Starting phenix.real_space_refine on Tue Jul 7 04:43:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxj_47289/07_2026/9dxj_47289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxj_47289/07_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_47289/07_2026/9dxj_47289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxj_47289/07_2026/9dxj_47289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dxj_47289/07_2026/9dxj_47289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxj_47289/07_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-dev-6108/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: 7.61, per 1000 atoms: 0.18 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: 3.59 Conformation dependent library (CDL) restraints added in 1.1 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: 7.74 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: 9.62 Time building geometry restraints manager: 4.88 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: 8.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.320 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 53.190 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.790 ------------------------------------------------------------------------------- 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 : 1.511 15.651 31990 Z= 1.091 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 1.49213 / 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 : 0.225 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: 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: 0.2015 time to fit residues: 37.8505 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 : 0.193 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: 0.0093 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: 0.0145 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 : 0.012 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 : 0.009 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 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 : 0.008 ------------------------------------------------------------------------------- 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: 3.9990 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 = 0.4635 r_free = 0.4635 target = 0.187442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.157051 restraints weight = 37695.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.163924 restraints weight = 21335.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.168862 restraints weight = 13581.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.172343 restraints weight = 9293.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.174866 restraints weight = 6752.687| |-----------------------------------------------------------------------------| r_work (final): 0.4488 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.205599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.155374 restraints weight = 9592.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.155105 restraints weight = 12207.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.157858 restraints weight = 8899.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.156545 restraints weight = 7241.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.156682 restraints weight = 5842.476| |-----------------------------------------------------------------------------| r_work (final): 0.4154 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.203204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.167255 restraints weight = 10221.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.169312 restraints weight = 4257.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.170884 restraints weight = 3247.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.171019 restraints weight = 2909.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.171036 restraints weight = 2793.330| |-----------------------------------------------------------------------------| r_work (final): 0.4330 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.183341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.173131 restraints weight = 6817.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.174247 restraints weight = 2979.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.174800 restraints weight = 2103.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.174832 restraints weight = 1766.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.174832 restraints weight = 1736.453| |-----------------------------------------------------------------------------| r_work (final): 0.4526 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.220718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.211701 restraints weight = 8227.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.213458 restraints weight = 5173.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.214414 restraints weight = 3882.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.215204 restraints weight = 3255.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.215483 restraints weight = 2762.764| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4362 moved from start: 10.6238 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= 1.957 Angle : 3.341 58.657 31990 Z= 1.823 Chirality : 0.177 1.798 3552 Planarity : 0.023 0.217 3300 Dihedral : 26.793 178.280 4984 Min Nonbonded Distance : 0.976 Molprobity Statistics. All-atom Clashscore : 205.91 Ramachandran Plot: Outliers : 4.32 % Allowed : 12.01 % Favored : 83.68 % Rotamer: Outliers : 5.51 % Allowed : 7.76 % Favored : 86.73 % Cbeta Deviations : 6.25 % 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: -3.22 (0.17), residues: 2132 helix: -0.87 (0.15), residues: 1116 sheet: -1.99 (0.36), residues: 164 loop : -3.96 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.005 ARG K 28 TYR 0.131 0.013 TYR I 10 PHE 0.079 0.006 PHE A 289 TRP 0.028 0.008 TRP K 167 HIS 0.049 0.010 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.04734 / 1.96 (23016) covalent geometry : angle 3.29984 / 1.82 (31966) hydrogen bonds : bond 0.29669 / 20.42 ( 1249) hydrogen bonds : angle 9.74762 / 7.04 ( 3415) metal coordination : bond 0.03382 / 2.23 ( 16) metal coordination : angle 19.47447 / 11.14 ( 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: 27 poor density : 132 time to evaluate : 0.242 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 39 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7540 (mp0) REVERT: I 124 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7949 (m) REVERT: I 141 PHE cc_start: 0.8483 (t80) cc_final: 0.8274 (t80) REVERT: I 158 LYS cc_start: 0.8889 (mttt) cc_final: 0.8324 (mttm) REVERT: I 178 LEU cc_start: 0.8091 (tp) cc_final: 0.7831 (tt) REVERT: I 184 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7010 (ttmm) REVERT: I 202 PHE cc_start: 0.8559 (t80) cc_final: 0.8054 (t80) REVERT: I 248 TYR cc_start: 0.3971 (OUTLIER) cc_final: 0.3415 (m-80) REVERT: I 388 HIS cc_start: 0.8832 (t-90) cc_final: 0.8585 (t-90) REVERT: I 431 TYR cc_start: 0.4473 (t80) cc_final: 0.3398 (t80) REVERT: I 503 MET cc_start: 0.7458 (ttm) cc_final: 0.7103 (ttm) outliers start: 27 outliers final: 14 residues processed: 151 average time/residue: 0.2024 time to fit residues: 36.7342 Evaluate side-chains 119 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.238 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: 0.0164 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: 0.0144 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: 0.0114 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 43 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 105 optimal weight: 0.0470 chunk 197 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 79 optimal weight: 0.1980 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.188270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.159799 restraints weight = 38171.