 70.20 - 105.30: 36 105.30 - 140.41: 6 140.41 - 175.51: 16 Dihedral angle restraints: 19500 sinusoidal: 12324 harmonic: 7176 Sorted by residual: dihedral pdb=" CD1 TYR I 363 " pdb=" CG TYR I 363 " pdb=" CD2 TYR I 363 " pdb=" HD2 TYR I 363 " ideal model delta harmonic sigma weight residual -180.00 -147.72 -32.28 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CD1 TYR A 363 " pdb=" CG TYR A 363 " pdb=" CD2 TYR A 363 " pdb=" HD2 TYR A 363 " ideal model delta harmonic sigma weight residual -180.00 -147.76 -32.24 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CG TYR A 363 " pdb=" CD1 TYR A 363 " pdb=" CE1 TYR A 363 " pdb=" HE1 TYR A 363 " ideal model delta harmonic sigma weight residual 180.00 -147.89 -32.11 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 19497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 3169 0.146 - 0.291: 130 0.291 - 0.437: 72 0.437 - 0.583: 140 0.583 - 0.728: 41 Chirality restraints: 3552 Sorted by residual: chirality pdb=" CG LEU K 19 " pdb=" CB LEU K 19 " pdb=" CD1 LEU K 19 " pdb=" CD2 LEU K 19 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CG LEU C 19 " pdb=" CB LEU C 19 " pdb=" CD1 LEU C 19 " pdb=" CD2 LEU C 19 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CB ILE C 61 " pdb=" CA ILE C 61 " pdb=" CG1 ILE C 61 " pdb=" CG2 ILE C 61 " both_signs ideal model delta sigma weight residual False 2.64 1.92 0.72 2.00e-01 2.50e+01 1.31e+01 ... (remaining 3549 not shown) Planarity restraints: 5510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT O -2 " -0.195 2.00e-02 2.50e+03 1.15e-01 3.99e+02 pdb=" N1 DT O -2 " 0.046 2.00e-02 2.50e+03 pdb=" C2 DT O -2 " 0.040 2.00e-02 2.50e+03 pdb=" O2 DT O -2 " -0.065 2.00e-02 2.50e+03 pdb=" N3 DT O -2 " 0.044 2.00e-02 2.50e+03 pdb=" C4 DT O -2 " -0.061 2.00e-02 2.50e+03 pdb=" O4 DT O -2 " -0.218 2.00e-02 2.50e+03 pdb=" C5 DT O -2 " 0.014 2.00e-02 2.50e+03 pdb=" C7 DT O -2 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT O -2 " 0.075 2.00e-02 2.50e+03 pdb=" H3 DT O -2 " 0.209 2.00e-02 2.50e+03 pdb=" H6 DT O -2 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 363 " -0.010 2.00e-02 2.50e+03 1.05e-01 3.33e+02 pdb=" CG TYR A 363 " -0.203 2.00e-02 2.50e+03 pdb=" CD1 TYR A 363 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 TYR A 363 " -0.083 2.00e-02 2.50e+03 pdb=" CE1 TYR A 363 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 363 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR A 363 " -0.083 2.00e-02 2.50e+03 pdb=" OH TYR A 363 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TYR A 363 " 0.116 2.00e-02 2.50e+03 pdb=" HD2 TYR A 363 " 0.122 2.00e-02 2.50e+03 pdb=" HE1 TYR A 363 " -0.132 2.00e-02 2.50e+03 pdb=" HE2 TYR A 363 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 363 " -0.010 2.00e-02 2.50e+03 1.05e-01 3.33e+02 pdb=" CG TYR I 363 " -0.202 2.00e-02 2.50e+03 pdb=" CD1 TYR I 363 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 TYR I 363 " -0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR I 363 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR I 363 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR I 363 " -0.083 2.00e-02 2.50e+03 pdb=" OH TYR I 363 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TYR I 363 " 0.116 2.00e-02 2.50e+03 pdb=" HD2 TYR I 363 " 0.123 2.00e-02 2.50e+03 pdb=" HE1 TYR I 363 " -0.132 2.00e-02 2.50e+03 pdb=" HE2 TYR I 363 " 0.036 2.00e-02 2.50e+03 ... (remaining 5507 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.98: 869 1.98 - 2.64: 54196 2.64 - 3.29: 134385 3.29 - 3.95: 168904 3.95 - 4.60: 260507 Nonbonded interactions: 618861 Sorted by model distance: nonbonded pdb=" OG SER A 22 " pdb=" P DA F 2 " model vdw 1.330 3.200 nonbonded pdb=" OG SER I 22 " pdb=" P DA N 2 " model vdw 1.331 3.200 nonbonded pdb=" O LEU C 243 " pdb="HE22 GLN C 293 " model vdw 1.447 2.450 nonbonded pdb=" O LEU K 243 " pdb="HE22 GLN K 293 " model vdw 1.447 2.450 nonbonded pdb=" H ALA K 215 " pdb=" OP2 DT O -14 " model vdw 1.449 2.450 ... (remaining 618856 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'I' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'P' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.250 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: 0.260 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 58.820 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 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 : 0.016 0.144 23032 Z= 1.029 Angle : 1.513 15.651 31990 Z= 1.094 Chirality : 0.149 0.728 3552 Planarity : 0.014 0.190 3300 Dihedral : 21.344 175.507 9632 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.58 % Favored : 94.04 % Rotamer: Outliers : 3.01 % Allowed : 5.92 % Favored : 91.07 % Cbeta Deviations : 3.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2132 helix: 0.28 (0.14), residues: 1132 sheet: -1.04 (0.27), residues: 328 loop : -1.04 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.005 ARG K 151 TYR 0.162 0.012 TYR A 363 PHE 0.108 0.006 PHE K 199 TRP 0.040 0.008 TRP C 167 HIS 0.013 0.004 HIS K 489 Details of bonding type rmsd/Z covalent geometry : bond 0.01586 / 1.03 (23016) covalent geometry : angle 1.49442 / 1.09 (31966) hydrogen bonds : bond 0.11508 / 7.82 ( 1249) hydrogen bonds : angle 5.54417 / 3.86 ( 3415) metal coordination : bond 0.00812 / 0.46 ( 16) metal coordination : angle 8.83825 / 5.57 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.4852 (ttmt) cc_final: 0.4373 (ptpp) REVERT: A 23 ARG cc_start: 0.3768 (OUTLIER) cc_final: 0.2806 (ptp-110) REVERT: A 46 LYS cc_start: 0.9341 (tttt) cc_final: 0.9111 (tmmt) REVERT: A 109 ASN cc_start: 0.8818 (m-40) cc_final: 0.8595 (m-40) REVERT: A 115 ARG cc_start: 0.8333 (mtt180) cc_final: 0.8033 (mpt180) REVERT: A 129 ASN cc_start: 0.8074 (t0) cc_final: 0.7218 (t0) REVERT: A 140 LEU cc_start: 0.8801 (mt) cc_final: 0.8590 (mt) REVERT: A 144 ARG cc_start: 0.8196 (tpt170) cc_final: 0.7994 (ttm-80) REVERT: A 158 LYS cc_start: 0.8577 (mttt) cc_final: 0.8078 (mttt) REVERT: A 161 TYR cc_start: 0.8515 (m-10) cc_final: 0.8258 (m-10) REVERT: A 197 LEU cc_start: 0.8024 (tp) cc_final: 0.7814 (tt) REVERT: A 232 LYS cc_start: 0.8634 (mttt) cc_final: 0.8129 (tppt) REVERT: A 277 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7642 (mm-40) REVERT: A 360 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5629 (t80) REVERT: A 382 ASP cc_start: 0.7114 (m-30) cc_final: 0.6762 (t0) REVERT: A 430 LYS cc_start: 0.7387 (mmtt) cc_final: 0.7027 (mmmt) REVERT: A 450 GLU cc_start: 0.7927 (tt0) cc_final: 0.7717 (tp30) REVERT: A 498 ASN cc_start: 0.7533 (t0) cc_final: 0.7056 (t0) outliers start: 12 outliers final: 5 residues processed: 157 average time/residue: 0.2150 time to fit residues: 40.4279 Evaluate side-chains 130 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.218 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.023 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0198 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0151 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0119 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0114 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 50.0000 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 GLN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN A 514 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.187274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.155669 restraints weight = 37221.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.162891 restraints weight = 21005.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.168019 restraints weight = 13317.