Starting phenix.real_space_refine on Mon Aug 10 06:54:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxh_47288/08_2026/9dxh_47288.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxh_47288/08_2026/9dxh_47288.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/9dxh_47288/08_2026/9dxh_47288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxh_47288/08_2026/9dxh_47288.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dxh_47288/08_2026/9dxh_47288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxh_47288/08_2026/9dxh_47288.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= 0.018 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 109 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42532 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "C" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "E" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1087 Classifications: {'DNA': 34} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1052 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "G" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 796 Classifications: {'DNA': 25} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 24} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 767 Classifications: {'DNA': 24} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 23} Chain: "I" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "K" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "M" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1087 Classifications: {'DNA': 34} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 33} Chain: "N" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1052 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "O" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 796 Classifications: {'DNA': 25} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 24} Chain: "P" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 767 Classifications: {'DNA': 24} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5206 SG CYS A 320 88.271 101.741 174.961 1.00186.55 S ATOM 5250 SG CYS A 323 86.510 99.391 172.823 1.00181.32 S ATOM 5738 SG CYS A 353 84.368 100.779 175.303 1.00189.90 S ATOM 5829 SG CYS A 358 86.898 98.308 176.517 1.00198.99 S ATOM 13987 SG CYS C 320 82.894 39.136 159.156 1.00192.18 S ATOM 14031 SG CYS C 323 84.322 38.454 155.715 1.00191.17 S ATOM 14519 SG CYS C 353 80.697 37.802 156.459 1.00167.59 S ATOM 14610 SG CYS C 358 83.402 35.569 158.062 1.00175.85 S ATOM 26470 SG CYS I 320 38.232 92.534 59.645 1.00186.55 S ATOM 26514 SG CYS I 323 41.446 92.357 61.407 1.00181.32 S ATOM 27002 SG CYS I 353 41.056 95.421 59.640 1.00189.90 S ATOM 27093 SG CYS I 358 41.625 92.381 57.542 1.00198.99 S ATOM 35251 SG CYS K 320 95.827 62.827 60.304 1.00192.18 S ATOM 35295 SG CYS K 323 96.137 60.479 63.259 1.00191.17 S ATOM 35783 SG CYS K 353 98.482 63.385 62.856 1.00167.59 S ATOM 35874 SG CYS K 358 98.706 60.404 60.419 1.00175.85 S Time building chain proxies: 7.12, per 1000 atoms: 0.17 Number of scatterers: 42532 At special positions: 0 Unit cell: (136.32, 144.84, 233.235, 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: 3.90 Conformation dependent library (CDL) restraints added in 947.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 353 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 358 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 323 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 320 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 353 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 320 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 323 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 358 " pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 353 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 358 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 323 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 320 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 353 " 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 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 25 sheets defined 56.6% alpha, 11.8% beta 108 base pairs and 181 stacking pairs defined. Time for finding SS restraints: 7.08 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.582A pdb=" N TYR A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) 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 83 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.730A pdb=" N LEU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 4.012A 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: 3.548A pdb=" N ASP A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.776A 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 224 Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 285 through 299 Processing helix chain 'A' and resid 362 through 380 removed outlier: 3.823A pdb=" N ASN A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.877A 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 505 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: 3.643A pdb=" N GLU C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 69 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 102 through 115 Processing helix chain 'C' and resid 129 through 164 removed outlier: 3.533A pdb=" N ALA C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) 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 244 Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.831A pdb=" N TYR C 248 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 299 removed outlier: 3.528A pdb=" N PHE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 380 Processing helix chain 'C' and resid 381 through 401 removed outlier: 5.533A pdb=" N ASP C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 433 removed outlier: 3.613A pdb=" N MET C 409 " --> pdb=" O THR C 405 " (cutoff:3.500A) 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 10 removed outlier: 3.581A pdb=" N TYR I 10 " --> pdb=" O ILE I 6 " (cutoff:3.500A) 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 83 Processing helix chain 'I' and resid 92 through 97 removed outlier: 3.729A pdb=" N LEU I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 4.011A 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: 3.548A pdb=" N ASP I 103 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 3.776A 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 224 Processing helix chain 'I' and resid 235 through 244 Processing helix chain 'I' and resid 245 through 250 removed outlier: 3.714A pdb=" N TYR I 248 " --> pdb=" O ASN I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 299 Processing helix chain 'I' and resid 362 through 380 removed outlier: 3.823A pdb=" N ASN I 378 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 3.877A 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 505 Processing helix chain 'I' and resid 531 through 537 Processing helix chain 'K' and resid 4 through 10 removed outlier: 3.853A pdb=" N TYR K 10 " --> pdb=" O ILE K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 31 Processing helix chain 'K' and resid 35 through 52 removed outlier: 3.642A pdb=" N GLU K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 69 Processing helix chain 'K' and resid 70 through 82 Processing helix chain 'K' and resid 92 through 96 Processing helix chain 'K' and resid 102 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 244 Processing helix chain 'K' and resid 245 through 250 removed outlier: 3.831A pdb=" N TYR K 248 " --> pdb=" O ASN K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 3.529A pdb=" N PHE K 289 " --> pdb=" O ASP K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 380 Processing helix chain 'K' and resid 381 through 401 removed outlier: 5.534A pdb=" N ASP K 398 " --> pdb=" O SER K 394 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP K 399 " --> pdb=" O LYS K 395 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER K 401 " --> pdb=" O GLU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 433 removed outlier: 3.613A pdb=" N MET K 409 " --> pdb=" O THR K 405 " (cutoff:3.500A) 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 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: 6.768A pdb=" N THR A 319 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N MET A 512 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.297A 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: 6.579A 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: 6.523A 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 Processing sheet with id=AB5, first strand: chain 'I' and resid 118 through 120 Processing sheet with id=AB6, first strand: chain 'I' and resid 176 through 179 Processing sheet with id=AB7, first strand: chain 'I' and resid 252 through 254 Processing sheet with id=AB8, first strand: chain 'I' and resid 257 through 259 Processing sheet with id=AB9, first strand: chain 'I' and resid 318 through 320 removed outlier: 6.315A pdb=" N GLN I 523 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 328 through 337 Processing sheet with id=AC2, first strand: chain 'K' and resid 55 through 59 removed outlier: 6.560A pdb=" N ILE K 88 " --> pdb=" O ILE K 119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 176 through 179 Processing sheet with id=AC4, first strand: chain 'K' and resid 252 through 254 Processing sheet with id=AC5, first strand: chain 'K' and resid 