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.166438 restraints weight = 22210.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.171189 restraints weight = 14161.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.174553 restraints weight = 9620.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.176952 restraints weight = 6911.363| |-----------------------------------------------------------------------------| r_work (final): 0.4526 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.203388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.152471 restraints weight = 9985.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.154041 restraints weight = 8889.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.150329 restraints weight = 9296.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.150280 restraints weight = 8320.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.151927 restraints weight = 6059.155| |-----------------------------------------------------------------------------| r_work (final): 0.4149 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.206051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.178941 restraints weight = 10205.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.178081 restraints weight = 7274.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.177960 restraints weight = 4972.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.178021 restraints weight = 4358.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.178084 restraints weight = 3751.339| |-----------------------------------------------------------------------------| r_work (final): 0.4368 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.189505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.181015 restraints weight = 6793.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.182454 restraints weight = 2856.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.182978 restraints weight = 1859.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.182984 restraints weight = 1623.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.182984 restraints weight = 1608.810| |-----------------------------------------------------------------------------| r_work (final): 0.4602 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.224803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.215306 restraints weight = 7970.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.217000 restraints weight = 5274.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.218263 restraints weight = 4168.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.218972 restraints weight = 3412.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.218981 restraints weight = 2977.315| |-----------------------------------------------------------------------------| r_work (final): 0.4782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4339 moved from start: 10.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.212 23032 Z= 1.423 Angle : 2.611 54.646 31990 Z= 1.441 Chirality : 0.133 1.380 3552 Planarity : 0.019 0.189 3300 Dihedral : 26.932 177.488 4984 Min Nonbonded Distance : 1.418 Molprobity Statistics. All-atom Clashscore : 165.35 Ramachandran Plot: Outliers : 1.88 % Allowed : 15.20 % Favored : 82.93 % Rotamer: Outliers : 2.65 % Allowed : 8.16 % Favored : 89.18 % Cbeta Deviations : 3.12 % 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: -3.33 (0.17), residues: 2132 helix: -0.80 (0.16), residues: 1088 sheet: -2.07 (0.40), residues: 148 loop : -4.15 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG C 153 TYR 0.097 0.009 TYR I 10 PHE 0.047 0.004 PHE I 138 TRP 0.058 0.015 TRP K 167 HIS 0.031 0.005 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.03216 / 1.42 (23016) covalent geometry : angle 2.58356 / 1.44 (31966) hydrogen bonds : bond 0.26366 / 18.37 ( 1249) hydrogen bonds : angle 9.22416 / 6.66 ( 3415) metal coordination : bond 0.01374 / 0.83 ( 16) metal coordination : angle 14.10230 / 7.97 ( 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 122 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.184 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 39 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8075 (pt0) REVERT: I 109 ASN cc_start: 0.8484 (m110) cc_final: 0.8182 (m-40) REVERT: I 153 ARG cc_start: 0.7634 (tmt170) cc_final: 0.6572 (ttt180) REVERT: I 158 LYS cc_start: 0.8907 (mttt) cc_final: 0.8206 (tptt) REVERT: I 244 GLN cc_start: 0.7963 (pt0) cc_final: 0.7407 (tm-30) REVERT: I 444 ARG cc_start: 0.6918 (mmm160) cc_final: 0.6636 (mmm160) REVERT: I 533 ASN cc_start: 0.8359 (t0) cc_final: 0.8131 (t0) outliers start: 13 outliers final: 5 residues processed: 121 average time/residue: 0.1697 time to fit residues: 25.0654 Evaluate side-chains 103 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0093 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 : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0144 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: 0.0114 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 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: 0.0111 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 : 0.008 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 180 optimal weight: 0.0030 chunk 179 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 203 optimal weight: 0.0070 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 288 GLN ** I 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.192445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.162380 restraints weight = 36406.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.169462 restraints weight = 21549.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.174683 restraints weight = 14185.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.178355 restraints weight = 9865.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.181224 restraints weight = 7212.336| |-----------------------------------------------------------------------------| r_work (final): 0.4544 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.203500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.157985 restraints weight = 9526.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.157132 restraints weight = 8443.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.158323 restraints weight = 7319.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.158833 restraints weight = 5409.