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.171696 restraints weight = 9091.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.174353 restraints weight = 6593.144| |-----------------------------------------------------------------------------| r_work (final): 0.4480 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.205656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.161266 restraints weight = 9680.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.160500 restraints weight = 6535.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.160234 restraints weight = 6220.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.160918 restraints weight = 5847.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.160190 restraints weight = 5589.690| |-----------------------------------------------------------------------------| r_work (final): 0.4188 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.203157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.168213 restraints weight = 10221.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.169272 restraints weight = 4077.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.169622 restraints weight = 3151.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.169622 restraints weight = 2959.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.169622 restraints weight = 2959.665| |-----------------------------------------------------------------------------| r_work (final): 0.4308 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.186234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.174916 restraints weight = 7995.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.176067 restraints weight = 3693.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.176555 restraints weight = 2459.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.176684 restraints weight = 2143.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.176693 restraints weight = 2040.768| |-----------------------------------------------------------------------------| r_work (final): 0.4519 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.221180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.212187 restraints weight = 8262.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.213884 restraints weight = 5089.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.214848 restraints weight = 3919.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.215615 restraints weight = 3327.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.215614 restraints weight = 2836.208| |-----------------------------------------------------------------------------| r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4364 moved from start: 10.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.519 23032 Z= 1.928 Angle : 3.354 61.753 31990 Z= 1.815 Chirality : 0.177 1.833 3552 Planarity : 0.023 0.212 3300 Dihedral : 26.812 176.635 4984 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 202.29 Ramachandran Plot: Outliers : 4.13 % Allowed : 12.57 % Favored : 83.30 % Rotamer: Outliers : 5.71 % Allowed : 7.96 % Favored : 86.33 % Cbeta Deviations : 6.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 4.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.17), residues: 2132 helix: -0.93 (0.15), residues: 1116 sheet: -2.00 (0.36), residues: 164 loop : -3.99 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.005 ARG A 28 TYR 0.131 0.013 TYR I 10 PHE 0.075 0.007 PHE I 289 TRP 0.032 0.009 TRP K 167 HIS 0.049 0.009 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.04697 / 1.93 (23016) covalent geometry : angle 3.31186 / 1.81 (31966) hydrogen bonds : bond 0.29927 / 20.58 ( 1249) hydrogen bonds : angle 9.76935 / 7.05 ( 3415) metal coordination : bond 0.03315 / 2.20 ( 16) metal coordination : angle 19.66146 / 11.25 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 39 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7592 (mp0) REVERT: I 124 VAL cc_start: 0.8209 (OUTLIER) cc_final: 0.7919 (m) REVERT: I 141 PHE cc_start: 0.8503 (t80) cc_final: 0.8282 (t80) REVERT: I 158 LYS cc_start: 0.8885 (mttt) cc_final: 0.8311 (mttm) REVERT: I 166 LYS cc_start: 0.4864 (OUTLIER) cc_final: 0.4645 (mttt) REVERT: I 178 LEU cc_start: 0.8080 (tp) cc_final: 0.7818 (tt) REVERT: I 183 SER cc_start: 0.4432 (m) cc_final: 0.4150 (m) REVERT: I 184 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7005 (ttmm) REVERT: I 202 PHE cc_start: 0.8584 (t80) cc_final: 0.8073 (t80) REVERT: I 388 HIS cc_start: 0.8830 (t-90) cc_final: 0.8589 (t-90) REVERT: I 431 TYR cc_start: 0.4478 (t80) cc_final: 0.3449 (t80) REVERT: I 503 MET cc_start: 0.7471 (ttm) cc_final: 0.7118 (ttm) outliers start: 28 outliers final: 16 residues processed: 151 average time/residue: 0.2099 time to fit residues: 38.0830 Evaluate side-chains 120 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.250 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0149 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0145 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0123 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0120 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 43 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 0.0770 chunk 179 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 514 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.187629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.158262 restraints weight = 38120.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.165027 restraints weight = 22079.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.169900 restraints weight = 14151.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.173383 restraints weight = 9673.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.175816 restraints weight = 6996.364| |-----------------------------------------------------------------------------| r_work (final): 0.4519 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.202861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.154346 restraints weight = 9922.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.153035 restraints weight = 7491.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.155964 restraints weight = 6756.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.152104 restraints weight = 6964.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.152497 restraints weight = 5627.417| |-----------------------------------------------------------------------------| r_work (final): 0.4134 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.205776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.172381 restraints weight = 10243.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.173485 restraints weight = 4300.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.173885 restraints weight = 3277.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.173901 restraints weight = 3038.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.173901 restraints weight = 3020.215| |-----------------------------------------------------------------------------| r_work (final): 0.4383 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.189561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.180948 restraints weight = 7148.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.182051 restraints weight = 3307.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.182258 restraints weight = 2392.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.182258 restraints weight = 2245.