257 through 259 Processing sheet with id=AC6, first strand: chain 'K' and resid 318 through 320 removed outlier: 6.563A pdb=" N GLN K 523 " --> pdb=" O THR K 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 328 through 337 1037 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 244 hydrogen bonds 488 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 181 stacking parallelities Total time for adding SS restraints: 10.28 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7512 1.03 - 1.23: 13442 1.23 - 1.43: 12007 1.43 - 1.62: 10285 1.62 - 1.82: 120 Bond restraints: 43366 Sorted by residual: bond pdb=" C6 DA E -5 " pdb=" N6 DA E -5 " ideal model delta sigma weight residual 1.335 1.227 0.108 8.00e-03 1.56e+04 1.81e+02 bond pdb=" C6 DA M -5 " pdb=" N6 DA M -5 " ideal model delta sigma weight residual 1.335 1.228 0.107 8.00e-03 1.56e+04 1.77e+02 bond pdb=" C6 DA G -3 " pdb=" N6 DA G -3 " ideal model delta sigma weight residual 1.335 1.230 0.105 8.00e-03 1.56e+04 1.73e+02 bond pdb=" C6 DA E -21 " pdb=" N6 DA E -21 " ideal model delta sigma weight residual 1.335 1.230 0.105 8.00e-03 1.56e+04 1.73e+02 bond pdb=" C6 DA O -3 " pdb=" N6 DA O -3 " ideal model delta sigma weight residual 1.335 1.231 0.104 8.00e-03 1.56e+04 1.71e+02 ... (remaining 43361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.54: 76621 7.54 - 15.09: 2022 15.09 - 22.63: 1 22.63 - 30.17: 0 30.17 - 37.72: 60 Bond angle restraints: 78704 Sorted by residual: angle pdb=" O5' DT F 5 " pdb=" C5' DT F 5 " pdb=" C4' DT F 5 " ideal model delta sigma weight residual 109.40 119.87 -10.47 8.00e-01 1.56e+00 1.71e+02 angle pdb=" O5' DT N 5 " pdb=" C5' DT N 5 " pdb=" C4' DT N 5 " ideal model delta sigma weight residual 109.40 119.78 -10.38 8.00e-01 1.56e+00 1.68e+02 angle pdb=" N9 DG F 6 " pdb=" C8 DG F 6 " pdb=" N7 DG F 6 " ideal model delta sigma weight residual 113.10 119.50 -6.40 5.00e-01 4.00e+00 1.64e+02 angle pdb=" N9 DG N 6 " pdb=" C8 DG N 6 " pdb=" N7 DG N 6 " ideal model delta sigma weight residual 113.10 119.47 -6.37 5.00e-01 4.00e+00 1.62e+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 71.28 37.72 3.00e+00 1.11e-01 1.58e+02 ... (remaining 78699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 18191 35.80 - 71.60: 1249 71.60 - 107.40: 40 107.40 - 143.20: 6 143.20 - 179.01: 14 Dihedral angle restraints: 19500 sinusoidal: 12324 harmonic: 7176 Sorted by residual: dihedral pdb=" CA TYR K 436 " pdb=" C TYR K 436 " pdb=" N SER K 437 " pdb=" CA SER K 437 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA TYR C 436 " pdb=" C TYR C 436 " pdb=" N SER C 437 " pdb=" CA SER C 437 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PRO C 521 " pdb=" C PRO C 521 " pdb=" N ALA C 522 " pdb=" CA ALA C 522 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 19497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 1267 0.153 - 0.305: 126 0.305 - 0.458: 598 0.458 - 0.611: 1224 0.611 - 0.763: 337 Chirality restraints: 3552 Sorted by residual: chirality pdb=" CG LEU C 302 " pdb=" CB LEU C 302 " pdb=" CD1 LEU C 302 " pdb=" CD2 LEU C 302 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CG LEU K 302 " pdb=" CB LEU K 302 " pdb=" CD1 LEU K 302 " pdb=" CD2 LEU K 302 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CG LEU I 111 " pdb=" CB LEU I 111 " pdb=" CD1 LEU I 111 " pdb=" CD2 LEU I 111 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 3549 not shown) Planarity restraints: 5510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT G -2 " 0.462 2.00e-02 2.50e+03 1.76e-01 9.26e+02 pdb=" N1 DT G -2 " -0.065 2.00e-02 2.50e+03 pdb=" C2 DT G -2 " -0.117 2.00e-02 2.50e+03 pdb=" O2 DT G -2 " -0.217 2.00e-02 2.50e+03 pdb=" N3 DT G -2 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT G -2 " 0.065 2.00e-02 2.50e+03 pdb=" O4 DT G -2 " 0.225 2.00e-02 2.50e+03 pdb=" C5 DT G -2 " -0.046 2.00e-02 2.50e+03 pdb=" C7 DT G -2 " -0.037 2.00e-02 2.50e+03 pdb=" C6 DT G -2 " -0.111 2.00e-02 2.50e+03 pdb=" H3 DT G -2 " -0.014 2.00e-02 2.50e+03 pdb=" H6 DT G -2 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 144 " -0.253 9.50e-02 1.11e+02 1.43e-01 3.07e+02 pdb=" NE ARG C 144 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 144 " 0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG C 144 " 0.099 2.00e-02 2.50e+03 pdb=" NH2 ARG C 144 " 0.074 2.00e-02 2.50e+03 pdb="HH11 ARG C 144 " 0.036 2.00e-02 2.50e+03 pdb="HH12 ARG C 144 " -0.229 2.00e-02 2.50e+03 pdb="HH21 ARG C 144 " -0.160 2.00e-02 2.50e+03 pdb="HH22 ARG C 144 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT O -12 " 0.223 2.00e-02 2.50e+03 1.01e-01 3.06e+02 pdb=" N1 DT O -12 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DT O -12 " -0.026 2.00e-02 2.50e+03 pdb=" O2 DT O -12 " -0.036 2.00e-02 2.50e+03 pdb=" N3 DT O -12 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT O -12 " 0.067 2.00e-02 2.50e+03 pdb=" O4 DT O -12 " 0.145 2.00e-02 2.50e+03 pdb=" C5 DT O -12 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT O -12 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT O -12 " -0.072 2.00e-02 2.50e+03 pdb=" H3 DT O -12 " -0.141 2.00e-02 2.50e+03 pdb=" H6 DT O -12 " -0.140 2.00e-02 2.50e+03 ... (remaining 5507 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 2080 2.11 - 2.73: 71968 2.73 - 3.35: 129487 3.35 - 3.98: 164899 3.98 - 4.60: 248433 Nonbonded interactions: 616867 Sorted by model distance: nonbonded pdb=" OD1 ASN K 235 " pdb=" H THR K 238 " model vdw 1.487 2.450 nonbonded pdb=" HZ2 LYS A 322 " pdb=" O CYS A 358 " model vdw 1.530 2.450 nonbonded pdb=" HZ2 LYS I 322 " pdb=" O CYS I 358 " model vdw 1.531 2.450 nonbonded pdb=" O VAL C 504 " pdb=" H ARG C 531 " model vdw 1.545 2.450 nonbonded pdb=" O VAL K 504 " pdb=" H ARG K 531 " model vdw 1.545 2.450 ... (remaining 616862 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 51.800 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 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 : 0.044 0.158 23032 Z= 2.711 Angle : 3.325 12.376 31990 Z= 2.504 Chirality : 0.415 0.763 3552 Planarity : 0.014 0.224 3300 Dihedral : 20.917 179.006 9632 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.64 % Allowed : 9.74 % Favored : 85.61 % Cbeta Deviations : 28.66 % 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: -1.50 (0.17), residues: 2132 helix: -0.59 (0.14), residues: 1138 sheet: -2.05 (0.30), residues: 280 loop : -0.87 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 137 TYR 0.160 0.015 TYR A 248 PHE 0.089 0.011 PHE A 138 TRP 0.042 0.014 TRP C 234 HIS 0.003 0.001 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.04361 / 2.71 (23016) covalent geometry : angle 3.32336 / 2.50 (31966) hydrogen bonds : bond 0.15331 / 10.37 ( 1281) hydrogen bonds : angle 6.91018 / 4.82 ( 3491) metal coordination : bond 0.02979 / 1.99 ( 16) metal coordination : angle 5.00570 / 3.37 ( 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 180 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8626 (mt) cc_final: 0.8386 (mp) REVERT: A 44 MET cc_start: 0.7768 (mmm) cc_final: 0.7433 (mmm) REVERT: A 59 MET cc_start: 0.2337 (OUTLIER) cc_final: 0.1447 (tpt) REVERT: A 74 LYS cc_start: 0.9251 (mttt) cc_final: 0.8794 (mttt) REVERT: A 103 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: A 119 ILE cc_start: 0.7786 (mt) cc_final: 0.7520 (mt) REVERT: A 134 ARG cc_start: 0.8298 (ttt180) cc_final: 0.8041 (ttt180) REVERT: A 135 GLN cc_start: 0.8860 (mp-120) cc_final: 0.8657 (tp40) REVERT: A 136 ILE cc_start: 0.9333 (mt) cc_final: 0.9095 (mt) REVERT: A 137 ARG cc_start: 0.8386 (mtp85) cc_final: 0.7200 (tmt170) REVERT: A 155 THR cc_start: 0.8594 (p) cc_final: 0.7849 (p) REVERT: A 158 LYS cc_start: 0.8984 (mttt) cc_final: 0.8463 (mttt) REVERT: A 272 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8124 (mp0) REVERT: A 428 PHE cc_start: 0.6346 (m-10) cc_final: 0.6027 (m-10) REVERT: A 430 LYS cc_start: 0.6725 (mmtt) cc_final: 0.6509 (mmmm) REVERT: A 450 GLU cc_start: 0.8096 (tt0) cc_final: 0.7853 (tp30) REVERT: A 496 LYS cc_start: 0.7382 (mmtt) cc_final: 0.7081 (mmtt) outliers start: 25 outliers final: 11 residues processed: 172 average time/residue: 0.1933 time to fit residues: 39.5859 Evaluate side-chains 146 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 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: 0.0154 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0088 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0069 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 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: 0.0107 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: 10.0000 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.0000 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.0980 chunk 200 optimal weight: 0.0770 overall best weight: 0.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN A 200 ASN ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 305 ASN A 356 ASN A 469 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.169807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.139898 restraints weight = 35455.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.146275 restraints weight = 20560.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.150639 restraints weight = 13319.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.153731 restraints weight = 9334.