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.158531 restraints weight = 4554.411| |-----------------------------------------------------------------------------| r_work (final): 0.4164 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.206949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.173344 restraints weight = 10292.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.174461 restraints weight = 4802.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.174851 restraints weight = 3799.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.174859 restraints weight = 3485.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.174859 restraints weight = 3468.982| |-----------------------------------------------------------------------------| r_work (final): 0.4395 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.184596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.172775 restraints weight = 3677.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.176467 restraints weight = 963.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.178368 restraints weight = 438.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.179613 restraints weight = 261.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.180262 restraints weight = 178.215| |-----------------------------------------------------------------------------| r_work (final): 0.4643 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.212600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.191120 restraints weight = 2550.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.197589 restraints weight = 835.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.201611 restraints weight = 434.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.203867 restraints weight = 274.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.205261 restraints weight = 190.303| |-----------------------------------------------------------------------------| r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4224 moved from start: 10.8511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.660 23032 Z= 1.185 Angle : 2.411 32.454 31990 Z= 1.340 Chirality : 0.122 1.092 3552 Planarity : 0.017 0.180 3300 Dihedral : 27.096 176.430 4984 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 139.36 Ramachandran Plot: Outliers : 1.50 % Allowed : 15.95 % Favored : 82.55 % Rotamer: Outliers : 2.45 % Allowed : 8.16 % Favored : 89.39 % Cbeta Deviations : 2.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.87 % 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: -3.41 (0.18), residues: 2132 helix: -1.07 (0.15), residues: 1140 sheet: -2.08 (0.41), residues: 148 loop : -4.05 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.003 ARG K 128 TYR 0.095 0.007 TYR A 10 PHE 0.050 0.004 PHE I 138 TRP 0.048 0.010 TRP K 167 HIS 0.027 0.004 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02483 / 1.19 (23016) covalent geometry : angle 2.37505 / 1.34 (31966) hydrogen bonds : bond 0.24305 / 16.83 ( 1249) hydrogen bonds : angle 9.44956 / 6.82 ( 3415) metal coordination : bond 0.01345 / 0.75 ( 16) metal coordination : angle 15.24865 / 8.71 ( 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 114 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.8494 (tptp) cc_final: 0.8096 (tppt) REVERT: I 108 VAL cc_start: 0.8843 (p) cc_final: 0.8586 (p) REVERT: I 109 ASN cc_start: 0.8400 (m110) cc_final: 0.8080 (m110) REVERT: I 151 ARG cc_start: 0.8486 (mmp80) cc_final: 0.7829 (tpt-90) REVERT: I 158 LYS cc_start: 0.8981 (mttt) cc_final: 0.8444 (tptt) REVERT: I 444 ARG cc_start: 0.6727 (mmm160) cc_final: 0.6425 (mmm160) REVERT: I 486 ASP cc_start: 0.8396 (m-30) cc_final: 0.8070 (m-30) outliers start: 12 outliers final: 4 residues processed: 113 average time/residue: 0.1793 time to fit residues: 24.8291 Evaluate side-chains 98 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.232 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: 0.0183 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: 0.0148 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: 0.0114 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 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: 0.0104 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: 0.7980 chunk 42 optimal weight: 0.8980 chunk 149 optimal weight: 0.0870 chunk 206 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.0030 chunk 179 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 overall best weight: 0.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 112 GLN 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 = 0.4673 r_free = 0.4673 target = 0.195107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.164454 restraints weight = 37098.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.171457 restraints weight = 22517.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.176856 restraints weight = 14916.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.180599 restraints weight = 10440.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.183481 restraints weight = 7627.985| |-----------------------------------------------------------------------------| r_work (final): 0.4578 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.204827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.166272 restraints weight = 9845.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.163093 restraints weight = 7373.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.164748 restraints weight = 7541.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.163500 restraints weight = 6646.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.163757 restraints weight = 5813.289| |-----------------------------------------------------------------------------| r_work (final): 0.4171 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.210366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.178008 restraints weight = 10253.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.179362 restraints weight = 4593.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.181419 restraints weight = 3474.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.181425 restraints weight = 2975.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.181425 restraints weight = 2968.587| |-----------------------------------------------------------------------------| r_work (final): 0.4451 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.197659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.187177 restraints weight = 8834.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.189078 restraints weight = 3496.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.189994 restraints weight = 2136.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.190214 restraints weight = 1710.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.190216 restraints weight = 1604.467| |-----------------------------------------------------------------------------| r_work (final): 0.4664 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.228191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.216833 restraints weight = 7869.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.219392 restraints weight = 4815.