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.182258 restraints weight = 2245.247| |-----------------------------------------------------------------------------| r_work (final): 0.4590 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.225071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.215475 restraints weight = 8155.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.217095 restraints weight = 5846.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.217454 restraints weight = 4763.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.218102 restraints weight = 4338.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.218229 restraints weight = 3940.077| |-----------------------------------------------------------------------------| r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4385 moved from start: 10.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.748 23032 Z= 1.305 Angle : 2.650 50.779 31990 Z= 1.457 Chirality : 0.130 1.397 3552 Planarity : 0.019 0.191 3300 Dihedral : 26.936 175.095 4984 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 162.97 Ramachandran Plot: Outliers : 2.63 % Allowed : 13.88 % Favored : 83.49 % Rotamer: Outliers : 3.88 % Allowed : 7.14 % Favored : 88.98 % Cbeta Deviations : 3.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.17), residues: 2132 helix: -0.83 (0.16), residues: 1088 sheet: -2.12 (0.40), residues: 148 loop : -4.17 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.003 ARG A 115 TYR 0.091 0.009 TYR A 10 PHE 0.054 0.004 PHE I 138 TRP 0.049 0.013 TRP I 167 HIS 0.041 0.006 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02785 / 1.31 (23016) covalent geometry : angle 2.62299 / 1.46 (31966) hydrogen bonds : bond 0.26703 / 18.59 ( 1249) hydrogen bonds : angle 9.43425 / 6.78 ( 3415) metal coordination : bond 0.01332 / 0.79 ( 16) metal coordination : angle 14.04314 / 7.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 39 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8106 (pt0) REVERT: I 151 ARG cc_start: 0.8457 (mmp-170) cc_final: 0.8242 (tpt-90) REVERT: I 158 LYS cc_start: 0.8900 (mttt) cc_final: 0.8272 (tptt) REVERT: I 178 LEU cc_start: 0.7397 (tp) cc_final: 0.7172 (tt) REVERT: I 288 GLN cc_start: 0.8408 (mt0) cc_final: 0.8183 (mt0) REVERT: I 444 ARG cc_start: 0.6813 (mmm160) cc_final: 0.6522 (mmm160) REVERT: I 486 ASP cc_start: 0.8451 (m-30) cc_final: 0.8244 (m-30) REVERT: I 503 MET cc_start: 0.7553 (ttm) cc_final: 0.7241 (ttm) REVERT: I 531 ARG cc_start: 0.6424 (ttp80) cc_final: 0.6167 (ttt-90) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.1983 time to fit residues: 31.5693 Evaluate side-chains 118 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.245 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0160 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0156 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0074 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0113 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 226 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 86 optimal weight: 30.0000 chunk 140 optimal weight: 0.9990 chunk 180 optimal weight: 0.0770 chunk 179 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 195 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 203 optimal weight: 0.2980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.193635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.159112 restraints weight = 39314.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.167085 restraints weight = 24470.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.172826 restraints weight = 16444.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.176916 restraints weight = 11638.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.179971 restraints weight = 8613.118| |-----------------------------------------------------------------------------| r_work (final): 0.4526 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.203939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.159057 restraints weight = 9318.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.158106 restraints weight = 6806.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.155516 restraints weight = 6114.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.155621 restraints weight = 5258.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.155655 restraints weight = 4627.716| |-----------------------------------------------------------------------------| r_work (final): 0.4170 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.208341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.174605 restraints weight = 10250.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.175823 restraints weight = 5031.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.177738 restraints weight = 3719.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.177776 restraints weight = 3338.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.177975 restraints weight = 3274.625| |-----------------------------------------------------------------------------| r_work (final): 0.4431 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.195048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.185871 restraints weight = 9078.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.187612 restraints weight = 3633.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.188554 restraints weight = 2381.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.188562 restraints weight = 1925.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.188562 restraints weight = 1904.328| |-----------------------------------------------------------------------------| r_work (final): 0.4640 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.228960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.218352 restraints weight = 7952.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.220300 restraints weight = 5449.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.221416 restraints weight = 4393.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.221427 restraints weight = 3825.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.221426 restraints weight = 3811.996| |-----------------------------------------------------------------------------| r_work (final): 0.4792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4315 moved from start: 10.8768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.667 23032 Z= 1.136 Angle : 2.314 32.559 31990 Z= 1.281 Chirality : 0.119 1.019 3552 Planarity : 0.020 0.325 3300 Dihedral : 27.023 174.515 4984 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 133.71 Ramachandran Plot: Outliers : 2.81 % Allowed : 15.38 % Favored : 81.80 % Rotamer: Outliers : 3.47 % Allowed : 9.18 % Favored : 87.35 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 4.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.18), residues: 2132 helix: -0.87 (0.15), residues: 1124 sheet: -2.03 (0.41), residues: 148 loop : -4.30 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG I 115 TYR 0.093 0.008 TYR I 10 PHE 0.049 0.004 PHE I 138 TRP 0.032 0.007 TRP K 167 HIS 0.041 0.005 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02324 / 1.14 (23016) covalent geometry : angle 2.27539 / 1.28 (31966) hydrogen bonds : bond 0.25663 / 17.79 ( 1249) hydrogen bonds : angle 9.60425 / 6.90 ( 3415) metal coordination : bond 0.01374 / 0.73 ( 16) metal coordination : angle 15.44750 / 8.