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.155876 restraints weight = 6955.686| |-----------------------------------------------------------------------------| r_work (final): 0.4339 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.218003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.159166 restraints weight = 9394.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.162043 restraints weight = 4791.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.163388 restraints weight = 3494.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.169990 restraints weight = 3082.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.170402 restraints weight = 2797.182| |-----------------------------------------------------------------------------| r_work (final): 0.4313 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.218167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.181292 restraints weight = 10835.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.181627 restraints weight = 4666.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.184877 restraints weight = 3301.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.184929 restraints weight = 3039.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.184978 restraints weight = 2855.793| |-----------------------------------------------------------------------------| r_work (final): 0.4331 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.189451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.182388 restraints weight = 7714.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.181218 restraints weight = 5526.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.181640 restraints weight = 4335.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.181885 restraints weight = 3657.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.181887 restraints weight = 3386.016| |-----------------------------------------------------------------------------| r_work (final): 0.4522 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.192830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.183964 restraints weight = 7940.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.185674 restraints weight = 3861.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.186693 restraints weight = 2599.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.187135 restraints weight = 2004.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.187177 restraints weight = 1751.371| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4450 moved from start: 10.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.157 23032 Z= 1.464 Angle : 2.618 56.254 31990 Z= 1.404 Chirality : 0.169 4.927 3552 Planarity : 0.017 0.219 3300 Dihedral : 25.897 175.032 4984 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 118.54 Ramachandran Plot: Outliers : 2.63 % Allowed : 12.01 % Favored : 85.37 % Rotamer: Outliers : 2.45 % Allowed : 7.14 % Favored : 90.41 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.97 % 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: -2.48 (0.17), residues: 2132 helix: -0.80 (0.15), residues: 1104 sheet: -1.62 (0.33), residues: 240 loop : -2.79 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 153 TYR 0.119 0.007 TYR I 237 PHE 0.028 0.003 PHE K 532 TRP 0.014 0.005 TRP C 167 HIS 0.030 0.006 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.03049 / 1.46 (23016) covalent geometry : angle 2.60070 / 1.40 (31966) hydrogen bonds : bond 0.25958 / 17.73 ( 1281) hydrogen bonds : angle 9.40660 / 6.70 ( 3491) metal coordination : bond 0.05378 / 2.84 ( 16) metal coordination : angle 11.41599 / 7.43 ( 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 152 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.231 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 3 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.3597 (tt) REVERT: I 31 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6118 (mtm-85) REVERT: I 46 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8904 (mttt) REVERT: I 85 TYR cc_start: 0.4708 (m-10) cc_final: 0.4266 (m-10) REVERT: I 112 GLN cc_start: 0.8369 (tp40) cc_final: 0.8072 (tp40) REVERT: I 134 ARG cc_start: 0.8856 (ttt180) cc_final: 0.8508 (ttm170) REVERT: I 154 MET cc_start: 0.7900 (mmt) cc_final: 0.7419 (mmt) REVERT: I 155 THR cc_start: 0.8834 (p) cc_final: 0.7784 (p) REVERT: I 158 LYS cc_start: 0.8765 (mttt) cc_final: 0.8336 (mttt) REVERT: I 185 LEU cc_start: 0.9029 (mt) cc_final: 0.8765 (mm) REVERT: I 202 PHE cc_start: 0.8517 (t80) cc_final: 0.8286 (t80) REVERT: I 224 GLN cc_start: 0.8992 (mt0) cc_final: 0.8739 (tm-30) REVERT: I 270 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7893 (pm20) REVERT: I 367 GLU cc_start: 0.8461 (pt0) cc_final: 0.8199 (pt0) REVERT: I 428 PHE cc_start: 0.6649 (m-10) cc_final: 0.6395 (m-10) outliers start: 12 outliers final: 2 residues processed: 147 average time/residue: 0.1970 time to fit residues: 34.9432 Evaluate side-chains 126 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.188 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: 0.0104 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 : 0.007 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: 0.0145 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: 0.0114 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 : 0.009 ------------------------------------------------------------------------------- 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: 0.9990 chunk 121 optimal weight: 0.0370 chunk 178 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN I 469 GLN ** I 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 514 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.169098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.137273 restraints weight = 39247.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.144258 restraints weight = 21752.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.149212 restraints weight = 13731.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.152742 restraints weight = 9377.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.155229 restraints weight = 6812.888| |-----------------------------------------------------------------------------| r_work (final): 0.4274 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.218315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.215847 restraints weight = 8738.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.216918 restraints weight = 3172.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.217637 restraints weight = 1334.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.218114 restraints weight = 639.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.218201 restraints weight = 291.670| |-----------------------------------------------------------------------------| r_work (final): 0.4720 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.218988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.179955 restraints weight = 10850.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.181561 restraints weight = 4527.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.185102 restraints weight = 3425.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.184626 restraints weight = 3207.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.184730 restraints weight = 2951.856| |-----------------------------------------------------------------------------| r_work (final): 0.4344 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.185602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.176664 restraints weight = 8020.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.178140 restraints weight = 3321.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.178794 restraints weight = 1824.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.178980 restraints weight = 1403.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.178980 restraints weight = 1275.493| |-----------------------------------------------------------------------------| r_work (final): 0.4533 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.200039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.191894 restraints weight = 7527.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.193442 restraints weight = 3020.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.194379 restraints weight = 2052.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.194379 restraints weight = 1538.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.194379 restraints weight = 1538.909| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4325 moved from start: 10.