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.220684 restraints weight = 3650.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.220684 restraints weight = 3088.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.220684 restraints weight = 3088.907| |-----------------------------------------------------------------------------| r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4194 moved from start: 10.9142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.647 23032 Z= 1.073 Angle : 2.132 29.879 31990 Z= 1.200 Chirality : 0.110 1.002 3552 Planarity : 0.015 0.144 3300 Dihedral : 26.979 174.683 4984 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 122.14 Ramachandran Plot: Outliers : 1.31 % Allowed : 16.89 % Favored : 81.80 % Rotamer: Outliers : 1.02 % Allowed : 6.53 % Favored : 92.45 % Cbeta Deviations : 2.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.87 % 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: -3.22 (0.18), residues: 2132 helix: -0.84 (0.15), residues: 1124 sheet: -2.14 (0.41), residues: 148 loop : -3.99 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 128 TYR 0.078 0.008 TYR I 10 PHE 0.049 0.004 PHE A 289 TRP 0.033 0.008 TRP A 167 HIS 0.020 0.003 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02161 / 1.07 (23016) covalent geometry : angle 2.09597 / 1.20 (31966) hydrogen bonds : bond 0.22476 / 15.62 ( 1249) hydrogen bonds : angle 9.17013 / 6.62 ( 3415) metal coordination : bond 0.01374 / 0.75 ( 16) metal coordination : angle 14.36550 / 8.23 ( 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 104 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.158 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: I 74 LYS cc_start: 0.8357 (tptp) cc_final: 0.7752 (tptp) REVERT: I 109 ASN cc_start: 0.8399 (m110) cc_final: 0.8039 (m-40) REVERT: I 135 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8448 (tm-30) REVERT: I 151 ARG cc_start: 0.8295 (mmp80) cc_final: 0.7523 (tpt170) REVERT: I 158 LYS cc_start: 0.9117 (mttt) cc_final: 0.8634 (tptp) REVERT: I 244 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: I 367 GLU cc_start: 0.8539 (tt0) cc_final: 0.8212 (tt0) REVERT: I 444 ARG cc_start: 0.6804 (mmm160) cc_final: 0.6314 (mmm160) REVERT: I 481 ILE cc_start: 0.9222 (mt) cc_final: 0.9016 (pt) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.2014 time to fit residues: 25.0872 Evaluate side-chains 91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.224 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: 0.0151 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 : 0.011 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: 0.0112 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 : 0.008 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 : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0106 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: 0.0010 chunk 9 optimal weight: 0.3980 chunk 129 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 3 optimal weight: 0.0670 chunk 131 optimal weight: 0.0050 chunk 115 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 24 optimal weight: 0.0270 overall best weight: 0.0996 ------------------------------------------------------------------------------- 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 = 0.4688 r_free = 0.4688 target = 0.197948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.166704 restraints weight = 37415.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.174004 restraints weight = 22889.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.179445 restraints weight = 15174.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.183249 restraints weight = 10650.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.186189 restraints weight = 7833.341| |-----------------------------------------------------------------------------| r_work (final): 0.4595 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.204424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.155053 restraints weight = 9017.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.161999 restraints weight = 4393.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.162808 restraints weight = 3299.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.162868 restraints weight = 2866.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.165909 restraints weight = 2841.268| |-----------------------------------------------------------------------------| r_work (final): 0.4216 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.210580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.177765 restraints weight = 10861.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.178854 restraints weight = 5232.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.179146 restraints weight = 4078.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.179146 restraints weight = 3847.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.179146 restraints weight = 3847.615| |-----------------------------------------------------------------------------| r_work (final): 0.4433 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.199838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.189125 restraints weight = 9222.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.191119 restraints weight = 3571.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.192127 restraints weight = 2183.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.192347 restraints weight = 1730.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.192347 restraints weight = 1655.109| |-----------------------------------------------------------------------------| r_work (final): 0.4684 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.231088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.219243 restraints weight = 8519.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.220825 restraints weight = 6147.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.222376 restraints weight = 4968.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.223570 restraints weight = 4170.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.223920 restraints weight = 3713.147| |-----------------------------------------------------------------------------| r_work (final): 0.4789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4166 moved from start: 10.9566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.678 23032 Z= 1.058 Angle : 2.020 33.691 31990 Z= 1.147 Chirality : 0.109 1.094 3552 Planarity : 0.014 0.128 3300 Dihedral : 27.112 174.395 4984 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 116.70 Ramachandran Plot: Outliers : 1.69 % Allowed : 15.76 % Favored : 82.55 % Rotamer: Outliers : 0.61 % Allowed : 4.90 % Favored : 94.49 % Cbeta Deviations : 2.