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 133 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7716 (tmm) REVERT: I 142 MET cc_start: 0.9125 (ttp) cc_final: 0.8922 (tmm) REVERT: I 151 ARG cc_start: 0.8123 (mmp-170) cc_final: 0.7878 (tpt170) REVERT: I 158 LYS cc_start: 0.8980 (mttt) cc_final: 0.8408 (tptt) REVERT: I 444 ARG cc_start: 0.6825 (mmm160) cc_final: 0.6515 (mmm160) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.2302 time to fit residues: 33.5703 Evaluate side-chains 108 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.250 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0156 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0150 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0118 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0113 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 74 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 149 optimal weight: 0.0770 chunk 206 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 179 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.194428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.163033 restraints weight = 37146.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.170052 restraints weight = 22554.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.175381 restraints weight = 15115.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.179305 restraints weight = 10695.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.182270 restraints weight = 7904.120| |-----------------------------------------------------------------------------| r_work (final): 0.4555 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.203410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.160546 restraints weight = 9667.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.158886 restraints weight = 7306.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.159478 restraints weight = 7325.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.157946 restraints weight = 5426.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.157946 restraints weight = 4992.715| |-----------------------------------------------------------------------------| r_work (final): 0.4170 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.210488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.178493 restraints weight = 10822.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.179691 restraints weight = 4709.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.180020 restraints weight = 3574.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.180020 restraints weight = 3381.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.180020 restraints weight = 3381.753| |-----------------------------------------------------------------------------| r_work (final): 0.4457 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.197888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.188119 restraints weight = 9574.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.189990 restraints weight = 3929.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.190992 restraints weight = 2514.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.191371 restraints weight = 2016.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.191406 restraints weight = 1814.014| |-----------------------------------------------------------------------------| r_work (final): 0.4674 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.230082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.219830 restraints weight = 8261.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.221589 restraints weight = 5740.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.222535 restraints weight = 4625.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.223339 restraints weight = 4049.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.223595 restraints weight = 3628.309| |-----------------------------------------------------------------------------| r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4221 moved from start: 10.9200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.678 23032 Z= 1.092 Angle : 2.114 32.449 31990 Z= 1.183 Chirality : 0.115 1.062 3552 Planarity : 0.016 0.209 3300 Dihedral : 26.904 174.350 4984 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 126.89 Ramachandran Plot: Outliers : 1.31 % Allowed : 16.32 % Favored : 82.36 % Rotamer: Outliers : 0.41 % Allowed : 5.92 % Favored : 93.67 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.17), residues: 2132 helix: -0.72 (0.15), residues: 1124 sheet: -1.98 (0.42), residues: 148 loop : -4.16 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG I 257 TYR 0.083 0.008 TYR I 10 PHE 0.038 0.004 PHE A 138 TRP 0.031 0.008 TRP I 167 HIS 0.015 0.002 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02208 / 1.09 (23016) covalent geometry : angle 2.07586 / 1.18 (31966) hydrogen bonds : bond 0.25002 / 17.27 ( 1249) hydrogen bonds : angle 9.48246 / 6.85 ( 3415) metal coordination : bond 0.01437 / 0.78 ( 16) metal coordination : angle 14.73610 / 8.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.8627 (tptp) cc_final: 0.8155 (tppt) REVERT: I 141 PHE cc_start: 0.7759 (t80) cc_final: 0.7504 (t80) REVERT: I 142 MET cc_start: 0.9063 (ttp) cc_final: 0.8767 (tmm) REVERT: I 151 ARG cc_start: 0.8085 (mmp-170) cc_final: 0.7867 (tpt170) REVERT: I 158 LYS cc_start: 0.8901 (mttt) cc_final: 0.8575 (tptt) REVERT: I 244 GLN cc_start: 0.8406 (pp30) cc_final: 0.7961 (pt0) REVERT: I 367 GLU cc_start: 0.8530 (tt0) cc_final: 0.8204 (tt0) REVERT: I 392 MET cc_start: 0.4691 (tpp) cc_final: 0.4281 (tpp) REVERT: I 444 ARG cc_start: 0.6804 (mmm160) cc_final: 0.6355 (mmm160) REVERT: I 486 ASP cc_start: 0.8217 (m-30) cc_final: 0.7965 (m-30) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 0.2277 time to fit residues: 27.3802 Evaluate side-chains 91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.228 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0152 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0147 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0116 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0114 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 131 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 218 optimal weight: 0.0270 chunk 172 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.197373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.162048 restraints weight = 38350.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.170214 restraints weight = 24331.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.176411 restraints weight = 16471.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.180898 restraints weight = 11649.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.184124 restraints weight = 8501.512| |-----------------------------------------------------------------------------| r_work (final): 0.4565 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.203217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.156550 restraints weight = 8907.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.159413 restraints weight = 4228.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.160277 restraints weight = 3295.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.160277 restraints weight = 3072.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.160277 restraints weight = 3072.053| |-----------------------------------------------------------------------------| r_work (final): 0.4231 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.211564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.188676 restraints weight = 10825.