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.202 23032 Z= 1.044 Angle : 1.940 44.769 31990 Z= 1.094 Chirality : 0.091 0.950 3552 Planarity : 0.014 0.152 3300 Dihedral : 26.246 174.030 4984 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 93.91 Ramachandran Plot: Outliers : 1.50 % Allowed : 12.38 % Favored : 86.12 % Rotamer: Outliers : 1.22 % Allowed : 4.90 % Favored : 93.88 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.16 % 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: -2.68 (0.18), residues: 2132 helix: -0.85 (0.15), residues: 1100 sheet: -2.16 (0.32), residues: 228 loop : -2.91 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG K 128 TYR 0.128 0.005 TYR I 237 PHE 0.027 0.003 PHE K 202 TRP 0.010 0.003 TRP K 167 HIS 0.019 0.004 HIS I 489 Details of bonding type rmsd/Z covalent geometry : bond 0.02021 / 1.04 (23016) covalent geometry : angle 1.93408 / 1.09 (31966) hydrogen bonds : bond 0.20489 / 13.91 ( 1281) hydrogen bonds : angle 8.51416 / 6.08 ( 3491) metal coordination : bond 0.01608 / 1.05 ( 16) metal coordination : angle 5.88881 / 3.72 ( 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 123 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 12 ILE cc_start: 0.7845 (pt) cc_final: 0.7397 (tp) REVERT: I 112 GLN cc_start: 0.8474 (tp40) cc_final: 0.8176 (tp40) REVERT: I 181 LYS cc_start: 0.9241 (mttt) cc_final: 0.8730 (tppt) REVERT: I 224 GLN cc_start: 0.8980 (mt0) cc_final: 0.8762 (tm-30) REVERT: I 270 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7891 (pm20) REVERT: I 392 MET cc_start: 0.5253 (mmt) cc_final: 0.4915 (tpt) REVERT: I 428 PHE cc_start: 0.6671 (m-10) cc_final: 0.6365 (m-10) REVERT: I 444 ARG cc_start: 0.6930 (mmp80) cc_final: 0.6715 (mmp80) REVERT: I 498 ASN cc_start: 0.7306 (t0) cc_final: 0.6780 (t0) REVERT: I 502 ARG cc_start: 0.8234 (mtp-110) cc_final: 0.7438 (tpp80) outliers start: 6 outliers final: 4 residues processed: 122 average time/residue: 0.1923 time to fit residues: 28.8424 Evaluate side-chains 119 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.233 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 : 0.012 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: 0.0141 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: 0.0109 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 : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0116 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- 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: 3.9990 chunk 90 optimal weight: 0.9990 chunk 86 optimal weight: 50.0000 chunk 140 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN I 368 ASN ** I 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.170441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.139964 restraints weight = 38129.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.146784 restraints weight = 21325.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.151612 restraints weight = 13498.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.155057 restraints weight = 9230.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.157501 restraints weight = 6701.560| |-----------------------------------------------------------------------------| r_work (final): 0.4353 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.217500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.164455 restraints weight = 7428.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.167654 restraints weight = 3514.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.170510 restraints weight = 2630.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.170524 restraints weight = 2398.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.170524 restraints weight = 2391.559| |-----------------------------------------------------------------------------| r_work (final): 0.4266 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.218439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.180495 restraints weight = 10475.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.183662 restraints weight = 4490.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.185804 restraints weight = 3238.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.185954 restraints weight = 2961.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.185953 restraints weight = 2898.736| |-----------------------------------------------------------------------------| r_work (final): 0.4333 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.190249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.181504 restraints weight = 8160.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.182716 restraints weight = 3334.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.183379 restraints weight = 1961.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.183606 restraints weight = 1476.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.183607 restraints weight = 1334.202| |-----------------------------------------------------------------------------| r_work (final): 0.4588 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.198799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.183542 restraints weight = 2735.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.190280 restraints weight = 677.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.193589 restraints weight = 245.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.195398 restraints weight = 126.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.196204 restraints weight = 80.294| |-----------------------------------------------------------------------------| r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4471 moved from start: 10.7386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.095 23032 Z= 0.984 Angle : 1.559 27.240 31990 Z= 0.913 Chirality : 0.080 0.530 3552 Planarity : 0.011 0.127 3300 Dihedral : 26.288 173.211 4984 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 76.76 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.95 % Favored : 86.49 % Rotamer: Outliers : 0.82 % Allowed : 5.92 % Favored : 93.27 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -2.52 (0.18), residues: 2132 helix: -0.76 (0.15), residues: 1116 sheet: -2.47 (0.31), residues: 228 loop : -2.66 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 115 TYR 0.116 0.004 TYR K 237 PHE 0.047 0.003 PHE A 138 TRP 0.010 0.002 TRP C 167 HIS 0.007 0.001 HIS I 489 Details of bonding type rmsd/Z covalent geometry : bond 0.01994 / 0.98 (23016) covalent geometry : angle 1.55410 / 0.91 (31966) hydrogen bonds : bond 0.17984 / 12.34 ( 1281) hydrogen bonds : angle 8.26076 / 5.91 ( 3491) metal coordination : bond 0.02046 / 1.41 ( 16) metal coordination : angle 4.81059 / 2.82 ( 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 126 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.9077 (mttt) cc_final: 0.8694 (mttt) REVERT: I 112 GLN cc_start: 0.8459 (tp40) cc_final: 0.8184 (tp40) REVERT: I 134 ARG cc_start: 0.8354 (ptt180) cc_final: 0.8090 (ptt-90) REVERT: I 146 GLU cc_start: 0.8648 (pt0) cc_final: 0.8412 (mt-10) REVERT: I 151 ARG cc_start: 0.8622 (mmp80) cc_final: 0.8355 (mmp80) REVERT: I 158 LYS cc_start: 0.8527 (mttt) cc_final: 0.7932 (mmtp) REVERT: I 202 PHE cc_start: 0.8509 (t80) cc_final: 0.8195 (t80) REVERT: I 224 GLN cc_start: 0.9126 (mt0) cc_final: 0.8790 (tm-30) REVERT: I 270 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7881 (pm20) REVERT: I 498 ASN cc_start: 0.7272 (t0) cc_final: 0.6439 (t0) REVERT: I 502 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.7636 (tpp80) outliers start: 4 outliers final: 2 residues processed: 126 average time/residue: 0.1977 time to fit residues: 30.3214 Evaluate side-chains 110 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.202 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: 0.0161 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 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: 0.0141 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0072 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0135 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: 0.1980 chunk 42 optimal weight: 0.1980 chunk 149 optimal weight: 0.1980 chunk 206 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 196 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 8 ASN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN I 498 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.174366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.143528 restraints weight = 37918.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.150439 restraints weight = 21225.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.155387 restraints weight = 13566.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.158870 restraints weight = 9366.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.161366 restraints weight = 6855.165| |-----------------------------------------------------------------------------| r_work (final): 0.4360 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.221227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.218553 restraints weight = 8496.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.220140 restraints weight = 3076.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.220822 restraints weight = 1248.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.221090 restraints weight = 572.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.221231 restraints weight = 346.250| |-----------------------------------------------------------------------------| r_work (final): 0.4746 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.219476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.182406 restraints weight = 10883.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.184113 restraints weight = 4431.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.184450 restraints weight = 3195.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.186762 restraints weight = 3036.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.186887 restraints weight = 2892.799| |-----------------------------------------------------------------------------| r_work (final): 0.4347 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.194410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.185575 restraints weight = 8301.