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 3.87 % 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 (0.18), residues: 2132 helix: -0.70 (0.16), residues: 1120 sheet: -1.84 (0.45), residues: 128 loop : -4.00 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 531 TYR 0.095 0.007 TYR I 237 PHE 0.032 0.004 PHE C 289 TRP 0.027 0.006 TRP A 167 HIS 0.026 0.004 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02104 / 1.06 (23016) covalent geometry : angle 1.98035 / 1.14 (31966) hydrogen bonds : bond 0.22410 / 15.53 ( 1249) hydrogen bonds : angle 9.20971 / 6.68 ( 3415) metal coordination : bond 0.01830 / 1.00 ( 16) metal coordination : angle 14.74443 / 8.20 ( 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 96 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.292 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: I 74 LYS cc_start: 0.8359 (tptp) cc_final: 0.7659 (tptp) REVERT: I 108 VAL cc_start: 0.8975 (p) cc_final: 0.8674 (p) REVERT: I 109 ASN cc_start: 0.8323 (m110) cc_final: 0.7929 (m-40) REVERT: I 135 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8357 (tm-30) REVERT: I 151 ARG cc_start: 0.8084 (mmp80) cc_final: 0.7435 (tpt170) REVERT: I 158 LYS cc_start: 0.9005 (mttt) cc_final: 0.8594 (tptt) REVERT: I 286 LYS cc_start: 0.8344 (tptt) cc_final: 0.8107 (tptt) REVERT: I 288 GLN cc_start: 0.6899 (mt0) cc_final: 0.6549 (mt0) REVERT: I 444 ARG cc_start: 0.6819 (mmm160) cc_final: 0.6385 (mmm160) outliers start: 3 outliers final: 3 residues processed: 96 average time/residue: 0.2171 time to fit residues: 24.7136 Evaluate side-chains 91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.182 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: 0.0151 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 : 0.013 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: 0.0143 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 : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0186 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 : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0068 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: 0.7980 chunk 26 optimal weight: 0.0570 chunk 227 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 184 optimal weight: 0.5980 chunk 203 optimal weight: 0.3980 chunk 161 optimal weight: 0.2980 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 = 0.4714 r_free = 0.4714 target = 0.201526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.169095 restraints weight = 37446.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.176787 restraints weight = 22477.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.182482 restraints weight = 14776.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.186368 restraints weight = 10348.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.189362 restraints weight = 7647.953| |-----------------------------------------------------------------------------| r_work (final): 0.4610 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.205135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.158357 restraints weight = 8626.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.161414 restraints weight = 4135.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.162285 restraints weight = 2991.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.161887 restraints weight = 2728.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.162016 restraints weight = 2815.104| |-----------------------------------------------------------------------------| r_work (final): 0.4268 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.213023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.180288 restraints weight = 11027.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.181249 restraints weight = 5726.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.181634 restraints weight = 4292.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.181633 restraints weight = 4025.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.181633 restraints weight = 4025.456| |-----------------------------------------------------------------------------| r_work (final): 0.4499 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.199851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.189630 restraints weight = 9349.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.191438 restraints weight = 3529.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.192343 restraints weight = 2194.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.192343 restraints weight = 1742.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.192343 restraints weight = 1742.730| |-----------------------------------------------------------------------------| r_work (final): 0.4688 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.210073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.190493 restraints weight = 2795.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.197136 restraints weight = 922.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.200869 restraints weight = 442.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.203221 restraints weight = 254.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.204578 restraints weight = 157.332| |-----------------------------------------------------------------------------| r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4091 moved from start: 11.0027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.659 23032 Z= 1.016 Angle : 1.919 26.692 31990 Z= 1.090 Chirality : 0.108 1.087 3552 Planarity : 0.013 0.134 3300 Dihedral : 27.169 175.523 4984 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 108.42 Ramachandran Plot: Outliers : 1.69 % Allowed : 14.63 % Favored : 83.68 % Rotamer: Outliers : 0.20 % Allowed : 5.10 % Favored : 94.69 % 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 (0.18), residues: 2132 helix: -0.89 (0.15), residues: 1164 sheet: -2.31 (0.41), residues: 148 loop : -3.76 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 128 TYR 0.090 0.007 TYR K 55 PHE 0.041 0.004 PHE C 309 TRP 0.022 0.006 TRP C 167 HIS 0.018 0.002 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02035 / 1.02 (23016) covalent geometry : angle 1.89149 / 1.09 (31966) hydrogen bonds : bond 0.20528 / 14.27 ( 1249) hydrogen bonds : angle 8.89474 / 6.46 ( 3415) metal coordination : bond 0.01356 / 0.77 ( 16) metal coordination : angle 12.02889 / 6.73 ( 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 94 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 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: I 74 LYS cc_start: 0.8284 (tptp) cc_final: 0.7564 (tptp) REVERT: I 108 VAL cc_start: 0.8846 (p) cc_final: 0.8515 (m) REVERT: I 109 ASN cc_start: 0.8358 (m110) cc_final: 0.8011 (m110) REVERT: I 137 ARG cc_start: 0.6848 (mtm110) cc_final: 0.6641 (ttp-110) REVERT: I 158 LYS cc_start: 0.8972 (mttt) cc_final: 0.8414 (tptp) REVERT: I 233 ARG cc_start: 0.7959 (ttt-90) cc_final: 0.7670 (ptm-80) REVERT: I 274 ILE cc_start: 0.8070 (tp) cc_final: 0.7745 (pt) REVERT: I 286 LYS cc_start: 0.8454 (tptt) cc_final: 0.8243 (tptt) REVERT: I 367 GLU cc_start: 0.8559 (tt0) cc_final: 0.8230 (tt0) REVERT: I 444 ARG cc_start: 0.6877 (mmm160) cc_final: 0.6418 (mmm160) REVERT: I 503 MET cc_start: 0.7719 (ttm) cc_final: 0.7465 (ttm) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.2040 time to fit residues: 22.9735 Evaluate side-chains 88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.219 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: 0.0148 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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0091 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: 0.0114 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 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 : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0109 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 180 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 29 optimal weight: 0.2980 chunk 210 optimal weight: 30.0000 overall best weight: 0.4560 ------------------------------------------------------------------------------- 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 = 0.4760 r_free = 0.4760 target = 0.211406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.178326 restraints weight = 36421.