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.187832 restraints weight = 10370.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.187486 restraints weight = 6712.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.187983 restraints weight = 5155.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.187693 restraints weight = 4978.179| |-----------------------------------------------------------------------------| r_work (final): 0.4478 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.192890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.183550 restraints weight = 4095.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.185199 restraints weight = 1747.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.186544 restraints weight = 1067.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.187579 restraints weight = 743.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.188226 restraints weight = 474.332| |-----------------------------------------------------------------------------| r_work (final): 0.4742 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.231174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.219429 restraints weight = 8356.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.220639 restraints weight = 6213.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.222028 restraints weight = 5331.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.222236 restraints weight = 4686.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.222738 restraints weight = 4454.632| |-----------------------------------------------------------------------------| r_work (final): 0.4805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4178 moved from start: 10.9657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.700 23032 Z= 1.047 Angle : 1.983 31.200 31990 Z= 1.122 Chirality : 0.108 1.025 3552 Planarity : 0.016 0.249 3300 Dihedral : 26.837 174.129 4984 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 114.47 Ramachandran Plot: Outliers : 1.88 % Allowed : 15.57 % Favored : 82.55 % Rotamer: Outliers : 0.61 % Allowed : 5.10 % Favored : 94.29 % Cbeta Deviations : 2.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.17), residues: 2132 helix: -0.59 (0.15), residues: 1120 sheet: -1.97 (0.44), residues: 128 loop : -4.15 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 531 TYR 0.078 0.008 TYR I 10 PHE 0.029 0.004 PHE C 138 TRP 0.026 0.006 TRP C 167 HIS 0.016 0.002 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02099 / 1.05 (23016) covalent geometry : angle 1.94944 / 1.12 (31966) hydrogen bonds : bond 0.24303 / 16.81 ( 1249) hydrogen bonds : angle 9.04405 / 6.54 ( 3415) metal coordination : bond 0.01755 / 1.01 ( 16) metal coordination : angle 13.42214 / 7.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.8490 (tptp) cc_final: 0.7802 (tptp) REVERT: I 109 ASN cc_start: 0.8205 (m-40) cc_final: 0.7868 (m-40) REVERT: I 142 MET cc_start: 0.8947 (ttp) cc_final: 0.8647 (tmm) REVERT: I 151 ARG cc_start: 0.8036 (mmp-170) cc_final: 0.7756 (tpt170) REVERT: I 158 LYS cc_start: 0.8887 (mttt) cc_final: 0.8649 (tptt) REVERT: I 367 GLU cc_start: 0.8490 (tt0) cc_final: 0.8203 (tt0) REVERT: I 392 MET cc_start: 0.4935 (tpp) cc_final: 0.4478 (tpp) REVERT: I 444 ARG cc_start: 0.7002 (mmm160) cc_final: 0.6546 (mmm160) outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 0.2077 time to fit residues: 24.5361 Evaluate side-chains 86 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.240 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0150 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0155 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0071 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0112 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 227 optimal weight: 5.9990 chunk 135 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 75 optimal weight: 0.0970 chunk 184 optimal weight: 0.0770 chunk 203 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 402 ASN I 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.210011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.176909 restraints weight = 37098.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.184056 restraints weight = 23305.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.189462 restraints weight = 16043.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.193451 restraints weight = 11568.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.196318 restraints weight = 8734.511| |-----------------------------------------------------------------------------| r_work (final): 0.4618 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.204748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.160383 restraints weight = 8893.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.166896 restraints weight = 4128.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.167644 restraints weight = 2958.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.167643 restraints weight = 2712.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.167643 restraints weight = 2712.594| |-----------------------------------------------------------------------------| r_work (final): 0.4258 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.212363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.189750 restraints weight = 10390.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.187330 restraints weight = 9729.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.187987 restraints weight = 5704.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.187940 restraints weight = 3953.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.187972 restraints weight = 4119.801| |-----------------------------------------------------------------------------| r_work (final): 0.4508 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.200830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.190852 restraints weight = 9165.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.192893 restraints weight = 3940.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.194131 restraints weight = 2364.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.194400 restraints weight = 1756.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.194400 restraints weight = 1635.047| |-----------------------------------------------------------------------------| r_work (final): 0.4703 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.231443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.220504 restraints weight = 8448.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.222521 restraints weight = 5922.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.224120 restraints weight = 4537.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.224885 restraints weight = 3720.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.225266 restraints weight = 3267.403| |-----------------------------------------------------------------------------| r_work (final): 0.4842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4077 moved from start: 11.0136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.687 23032 Z= 1.025 Angle : 1.881 31.591 31990 Z= 1.068 Chirality : 0.107 1.144 3552 Planarity : 0.013 0.131 3300 Dihedral : 26.911 173.860 4984 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 104.09 Ramachandran Plot: Outliers : 1.50 % Allowed : 15.38 % Favored : 83.11 % Rotamer: Outliers : 0.20 % Allowed : 4.90 % Favored : 94.90 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.18), residues: 2132 helix: -0.74 (0.15), residues: 1148 sheet: -2.15 (0.41), residues: 148 loop : -4.18 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG K 98 TYR 0.068 0.008 TYR I 10 PHE 0.043 0.004 PHE C 309 TRP 0.016 0.004 TRP K 167 HIS 0.050 0.006 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02037 / 1.03 (23016) covalent geometry : angle 1.85283 / 1.07 (31966) hydrogen bonds : bond 0.22511 / 15.55 ( 1249) hydrogen bonds : angle 8.78373 / 6.34 ( 3415) metal coordination : bond 0.01323 / 0.77 ( 16) metal coordination : angle 11.93394 / 6.