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.186703 restraints weight = 3267.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.187227 restraints weight = 1979.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.187530 restraints weight = 1600.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.187562 restraints weight = 1418.504| |-----------------------------------------------------------------------------| r_work (final): 0.4600 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.206034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.196003 restraints weight = 7710.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.198130 restraints weight = 2971.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.199148 restraints weight = 1851.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.199210 restraints weight = 1507.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.199246 restraints weight = 1477.945| |-----------------------------------------------------------------------------| r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4221 moved from start: 10.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 1.214 23032 Z= 0.944 Angle : 1.469 27.988 31990 Z= 0.870 Chirality : 0.077 0.491 3552 Planarity : 0.012 0.128 3300 Dihedral : 26.355 174.161 4984 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 68.43 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.51 % Favored : 88.93 % Rotamer: Outliers : 0.20 % Allowed : 3.88 % Favored : 95.92 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.16 % 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: -2.52 (0.18), residues: 2132 helix: -0.86 (0.15), residues: 1104 sheet: -2.55 (0.31), residues: 228 loop : -2.43 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG C 128 TYR 0.092 0.004 TYR I 237 PHE 0.028 0.002 PHE K 138 TRP 0.012 0.003 TRP C 167 HIS 0.004 0.001 HIS I 489 Details of bonding type rmsd/Z covalent geometry : bond 0.02124 / 0.94 (23016) covalent geometry : angle 1.46390 / 0.87 (31966) hydrogen bonds : bond 0.17222 / 11.87 ( 1281) hydrogen bonds : angle 8.07393 / 5.80 ( 3491) metal coordination : bond 0.01611 / 1.14 ( 16) metal coordination : angle 4.68303 / 2.85 ( 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 120 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.9151 (mttt) cc_final: 0.8755 (mttt) REVERT: I 112 GLN cc_start: 0.8255 (tp40) cc_final: 0.7890 (tp40) REVERT: I 123 LYS cc_start: 0.7410 (tttt) cc_final: 0.7182 (tttp) REVERT: I 134 ARG cc_start: 0.8246 (ptt180) cc_final: 0.7975 (ptt180) REVERT: I 154 MET cc_start: 0.8313 (mmt) cc_final: 0.7424 (mmt) REVERT: I 158 LYS cc_start: 0.8721 (mttt) cc_final: 0.8054 (mttm) REVERT: I 224 GLN cc_start: 0.9061 (mt0) cc_final: 0.8796 (tm-30) REVERT: I 236 GLN cc_start: 0.6781 (pt0) cc_final: 0.6432 (pt0) REVERT: I 268 ARG cc_start: 0.7554 (mmm160) cc_final: 0.7180 (mmp80) REVERT: I 270 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7827 (pm20) REVERT: I 273 GLN cc_start: 0.8343 (mt0) cc_final: 0.7858 (mt0) REVERT: I 392 MET cc_start: 0.5788 (mmt) cc_final: 0.5538 (mmt) REVERT: I 429 ASP cc_start: 0.7869 (m-30) cc_final: 0.7666 (m-30) REVERT: I 502 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.7554 (tpp80) REVERT: I 515 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8309 (mmtp) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.2138 time to fit residues: 30.9034 Evaluate side-chains 116 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.241 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0154 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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 : 0.012 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: 0.0117 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 129 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 131 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 172 optimal weight: 0.0870 chunk 24 optimal weight: 0.0770 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 5 ASN ** I 40 GLN ** 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 = 0.4519 r_free = 0.4519 target = 0.174906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.145156 restraints weight = 36940.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.151849 restraints weight = 21004.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.156366 restraints weight = 13572.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.159620 restraints weight = 9520.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.161881 restraints weight = 7073.931| |-----------------------------------------------------------------------------| r_work (final): 0.4396 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.220492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.213465 restraints weight = 8310.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.215580 restraints weight = 2810.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.216262 restraints weight = 1236.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.216262 restraints weight = 809.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.216262 restraints weight = 809.458| |-----------------------------------------------------------------------------| r_work (final): 0.4636 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.219499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.183304 restraints weight = 10508.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.183623 restraints weight = 4596.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.187505 restraints weight = 3341.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.187625 restraints weight = 2766.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.187625 restraints weight = 2713.389| |-----------------------------------------------------------------------------| r_work (final): 0.4347 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.196030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.186770 restraints weight = 8244.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.188290 restraints weight = 3000.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.188931 restraints weight = 1755.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.188931 restraints weight = 1409.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.188931 restraints weight = 1409.569| |-----------------------------------------------------------------------------| r_work (final): 0.4601 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.207043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.199178 restraints weight = 6766.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.200028 restraints weight = 3307.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.200046 restraints weight = 2562.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.201038 restraints weight = 2526.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.201204 restraints weight = 2081.131| |-----------------------------------------------------------------------------| r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4288 moved from start: 10.8117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.450 23032 Z= 0.810 Angle : 1.338 20.907 31990 Z= 0.806 Chirality : 0.074 0.483 3552 Planarity : 0.010 0.112 3300 Dihedral : 26.383 173.189 4984 Min Nonbonded Distance : 1.473 Molprobity Statistics. All-atom Clashscore : 64.76 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.26 % Favored : 88.37 % Rotamer: Outliers : 0.61 % Allowed : 3.47 % Favored : 95.92 % Cbeta Deviations : 1.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.97 % 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: -2.44 (0.18), residues: 2132 helix: -0.75 (0.15), residues: 1108 sheet: -2.43 (0.31), residues: 228 loop : -2.51 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 115 TYR 0.080 0.004 TYR C 237 PHE 0.021 0.002 PHE I 202 TRP 0.008 0.002 TRP A 167 HIS 0.003 0.001 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01117 / 0.81 (23016) covalent geometry : angle 1.33201 / 0.81 (31966) hydrogen bonds : bond 0.16348 / 11.28 ( 1281) hydrogen bonds : angle 7.93132 / 5.69 ( 3491) metal coordination : bond 0.01783 / 1.26 ( 16) metal coordination : angle 4.81832 / 2.92 ( 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 126 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 26 MET cc_start: 0.8047 (mpp) cc_final: 0.7703 (pmm) REVERT: I 112 GLN cc_start: 0.8430 (tp40) cc_final: 0.8096 (tp40) REVERT: I 153 ARG cc_start: 0.7842 (tpt170) cc_final: 0.7520 (tmt-80) REVERT: I 180 LYS cc_start: 0.8738 (ptpp) cc_final: 0.8274 (mmtt) REVERT: I 216 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8361 (mt) REVERT: I 268 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7204 (mmp80) REVERT: I 270 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7841 (pm20) REVERT: I 273 GLN cc_start: 0.8263 (mt0) cc_final: 0.7821 (mt0) REVERT: I 392 MET cc_start: 0.5604 (mmt) cc_final: 0.5375 (mmt) REVERT: I 478 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7779 (ttt180) REVERT: I 515 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8304 (pttt) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.2142 time to fit residues: 32.1318 Evaluate side-chains 114 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.199 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: 0.0143 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 : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0124 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: 0.0107 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: 0.0050 chunk 26 optimal weight: 0.1980 chunk 227 optimal weight: 3.9990 chunk 135 optimal weight: 0.0670 chunk 112 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 0.0000 chunk 184 optimal weight: 0.9980 chunk 203 optimal weight: 0.3980 chunk 161 optimal weight: 0.0050 overall best weight: 0.0550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 HIS ** 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 = 0.4569 r_free = 0.4569 target = 0.183531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.154629 restraints weight = 36762.