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.185807 restraints weight = 22010.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.191302 restraints weight = 14699.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.195216 restraints weight = 10461.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.198162 restraints weight = 7826.026| |-----------------------------------------------------------------------------| r_work (final): 0.4622 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.204898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.155377 restraints weight = 8350.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.158743 restraints weight = 3978.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.164761 restraints weight = 2979.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.165574 restraints weight = 2487.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.165593 restraints weight = 2324.414| |-----------------------------------------------------------------------------| r_work (final): 0.4260 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.214230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.180892 restraints weight = 11122.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.181998 restraints weight = 5611.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.182356 restraints weight = 4166.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.182356 restraints weight = 3918.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.182356 restraints weight = 3918.351| |-----------------------------------------------------------------------------| r_work (final): 0.4500 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.199674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.186992 restraints weight = 3460.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.190095 restraints weight = 1103.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.192074 restraints weight = 547.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.193517 restraints weight = 327.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.194125 restraints weight = 222.919| |-----------------------------------------------------------------------------| r_work (final): 0.4615 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.208960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.192072 restraints weight = 2762.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.198686 restraints weight = 926.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.202213 restraints weight = 429.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.204335 restraints weight = 225.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.205564 restraints weight = 124.799| |-----------------------------------------------------------------------------| r_work (final): 0.4866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4080 moved from start: 11.0342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.699 23032 Z= 1.001 Angle : 1.842 26.407 31990 Z= 1.058 Chirality : 0.102 0.877 3552 Planarity : 0.013 0.130 3300 Dihedral : 27.155 174.440 4984 Min Nonbonded Distance : 1.418 Molprobity Statistics. All-atom Clashscore : 103.39 Ramachandran Plot: Outliers : 1.50 % Allowed : 15.01 % Favored : 83.49 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: -0.78 (0.16), residues: 1132 sheet: -2.15 (0.42), residues: 148 loop : -3.85 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 257 TYR 0.103 0.007 TYR A 55 PHE 0.034 0.004 PHE A 289 TRP 0.031 0.007 TRP I 167 HIS 0.046 0.005 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.02015 / 1.00 (23016) covalent geometry : angle 1.81267 / 1.06 (31966) hydrogen bonds : bond 0.20483 / 14.27 ( 1249) hydrogen bonds : angle 8.92235 / 6.48 ( 3415) metal coordination : bond 0.01416 / 0.80 ( 16) metal coordination : angle 12.08773 / 6.78 ( 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 93 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.230 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 108 VAL cc_start: 0.8826 (p) cc_final: 0.8506 (m) REVERT: I 109 ASN cc_start: 0.8422 (m110) cc_final: 0.8085 (m110) REVERT: I 151 ARG cc_start: 0.8074 (mmp80) cc_final: 0.7304 (tpt170) REVERT: I 158 LYS cc_start: 0.9040 (mttt) cc_final: 0.8480 (tptt) REVERT: I 233 ARG cc_start: 0.8024 (ttt-90) cc_final: 0.7748 (ptm-80) REVERT: I 367 GLU cc_start: 0.8586 (tt0) cc_final: 0.8235 (tt0) REVERT: I 441 PHE cc_start: 0.6592 (t80) cc_final: 0.6322 (t80) REVERT: I 444 ARG cc_start: 0.6880 (mmm160) cc_final: 0.6408 (mmm160) REVERT: I 503 MET cc_start: 0.7828 (ttm) cc_final: 0.7619 (ttm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1984 time to fit residues: 22.3354 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 : 0.255 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: 0.0167 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: 0.0091 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 : 0.009 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 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: 0.0118 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 : 0.008 ------------------------------------------------------------------------------- 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: 0.4980 chunk 180 optimal weight: 0.6980 chunk 93 optimal weight: 40.0000 chunk 197 optimal weight: 0.0060 chunk 69 optimal weight: 0.0770 chunk 52 optimal weight: 0.0770 chunk 34 optimal weight: 0.0170 chunk 203 optimal weight: 0.0270 chunk 229 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 overall best weight: 0.0408 ------------------------------------------------------------------------------- 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 = 0.4789 r_free = 0.4789 target = 0.212826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.180477 restraints weight = 36904.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.188266 restraints weight = 22260.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.193710 restraints weight = 14669.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.197681 restraints weight = 10313.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.200586 restraints weight = 7604.602| |-----------------------------------------------------------------------------| r_work (final): 0.4659 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.205953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.156392 restraints weight = 8904.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.163145 restraints weight = 4306.