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.8391 (tptp) cc_final: 0.7612 (tptp) REVERT: I 109 ASN cc_start: 0.8213 (m-40) cc_final: 0.7830 (m110) REVERT: I 133 MET cc_start: 0.7502 (tmm) cc_final: 0.6946 (tmm) REVERT: I 151 ARG cc_start: 0.7948 (mmp-170) cc_final: 0.7597 (tpt170) REVERT: I 158 LYS cc_start: 0.8852 (mttt) cc_final: 0.8580 (tptt) REVERT: I 367 GLU cc_start: 0.8515 (tt0) cc_final: 0.8279 (tt0) REVERT: I 444 ARG cc_start: 0.6583 (mmm160) cc_final: 0.6139 (mmm160) REVERT: I 484 ILE cc_start: 0.8538 (mm) cc_final: 0.8285 (mm) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.2159 time to fit residues: 23.0582 Evaluate side-chains 85 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.242 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0156 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0161 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0118 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0108 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 46 optimal weight: 0.1980 chunk 202 optimal weight: 50.0000 chunk 87 optimal weight: 0.4980 chunk 172 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 61 optimal weight: 0.0060 chunk 29 optimal weight: 0.2980 chunk 210 optimal weight: 20.0000 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.211474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.177147 restraints weight = 36771.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.184734 restraints weight = 22458.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.190582 restraints weight = 15191.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.194896 restraints weight = 10922.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.198028 restraints weight = 8113.383| |-----------------------------------------------------------------------------| r_work (final): 0.4633 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.204487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.156282 restraints weight = 8665.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.161763 restraints weight = 4139.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.163777 restraints weight = 3108.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.164272 restraints weight = 2783.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.164272 restraints weight = 2652.447| |-----------------------------------------------------------------------------| r_work (final): 0.4259 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.214052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.181723 restraints weight = 10400.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.182881 restraints weight = 4698.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.183137 restraints weight = 3731.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.183137 restraints weight = 3551.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.183137 restraints weight = 3551.359| |-----------------------------------------------------------------------------| r_work (final): 0.4485 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.201208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.191258 restraints weight = 9158.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.193201 restraints weight = 3815.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.194181 restraints weight = 2249.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.194405 restraints weight = 1760.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.194405 restraints weight = 1654.265| |-----------------------------------------------------------------------------| r_work (final): 0.4704 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.232498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.221591 restraints weight = 7715.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.223828 restraints weight = 5139.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.225340 restraints weight = 3865.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.226414 restraints weight = 3141.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.226804 restraints weight = 2649.454| |-----------------------------------------------------------------------------| r_work (final): 0.4851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4076 moved from start: 11.0467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.683 23032 Z= 0.999 Angle : 1.802 32.007 31990 Z= 1.034 Chirality : 0.101 1.001 3552 Planarity : 0.013 0.144 3300 Dihedral : 26.917 173.859 4984 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 99.22 Ramachandran Plot: Outliers : 1.31 % Allowed : 15.95 % Favored : 82.74 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 1.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.18), residues: 2132 helix: -0.62 (0.16), residues: 1136 sheet: -2.12 (0.42), residues: 148 loop : -4.09 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG I 137 TYR 0.060 0.006 TYR I 10 PHE 0.028 0.003 PHE I 289 TRP 0.016 0.003 TRP I 167 HIS 0.041 0.005 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01976 / 1.00 (23016) covalent geometry : angle 1.77220 / 1.03 (31966) hydrogen bonds : bond 0.21753 / 15.01 ( 1249) hydrogen bonds : angle 8.64867 / 6.27 ( 3415) metal coordination : bond 0.01393 / 0.77 ( 16) metal coordination : angle 12.05365 / 6.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.251 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: I 74 LYS cc_start: 0.8361 (tptp) cc_final: 0.7716 (tptp) REVERT: I 109 ASN cc_start: 0.8278 (m-40) cc_final: 0.7877 (m-40) REVERT: I 151 ARG cc_start: 0.7813 (mmp-170) cc_final: 0.7493 (mmp80) REVERT: I 158 LYS cc_start: 0.9012 (mttt) cc_final: 0.8611 (tptt) REVERT: I 233 ARG cc_start: 0.7773 (ttt-90) cc_final: 0.7468 (ptm-80) REVERT: I 367 GLU cc_start: 0.8635 (tt0) cc_final: 0.8329 (tt0) REVERT: I 392 MET cc_start: 0.4308 (tpt) cc_final: 0.3835 (tpp) REVERT: I 444 ARG cc_start: 0.6518 (mmm160) cc_final: 0.6039 (mmm160) REVERT: I 484 ILE cc_start: 0.8498 (mm) cc_final: 0.8227 (mm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2327 time to fit residues: 24.9751 Evaluate side-chains 87 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.252 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0196 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0159 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0126 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0120 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 219 optimal weight: 0.6980 chunk 180 optimal weight: 0.0370 chunk 93 optimal weight: 50.0000 chunk 197 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 203 optimal weight: 0.0870 chunk 229 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.207151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.174101 restraints weight = 36587.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.181583 restraints weight = 22528.