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.160996 restraints weight = 21360.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.165344 restraints weight = 13994.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.168420 restraints weight = 9941.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.170516 restraints weight = 7447.357| |-----------------------------------------------------------------------------| r_work (final): 0.4411 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.220276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.162818 restraints weight = 8243.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.166064 restraints weight = 3973.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.172812 restraints weight = 2974.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.173275 restraints weight = 2583.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.173354 restraints weight = 2461.453| |-----------------------------------------------------------------------------| r_work (final): 0.4334 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.220375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.182449 restraints weight = 10335.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.183602 restraints weight = 4472.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.187123 restraints weight = 3438.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.186676 restraints weight = 3121.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.186676 restraints weight = 2911.027| |-----------------------------------------------------------------------------| r_work (final): 0.4358 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.197709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.188923 restraints weight = 8299.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.190293 restraints weight = 3377.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.190866 restraints weight = 2025.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.191104 restraints weight = 1679.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.191104 restraints weight = 1570.857| |-----------------------------------------------------------------------------| r_work (final): 0.4611 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.212970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.203115 restraints weight = 6986.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.204393 restraints weight = 3498.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.205281 restraints weight = 2734.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.205281 restraints weight = 2453.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.205281 restraints weight = 2451.647| |-----------------------------------------------------------------------------| r_work (final): 0.4677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4257 moved from start: 10.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.309 23032 Z= 0.690 Angle : 1.369 21.165 31990 Z= 0.832 Chirality : 0.075 0.591 3552 Planarity : 0.010 0.114 3300 Dihedral : 26.458 173.071 4984 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 61.12 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.44 % Favored : 88.18 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 1.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.97 % 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: -2.45 (0.18), residues: 2132 helix: -0.63 (0.15), residues: 1104 sheet: -2.39 (0.31), residues: 228 loop : -2.73 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 115 TYR 0.076 0.004 TYR C 237 PHE 0.017 0.002 PHE C 138 TRP 0.008 0.003 TRP C 167 HIS 0.008 0.002 HIS C 489 Details of bonding type rmsd/Z covalent geometry : bond 0.01001 / 0.69 (23016) covalent geometry : angle 1.36309 / 0.83 (31966) hydrogen bonds : bond 0.19334 / 13.06 ( 1281) hydrogen bonds : angle 7.82312 / 5.64 ( 3491) metal coordination : bond 0.01659 / 1.18 ( 16) metal coordination : angle 4.79779 / 2.90 ( 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 116 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 112 GLN cc_start: 0.8295 (tp40) cc_final: 0.8093 (tp-100) REVERT: I 134 ARG cc_start: 0.8148 (ptt180) cc_final: 0.7910 (ptt180) REVERT: I 151 ARG cc_start: 0.8433 (mmp80) cc_final: 0.7905 (tpt170) REVERT: I 153 ARG cc_start: 0.7636 (tpt170) cc_final: 0.7374 (tmt-80) REVERT: I 270 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7820 (pm20) REVERT: I 273 GLN cc_start: 0.8226 (mt0) cc_final: 0.7732 (mt0) REVERT: I 290 GLN cc_start: 0.9036 (mt0) cc_final: 0.8692 (mt0) REVERT: I 366 VAL cc_start: 0.8907 (m) cc_final: 0.8646 (m) REVERT: I 392 MET cc_start: 0.5625 (mmt) cc_final: 0.5384 (mmt) REVERT: I 515 LYS cc_start: 0.8543 (mmtt) cc_final: 0.7957 (pttt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2106 time to fit residues: 29.3310 Evaluate side-chains 112 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.201 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: 0.0153 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: 0.0146 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: 0.0111 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 : 0.005 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: 0.0144 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 : 0.012 ------------------------------------------------------------------------------- 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: 0.0020 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 202 optimal weight: 30.0000 chunk 87 optimal weight: 0.8980 chunk 172 optimal weight: 0.0050 chunk 86 optimal weight: 40.0000 chunk 61 optimal weight: 0.0270 chunk 29 optimal weight: 0.0970 chunk 210 optimal weight: 9.9990 overall best weight: 0.2058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 HIS ** 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 = 0.4540 r_free = 0.4540 target = 0.177842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.149203 restraints weight = 36655.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.155507 restraints weight = 21433.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.159918 restraints weight = 14057.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.163086 restraints weight = 9939.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.165434 restraints weight = 7431.277| |-----------------------------------------------------------------------------| r_work (final): 0.4432 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.220957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.169789 restraints weight = 8355.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.167811 restraints weight = 6286.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.168517 restraints weight = 4883.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.168519 restraints weight = 4123.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.168519 restraints weight = 4121.586| |-----------------------------------------------------------------------------| r_work (final): 0.4306 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.220235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.182028 restraints weight = 10341.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.183643 restraints weight = 4521.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.187205 restraints weight = 3329.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.187501 restraints weight = 3133.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.187106 restraints weight = 3017.957| |-----------------------------------------------------------------------------| r_work (final): 0.4371 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.198164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.189817 restraints weight = 7961.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.191433 restraints weight = 2974.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.191985 restraints weight = 1742.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.191984 restraints weight = 1498.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.191984 restraints weight = 1498.458| |-----------------------------------------------------------------------------| r_work (final): 0.4615 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.212868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.182080 restraints weight = 2343.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.190151 restraints weight = 874.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.194543 restraints weight = 444.