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.164405 restraints weight = 3100.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.165902 restraints weight = 2676.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.166028 restraints weight = 2551.046| |-----------------------------------------------------------------------------| r_work (final): 0.4284 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.216310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.182668 restraints weight = 10689.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.183922 restraints weight = 5009.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.184377 restraints weight = 3746.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.184376 restraints weight = 3455.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.184376 restraints weight = 3455.925| |-----------------------------------------------------------------------------| r_work (final): 0.4488 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.203074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.192018 restraints weight = 10044.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.194144 restraints weight = 3867.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.194953 restraints weight = 2257.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.195083 restraints weight = 1779.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.195145 restraints weight = 1701.409| |-----------------------------------------------------------------------------| r_work (final): 0.4693 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.211930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.194237 restraints weight = 3039.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.200807 restraints weight = 950.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.204702 restraints weight = 484.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.206952 restraints weight = 254.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.208365 restraints weight = 148.162| |-----------------------------------------------------------------------------| r_work (final): 0.4782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4048 moved from start: 11.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.684 23032 Z= 0.994 Angle : 1.821 27.031 31990 Z= 1.042 Chirality : 0.101 0.886 3552 Planarity : 0.013 0.138 3300 Dihedral : 27.200 174.790 4984 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 97.84 Ramachandran Plot: Outliers : 1.50 % Allowed : 14.82 % Favored : 83.68 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 1.37 % 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: -2.87 (0.18), residues: 2132 helix: -0.59 (0.16), residues: 1112 sheet: -2.11 (0.42), residues: 148 loop : -3.69 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 257 TYR 0.110 0.008 TYR I 237 PHE 0.052 0.005 PHE I 199 TRP 0.027 0.007 TRP I 167 HIS 0.033 0.004 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01988 / 0.99 (23016) covalent geometry : angle 1.79181 / 1.04 (31966) hydrogen bonds : bond 0.19846 / 13.84 ( 1249) hydrogen bonds : angle 8.72758 / 6.33 ( 3415) metal coordination : bond 0.01416 / 0.78 ( 16) metal coordination : angle 12.05037 / 6.78 ( 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 92 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.229 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 151 ARG cc_start: 0.8044 (mmp80) cc_final: 0.7165 (tpt170) REVERT: I 158 LYS cc_start: 0.9024 (mttt) cc_final: 0.8473 (tptt) REVERT: I 367 GLU cc_start: 0.8549 (tt0) cc_final: 0.8230 (tt0) REVERT: I 444 ARG cc_start: 0.6884 (mmm160) cc_final: 0.6390 (mmm160) REVERT: I 486 ASP cc_start: 0.8167 (m-30) cc_final: 0.7936 (m-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1950 time to fit residues: 21.5630 Evaluate side-chains 82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.225 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: 0.0169 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: 0.0146 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 : 0.009 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: 0.0111 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 171 optimal weight: 0.0980 chunk 219 optimal weight: 0.0470 chunk 119 optimal weight: 0.0770 chunk 194 optimal weight: 0.5980 chunk 175 optimal weight: 0.0020 chunk 155 optimal weight: 0.0040 chunk 94 optimal weight: 30.0000 chunk 123 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 214 optimal weight: 40.0000 chunk 109 optimal weight: 1.9990 overall best weight: 0.0456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4819 r_free = 0.4819 target = 0.216075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.176427 restraints weight = 37907.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.185077 restraints weight = 24421.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.191745 restraints weight = 16877.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.196533 restraints weight = 12216.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.199784 restraints weight = 9188.435| |-----------------------------------------------------------------------------| r_work (final): 0.4662 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.206411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.154960 restraints weight = 8953.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.158511 restraints weight = 4508.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.163004 restraints weight = 3392.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.163012 restraints weight = 2960.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.163012 restraints weight = 2913.402| |-----------------------------------------------------------------------------| r_work (final): 0.4292 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.217035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.183410 restraints weight = 10973.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.184867 restraints weight = 5046.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.187659 restraints weight = 3617.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.187788 restraints weight = 3061.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.187788 restraints weight = 2958.480| |-----------------------------------------------------------------------------| r_work (final): 0.4518 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.204368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.193497 restraints weight = 9512.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.195683 restraints weight = 3606.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.196524 restraints weight = 1924.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.196712 restraints weight = 1467.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.196712 restraints weight = 1377.300| |-----------------------------------------------------------------------------| r_work (final): 0.4700 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.232371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.221568 restraints weight = 7626.