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.187279 restraints weight = 15218.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.191347 restraints weight = 10867.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.194524 restraints weight = 8115.900| |-----------------------------------------------------------------------------| r_work (final): 0.4686 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.205152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.155576 restraints weight = 9111.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.160570 restraints weight = 4484.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.162503 restraints weight = 3341.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.162504 restraints weight = 3043.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.162504 restraints weight = 3042.945| |-----------------------------------------------------------------------------| r_work (final): 0.4272 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.214371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.182313 restraints weight = 10812.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.183464 restraints weight = 4795.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.183589 restraints weight = 3648.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.183589 restraints weight = 3530.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.183589 restraints weight = 3530.602| |-----------------------------------------------------------------------------| r_work (final): 0.4489 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.200536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.190185 restraints weight = 9819.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.192240 restraints weight = 4141.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.193181 restraints weight = 2359.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.193414 restraints weight = 1806.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.193414 restraints weight = 1703.051| |-----------------------------------------------------------------------------| r_work (final): 0.4686 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.231453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.220581 restraints weight = 8379.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.222973 restraints weight = 5638.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.224590 restraints weight = 4130.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.225419 restraints weight = 3202.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.225707 restraints weight = 2713.890| |-----------------------------------------------------------------------------| r_work (final): 0.4853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4028 moved from start: 11.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.633 23032 Z= 1.002 Angle : 1.782 31.446 31990 Z= 1.029 Chirality : 0.099 0.896 3552 Planarity : 0.011 0.121 3300 Dihedral : 26.924 174.301 4984 Min Nonbonded Distance : 1.458 Molprobity Statistics. All-atom Clashscore : 98.80 Ramachandran Plot: Outliers : 1.69 % Allowed : 15.38 % Favored : 82.93 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 1.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.18), residues: 2132 helix: -0.66 (0.16), residues: 1132 sheet: -2.03 (0.42), residues: 148 loop : -4.09 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 137 TYR 0.070 0.006 TYR I 10 PHE 0.019 0.003 PHE K 73 TRP 0.013 0.004 TRP K 167 HIS 0.037 0.004 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01990 / 1.00 (23016) covalent geometry : angle 1.75356 / 1.03 (31966) hydrogen bonds : bond 0.20660 / 14.23 ( 1249) hydrogen bonds : angle 8.58164 / 6.21 ( 3415) metal coordination : bond 0.01410 / 0.78 ( 16) metal coordination : angle 11.74629 / 6.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.8285 (tptp) cc_final: 0.7801 (tptp) REVERT: I 109 ASN cc_start: 0.8260 (m-40) cc_final: 0.7868 (m-40) REVERT: I 137 ARG cc_start: 0.6829 (ttp-110) cc_final: 0.5841 (tmt170) REVERT: I 151 ARG cc_start: 0.7719 (mmp-170) cc_final: 0.7316 (mmp80) REVERT: I 158 LYS cc_start: 0.9160 (mttt) cc_final: 0.8630 (tptp) REVERT: I 367 GLU cc_start: 0.8655 (tt0) cc_final: 0.8371 (tt0) REVERT: I 392 MET cc_start: 0.4150 (tpt) cc_final: 0.3596 (tpp) REVERT: I 444 ARG cc_start: 0.6562 (mmm160) cc_final: 0.6094 (mmm160) REVERT: I 503 MET cc_start: 0.7812 (ttm) cc_final: 0.7138 (ttm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2088 time to fit residues: 22.6170 Evaluate side-chains 89 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.278 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0203 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0157 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0079 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0115 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 171 optimal weight: 0.6980 chunk 219 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 194 optimal weight: 0.8980 chunk 175 optimal weight: 0.5980 chunk 155 optimal weight: 0.1980 chunk 94 optimal weight: 50.0000 chunk 123 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.210167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.176516 restraints weight = 36314.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.184396 restraints weight = 22246.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.190181 restraints weight = 14920.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.194206 restraints weight = 10613.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.197150 restraints weight = 7901.422| |-----------------------------------------------------------------------------| r_work (final): 0.4672 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.204832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.155547 restraints weight = 8885.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.162043 restraints weight = 4224.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.165793 restraints weight = 3076.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.166780 restraints weight = 2654.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.166791 restraints weight = 2503.861| |-----------------------------------------------------------------------------| r_work (final): 0.4255 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.215691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.183385 restraints weight = 11049.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.184535 restraints weight = 4787.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.185167 restraints weight = 3701.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.185167 restraints weight = 3508.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.185167 restraints weight = 3508.508| |-----------------------------------------------------------------------------| r_work (final): 0.4485 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.200616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.189998 restraints weight = 9908.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.191848 restraints weight = 4342.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.192771 restraints weight = 2523.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.192954 restraints weight = 1974.