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.196577 restraints weight = 282.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.197861 restraints weight = 214.070| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4272 moved from start: 10.8655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.309 23032 Z= 0.594 Angle : 1.288 21.294 31990 Z= 0.760 Chirality : 0.073 0.464 3552 Planarity : 0.013 0.207 3300 Dihedral : 26.465 172.714 4984 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 62.03 Ramachandran Plot: Outliers : 0.75 % Allowed : 10.51 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.35 % 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: -2.40 (0.18), residues: 2132 helix: -0.66 (0.16), residues: 1112 sheet: -2.39 (0.32), residues: 228 loop : -2.61 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG I 128 TYR 0.078 0.003 TYR K 237 PHE 0.017 0.002 PHE C 138 TRP 0.006 0.003 TRP A 167 HIS 0.006 0.001 HIS C 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00912 / 0.59 (23016) covalent geometry : angle 1.28128 / 0.76 (31966) hydrogen bonds : bond 0.20950 / 14.55 ( 1281) hydrogen bonds : angle 7.71639 / 5.52 ( 3491) metal coordination : bond 0.01616 / 1.15 ( 16) metal coordination : angle 4.90106 / 2.97 ( 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 119 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 LYS cc_start: 0.9087 (mttt) cc_final: 0.8733 (mttt) REVERT: I 153 ARG cc_start: 0.7719 (tpt170) cc_final: 0.7347 (tmt-80) REVERT: I 180 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8575 (mmtt) REVERT: I 246 GLU cc_start: 0.8385 (mp0) cc_final: 0.8104 (mp0) REVERT: I 270 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7874 (pm20) REVERT: I 273 GLN cc_start: 0.8201 (mt0) cc_final: 0.7764 (mt0) REVERT: I 290 GLN cc_start: 0.9005 (mt0) cc_final: 0.8700 (mt0) REVERT: I 366 VAL cc_start: 0.8876 (m) cc_final: 0.8626 (m) REVERT: I 392 MET cc_start: 0.5737 (mmt) cc_final: 0.5453 (mmt) REVERT: I 478 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7564 (ttt180) REVERT: I 502 ARG cc_start: 0.8788 (mtp-110) cc_final: 0.8011 (tpp80) REVERT: I 515 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8045 (pttt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2128 time to fit residues: 30.2707 Evaluate side-chains 113 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.239 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: 0.0153 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0147 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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: 0.0113 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: 0.0108 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- 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: 0.9980 chunk 180 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.0010 chunk 34 optimal weight: 0.0470 chunk 203 optimal weight: 0.4980 chunk 229 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 HIS ** 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 = 0.4544 r_free = 0.4544 target = 0.180813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.151809 restraints weight = 35574.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.158007 restraints weight = 21210.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.162403 restraints weight = 14009.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.165428 restraints weight = 9963.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.167873 restraints weight = 7520.525| |-----------------------------------------------------------------------------| r_work (final): 0.4415 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.220207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.168931 restraints weight = 7972.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.170123 restraints weight = 5315.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.169873 restraints weight = 3587.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.169997 restraints weight = 3370.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.169971 restraints weight = 3182.547| |-----------------------------------------------------------------------------| r_work (final): 0.4290 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.219513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.181368 restraints weight = 10638.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.183128 restraints weight = 4582.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.185792 restraints weight = 3484.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.186060 restraints weight = 3136.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.186852 restraints weight = 2904.055| |-----------------------------------------------------------------------------| r_work (final): 0.4356 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.199936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.190848 restraints weight = 8013.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.192601 restraints weight = 2794.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.193354 restraints weight = 1718.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.193358 restraints weight = 1450.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.193357 restraints weight = 1447.037| |-----------------------------------------------------------------------------| r_work (final): 0.4623 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.203795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.176625 restraints weight = 2603.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.182749 restraints weight = 886.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.186376 restraints weight = 447.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.188719 restraints weight = 295.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.190063 restraints weight = 224.087| |-----------------------------------------------------------------------------| r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4225 moved from start: 10.8925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.309 23032 Z= 0.568 Angle : 1.256 21.224 31990 Z= 0.742 Chirality : 0.074 0.461 3552 Planarity : 0.012 0.144 3300 Dihedral : 26.461 176.623 4984 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 59.54 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.13 % Favored : 89.31 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.55 % 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: -2.34 (0.18), residues: 2132 helix: -0.58 (0.16), residues: 1120 sheet: -2.28 (0.33), residues: 220 loop : -2.68 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 531 TYR 0.044 0.003 TYR C 396 PHE 0.025 0.002 PHE A 138 TRP 0.008 0.002 TRP K 167 HIS 0.005 0.001 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.57 (23016) covalent geometry : angle 1.24831 / 0.74 (31966) hydrogen bonds : bond 0.20189 / 13.87 ( 1281) hydrogen bonds : angle 7.52789 / 5.36 ( 3491) metal coordination : bond 0.01555 / 1.13 ( 16) metal coordination : angle 5.20587 / 3.17 ( 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 126 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 27 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6903 (tt0) REVERT: I 74 LYS cc_start: 0.9138 (mttt) cc_final: 0.8765 (mttt) REVERT: I 153 ARG cc_start: 0.7534 (tpt170) cc_final: 0.7300 (tmt-80) REVERT: I 270 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7865 (pm20) REVERT: I 273 GLN cc_start: 0.8279 (mt0) cc_final: 0.7868 (mt0) REVERT: I 366 VAL cc_start: 0.8944 (m) cc_final: 0.8675 (m) REVERT: I 478 ARG cc_start: 0.8385 (ttp80) cc_final: 0.7710 (ttt180) REVERT: I 498 ASN cc_start: 0.7800 (t0) cc_final: 0.6917 (t0) REVERT: I 502 ARG cc_start: 0.8714 (mtp-110) cc_final: 0.8120 (tpp80) REVERT: I 515 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7796 (pttt) REVERT: I 534 PHE cc_start: 0.7293 (t80) cc_final: 0.6993 (t80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1975 time to fit residues: 30.1431 Evaluate side-chains 118 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.226 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: 0.0172 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: 0.0146 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 : 0.011 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 : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0129 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: 1.9990 chunk 219 optimal weight: 0.7980 chunk 119 optimal weight: 0.0670 chunk 194 optimal weight: 0.7980 chunk 175 optimal weight: 0.3980 chunk 155 optimal weight: 0.3980 chunk 94 optimal weight: 30.0000 chunk 123 optimal weight: 0.0670 chunk 59 optimal weight: 0.0170 chunk 214 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 HIS ** 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 = 0.4562 r_free = 0.4562 target = 0.182388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.152756 restraints weight = 35668.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.159164 restraints weight = 21201.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.163814 restraints weight = 13937.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.167102 restraints weight = 9835.