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.223780 restraints weight = 4832.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.225322 restraints weight = 3538.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.225671 restraints weight = 2827.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.226177 restraints weight = 2573.609| |-----------------------------------------------------------------------------| r_work (final): 0.4811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4047 moved from start: 11.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.658 23032 Z= 0.987 Angle : 1.744 25.327 31990 Z= 1.010 Chirality : 0.098 0.806 3552 Planarity : 0.012 0.131 3300 Dihedral : 27.178 174.664 4984 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 95.22 Ramachandran Plot: Outliers : 1.69 % Allowed : 14.26 % Favored : 84.05 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 1.17 % 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: -2.78 (0.18), residues: 2132 helix: -0.60 (0.16), residues: 1108 sheet: -1.79 (0.46), residues: 128 loop : -3.56 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG I 137 TYR 0.093 0.007 TYR A 55 PHE 0.039 0.004 PHE I 202 TRP 0.019 0.005 TRP A 167 HIS 0.026 0.003 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01965 / 0.99 (23016) covalent geometry : angle 1.71810 / 1.01 (31966) hydrogen bonds : bond 0.19969 / 14.01 ( 1249) hydrogen bonds : angle 8.52624 / 6.19 ( 3415) metal coordination : bond 0.01275 / 0.76 ( 16) metal coordination : angle 11.14363 / 6.24 ( 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 91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.190 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: I 151 ARG cc_start: 0.8040 (mmp80) cc_final: 0.7455 (tpt170) REVERT: I 158 LYS cc_start: 0.8979 (mttt) cc_final: 0.8384 (tptt) REVERT: I 272 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7830 (mp0) REVERT: I 367 GLU cc_start: 0.8514 (tt0) cc_final: 0.8176 (tt0) REVERT: I 444 ARG cc_start: 0.7177 (mmm160) cc_final: 0.6678 (mmm160) REVERT: I 486 ASP cc_start: 0.8208 (m-30) cc_final: 0.7968 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1623 time to fit residues: 18.4330 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 : 0.217 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 : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0094 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: 0.0150 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 : 0.012 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: 0.0115 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 : 0.009 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 : 0.011 ------------------------------------------------------------------------------- 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: 0.2980 chunk 224 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.0060 chunk 163 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4820 r_free = 0.4820 target = 0.217785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.179543 restraints weight = 37930.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.187726 restraints weight = 24532.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.194233 restraints weight = 17086.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.199039 restraints weight = 12373.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.202570 restraints weight = 9283.213| |-----------------------------------------------------------------------------| r_work (final): 0.4649 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.205642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.156257 restraints weight = 8423.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.162112 restraints weight = 4110.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.163053 restraints weight = 3035.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.166510 restraints weight = 2746.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.166689 restraints weight = 2488.499| |-----------------------------------------------------------------------------| r_work (final): 0.4277 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.216139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.183291 restraints weight = 11300.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.184436 restraints weight = 4983.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.184662 restraints weight = 3844.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.184856 restraints weight = 3627.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.184863 restraints weight = 3627.695| |-----------------------------------------------------------------------------| r_work (final): 0.4486 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.204225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.193227 restraints weight = 9176.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.194972 restraints weight = 3763.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.195910 restraints weight = 2057.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.196186 restraints weight = 1488.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.196186 restraints weight = 1376.535| |-----------------------------------------------------------------------------| r_work (final): 0.4693 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.229832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.218894 restraints weight = 8154.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.221137 restraints weight = 5299.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.222493 restraints weight = 3828.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.223035 restraints weight = 3061.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.223767 restraints weight = 2704.109| |-----------------------------------------------------------------------------| r_work (final): 0.4779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4114 moved from start: 11.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.699 23032 Z= 0.984 Angle : 1.713 25.040 31990 Z= 0.988 Chirality : 0.094 0.746 3552 Planarity : 0.012 0.130 3300 Dihedral : 27.238 175.231 4984 Min Nonbonded Distance : 1.429 Molprobity Statistics. All-atom Clashscore : 92.47 Ramachandran Plot: Outliers : 1.88 % Allowed : 14.45 % Favored : 83.68 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -2.66 (0.18), residues: 2132 helix: -0.46 (0.16), residues: 1104 sheet: -1.69 (0.47), residues: 128 loop : -3.55 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG K 137 TYR 0.108 0.008 TYR I 237 PHE 0.035 0.004 PHE I 202 TRP 0.017 0.004 TRP K 234 HIS 0.015 0.002 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01970 / 0.98 (23016) covalent geometry : angle 1.69105 / 0.99 (31966) hydrogen bonds : bond 0.19405 / 13.57 ( 1249) hydrogen bonds : angle 8.37236 / 6.06 ( 3415) metal coordination : bond 0.01061 / 0.58 ( 16) metal coordination : angle 10.05798 / 5.63 ( 24) =============================================================================== Job complete usr+sys time: 4229.24 seconds wall clock time: 74 minutes 18.86 seconds (4458.86 seconds total)