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.192985 restraints weight = 1742.636| |-----------------------------------------------------------------------------| r_work (final): 0.4675 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.230473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.220219 restraints weight = 7808.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.222553 restraints weight = 5107.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.224102 restraints weight = 3685.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.225026 restraints weight = 2858.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.225596 restraints weight = 2385.683| |-----------------------------------------------------------------------------| r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4044 moved from start: 11.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.647 23032 Z= 0.989 Angle : 1.729 32.046 31990 Z= 1.001 Chirality : 0.095 0.988 3552 Planarity : 0.012 0.123 3300 Dihedral : 26.762 174.672 4984 Min Nonbonded Distance : 1.464 Molprobity Statistics. All-atom Clashscore : 96.31 Ramachandran Plot: Outliers : 1.88 % Allowed : 17.07 % Favored : 81.05 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 1.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 2.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.18), residues: 2132 helix: -0.53 (0.16), residues: 1096 sheet: -1.86 (0.48), residues: 112 loop : -3.83 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG A 128 TYR 0.104 0.008 TYR C 237 PHE 0.052 0.004 PHE A 199 TRP 0.013 0.004 TRP A 167 HIS 0.033 0.004 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01973 / 0.99 (23016) covalent geometry : angle 1.69970 / 1.00 (31966) hydrogen bonds : bond 0.20236 / 13.88 ( 1249) hydrogen bonds : angle 8.47410 / 6.12 ( 3415) metal coordination : bond 0.01477 / 0.81 ( 16) metal coordination : angle 11.70468 / 6.62 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.8226 (tptp) cc_final: 0.7719 (tptp) REVERT: I 107 ILE cc_start: 0.8783 (pt) cc_final: 0.8561 (pt) REVERT: I 109 ASN cc_start: 0.8215 (m-40) cc_final: 0.7828 (m-40) REVERT: I 137 ARG cc_start: 0.6700 (ttp-110) cc_final: 0.5720 (tmt170) REVERT: I 151 ARG cc_start: 0.7631 (mmp-170) cc_final: 0.7344 (mmp80) REVERT: I 158 LYS cc_start: 0.9172 (mttt) cc_final: 0.8632 (tptt) REVERT: I 367 GLU cc_start: 0.8671 (tt0) cc_final: 0.8425 (tt0) REVERT: I 392 MET cc_start: 0.4186 (tpt) cc_final: 0.3641 (tpp) REVERT: I 444 ARG cc_start: 0.6589 (mmm160) cc_final: 0.6136 (mmm160) REVERT: I 484 ILE cc_start: 0.8516 (mm) cc_final: 0.8294 (mm) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2153 time to fit residues: 25.0088 Evaluate side-chains 93 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.227 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0154 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0125 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0116 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0108 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 58 optimal weight: 0.1980 chunk 224 optimal weight: 2.9990 chunk 161 optimal weight: 0.2980 chunk 227 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 99 optimal weight: 0.0070 chunk 105 optimal weight: 0.0980 chunk 163 optimal weight: 0.8980 chunk 179 optimal weight: 0.5980 overall best weight: 0.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.213781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.180878 restraints weight = 35831.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.188233 restraints weight = 22569.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.193520 restraints weight = 15479.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.197641 restraints weight = 11254.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.200675 restraints weight = 8468.604| |-----------------------------------------------------------------------------| r_work (final): 0.4682 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.206261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.157488 restraints weight = 8720.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.160965 restraints weight = 4168.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.166661 restraints weight = 3138.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.167422 restraints weight = 2721.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.167542 restraints weight = 2570.671| |-----------------------------------------------------------------------------| r_work (final): 0.4273 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.216461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.184493 restraints weight = 10648.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.186048 restraints weight = 4877.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.186741 restraints weight = 3502.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.186743 restraints weight = 3345.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.186742 restraints weight = 3343.814| |-----------------------------------------------------------------------------| r_work (final): 0.4489 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.200410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.190444 restraints weight = 9235.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.192443 restraints weight = 3842.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.193206 restraints weight = 2113.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.193449 restraints weight = 1526.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.193449 restraints weight = 1403.864| |-----------------------------------------------------------------------------| r_work (final): 0.4678 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.233192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.222113 restraints weight = 7824.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.224480 restraints weight = 4992.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.226034 restraints weight = 3606.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.226873 restraints weight = 2862.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.227087 restraints weight = 2488.305| |-----------------------------------------------------------------------------| r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4010 moved from start: 11.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.652 23032 Z= 0.981 Angle : 1.720 31.248 31990 Z= 0.995 Chirality : 0.095 1.039 3552 Planarity : 0.017 0.338 3300 Dihedral : 26.763 174.960 4984 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 91.77 Ramachandran Plot: Outliers : 1.88 % Allowed : 16.32 % Favored : 81.80 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 1.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.18), residues: 2132 helix: -0.56 (0.16), residues: 1104 sheet: -2.00 (0.48), residues: 112 loop : -3.72 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG I 531 TYR 0.115 0.008 TYR I 237 PHE 0.053 0.004 PHE I 534 TRP 0.013 0.004 TRP C 167 HIS 0.025 0.003 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01942 / 0.98 (23016) covalent geometry : angle 1.69324 / 0.99 (31966) hydrogen bonds : bond 0.20043 / 13.79 ( 1249) hydrogen bonds : angle 8.38100 / 6.04 ( 3415) metal coordination : bond 0.01315 / 0.70 ( 16) metal coordination : angle 11.07865 / 6.21 ( 24) =============================================================================== Job complete usr+sys time: 4444.67 seconds wall clock time: 78 minutes 8.18 seconds (4688.18 seconds total)