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.169338 restraints weight = 7321.407| |-----------------------------------------------------------------------------| r_work (final): 0.4541 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.220771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.166122 restraints weight = 8571.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.167361 restraints weight = 5493.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.168909 restraints weight = 3880.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.168642 restraints weight = 3584.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.168761 restraints weight = 3503.143| |-----------------------------------------------------------------------------| r_work (final): 0.4298 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.219910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.187837 restraints weight = 10782.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.187641 restraints weight = 6093.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.188270 restraints weight = 4568.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.188091 restraints weight = 3943.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.188242 restraints weight = 3976.194| |-----------------------------------------------------------------------------| r_work (final): 0.4387 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.201505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.192614 restraints weight = 7958.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.194451 restraints weight = 2920.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.195212 restraints weight = 1784.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.195220 restraints weight = 1478.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.195220 restraints weight = 1473.661| |-----------------------------------------------------------------------------| r_work (final): 0.4652 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.216897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.207739 restraints weight = 6194.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.208985 restraints weight = 2970.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.209983 restraints weight = 2140.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.210457 restraints weight = 1693.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.210457 restraints weight = 1557.593| |-----------------------------------------------------------------------------| r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4163 moved from start: 10.9179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.310 23032 Z= 0.566 Angle : 1.242 21.419 31990 Z= 0.728 Chirality : 0.073 0.441 3552 Planarity : 0.012 0.165 3300 Dihedral : 26.466 172.311 4984 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 57.49 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.63 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.74 % 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: -2.31 (0.18), residues: 2132 helix: -0.63 (0.15), residues: 1116 sheet: -2.14 (0.32), residues: 220 loop : -2.57 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 128 TYR 0.053 0.004 TYR C 237 PHE 0.019 0.002 PHE K 138 TRP 0.007 0.002 TRP A 167 HIS 0.021 0.003 HIS C 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.57 (23016) covalent geometry : angle 1.23425 / 0.73 (31966) hydrogen bonds : bond 0.19563 / 13.46 ( 1281) hydrogen bonds : angle 7.72468 / 5.50 ( 3491) metal coordination : bond 0.01548 / 1.11 ( 16) metal coordination : angle 5.12469 / 3.12 ( 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 121 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 27 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6886 (tt0) REVERT: I 74 LYS cc_start: 0.9105 (mttt) cc_final: 0.8727 (mttt) REVERT: I 92 GLU cc_start: 0.7314 (tp30) cc_final: 0.7006 (tt0) REVERT: I 270 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7861 (pm20) REVERT: I 366 VAL cc_start: 0.8979 (m) cc_final: 0.8704 (m) REVERT: I 478 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7352 (ttt180) REVERT: I 515 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7679 (pttt) REVERT: I 534 PHE cc_start: 0.7260 (t80) cc_final: 0.6992 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2023 time to fit residues: 29.6595 Evaluate side-chains 109 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.228 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0152 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0140 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: 0.0114 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 : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0108 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 ------------------------------------------------------------------------------- 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: 0.0770 chunk 224 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.0970 chunk 163 optimal weight: 0.0970 chunk 179 optimal weight: 0.4980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 487 GLN ** I 489 HIS ** 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 = 0.4587 r_free = 0.4587 target = 0.187248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.157980 restraints weight = 35745.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.164737 restraints weight = 20703.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.169360 restraints weight = 13340.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.172646 restraints weight = 9320.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.175032 restraints weight = 6891.610| |-----------------------------------------------------------------------------| r_work (final): 0.4548 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.220936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.168319 restraints weight = 8095.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.170787 restraints weight = 5414.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.169859 restraints weight = 3812.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.170488 restraints weight = 4388.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.170656 restraints weight = 3613.989| |-----------------------------------------------------------------------------| r_work (final): 0.4336 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.219769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.183536 restraints weight = 10394.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.185086 restraints weight = 4384.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.185571 restraints weight = 3161.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.188422 restraints weight = 2981.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.188376 restraints weight = 2802.486| |-----------------------------------------------------------------------------| r_work (final): 0.4364 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.204763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.191779 restraints weight = 3399.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.195180 restraints weight = 850.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.196691 restraints weight = 331.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.197366 restraints weight = 195.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.197538 restraints weight = 155.184| |-----------------------------------------------------------------------------| r_work (final): 0.4803 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.209080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.188043 restraints weight = 2265.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.196702 restraints weight = 671.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.200951 restraints weight = 298.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.202562 restraints weight = 179.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.204092 restraints weight = 129.935| |-----------------------------------------------------------------------------| r_work (final): 0.4826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4120 moved from start: 10.9434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.310 23032 Z= 0.558 Angle : 1.203 20.911 31990 Z= 0.707 Chirality : 0.072 0.403 3552 Planarity : 0.013 0.230 3300 Dihedral : 26.425 174.626 4984 Min Nonbonded Distance : 1.467 Molprobity Statistics. All-atom Clashscore : 55.19 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.63 % Favored : 87.99 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.74 % 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: -2.16 (0.18), residues: 2132 helix: -0.47 (0.16), residues: 1104 sheet: -2.17 (0.32), residues: 220 loop : -2.50 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG K 128 TYR 0.093 0.004 TYR C 237 PHE 0.011 0.002 PHE C 138 TRP 0.006 0.002 TRP I 167 HIS 0.013 0.002 HIS C 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.56 (23016) covalent geometry : angle 1.19480 / 0.71 (31966) hydrogen bonds : bond 0.15596 / 10.71 ( 1281) hydrogen bonds : angle 7.62827 / 5.42 ( 3491) metal coordination : bond 0.01494 / 1.09 ( 16) metal coordination : angle 5.18559 / 3.19 ( 24) =============================================================================== Job complete usr+sys time: 4412.71 seconds wall clock time: 77 minutes 16.47 seconds (4636.47 seconds total)