Starting phenix.real_space_refine on Tue Jul 7 04:36:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxh_47288/07_2026/9dxh_47288.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxh_47288/07_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_47288/07_2026/9dxh_47288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxh_47288/07_2026/9dxh_47288.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dxh_47288/07_2026/9dxh_47288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxh_47288/07_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42532 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "C" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "E" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1087 Classifications: {'DNA': 34} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1052 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "G" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 796 Classifications: {'DNA': 25} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 24} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 767 Classifications: {'DNA': 24} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 23} Chain: "I" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "K" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8781 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "M" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1087 Classifications: {'DNA': 34} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 33} Chain: "N" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1052 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "O" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 796 Classifications: {'DNA': 25} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 24} Chain: "P" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 767 Classifications: {'DNA': 24} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5206 SG CYS A 320 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: 7.49, per 1000 atoms: 0.18 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: 3.73 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 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: 6.93 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: 10.55 Time building geometry restraints manager: 5.25 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: 6.550 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: 0.270 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 54.460 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.130 ------------------------------------------------------------------------------- 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 : 3.323 12.376 31990 Z= 2.501 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 3.32162 / 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 : 0.223 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: 0.2090 time to fit residues: 42.5147 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 : 0.201 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 : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0168 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0149 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 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=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: 5.9990 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 = 0.4482 r_free = 0.4482 target = 0.169688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.139705 restraints weight = 35483.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.146026 restraints weight = 20738.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.150368 restraints weight = 13473.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.153460 restraints weight = 9468.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.155629 restraints weight = 7075.980| |-----------------------------------------------------------------------------| r_work (final): 0.4337 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.217990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.159072 restraints weight = 9392.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.161958 restraints weight = 4481.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.169281 restraints weight = 3403.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.169785 restraints weight = 2843.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.169872 restraints weight = 2669.162| |-----------------------------------------------------------------------------| r_work (final): 0.4262 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.218166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.183011 restraints weight = 10834.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.182916 restraints weight = 4493.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.183536 restraints weight = 3235.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.183618 restraints weight = 3018.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.183602 restraints weight = 2980.550| |-----------------------------------------------------------------------------| r_work (final): 0.4339 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.189387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.180925 restraints weight = 7654.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.181768 restraints weight = 4324.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.182033 restraints weight = 3250.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.182033 restraints weight = 2912.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.182033 restraints weight = 2912.873| |-----------------------------------------------------------------------------| r_work (final): 0.4545 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.192998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.183182 restraints weight = 8232.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.185124 restraints weight = 4071.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.185873 restraints weight = 2710.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.186710 restraints weight = 2176.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.186983 restraints weight = 1885.580| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4422 moved from start: 10.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.162 23032 Z= 1.464 Angle : 2.620 53.816 31990 Z= 1.401 Chirality : 0.169 4.894 3552 Planarity : 0.017 0.217 3300 Dihedral : 26.024 174.832 4984 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 119.03 Ramachandran Plot: Outliers : 2.63 % Allowed : 11.82 % Favored : 85.55 % Rotamer: Outliers : 2.45 % Allowed : 7.35 % Favored : 90.20 % Cbeta Deviations : 1.56 % 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: -2.42 (0.18), residues: 2132 helix: -0.76 (0.15), residues: 1104 sheet: -1.60 (0.33), residues: 240 loop : -2.75 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG K 153 TYR 0.114 0.007 TYR I 237 PHE 0.026 0.003 PHE I 532 TRP 0.013 0.005 TRP C 167 HIS 0.041 0.007 HIS I 489 Details of bonding type rmsd/Z covalent geometry : bond 0.03066 / 1.46 (23016) covalent geometry : angle 2.60277 / 1.40 (31966) hydrogen bonds : bond 0.25850 / 17.62 ( 1281) hydrogen bonds : angle 9.40348 / 6.70 ( 3491) metal coordination : bond 0.05296 / 2.79 ( 16) metal coordination : angle 11.22099 / 7.31 ( 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 : 0.167 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: 0.4616 (OUTLIER) cc_final: 0.3226 (tt) REVERT: I 31 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6150 (mtm-85) REVERT: I 46 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8893 (mttt) REVERT: I 85 TYR cc_start: 0.4743 (m-10) cc_final: 0.4326 (m-10) REVERT: I 112 GLN cc_start: 0.8395 (tp40) cc_final: 0.8074 (tp40) REVERT: I 134 ARG cc_start: 0.8863 (ttt180) cc_final: 0.8574 (ttm170) REVERT: I 154 MET cc_start: 0.7883 (mmt) cc_final: 0.7370 (mmt) REVERT: I 158 LYS cc_start: 0.8764 (mttt) cc_final: 0.8297 (mttt) REVERT: I 185 LEU cc_start: 0.9022 (mt) cc_final: 0.8756 (mm) REVERT: I 224 GLN cc_start: 0.9004 (mt0) cc_final: 0.8736 (tm-30) REVERT: I 270 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7907 (pm20) REVERT: I 367 GLU cc_start: 0.8456 (pt0) cc_final: 0.8194 (pt0) REVERT: I 428 PHE cc_start: 0.6654 (m-10) cc_final: 0.6400 (m-10) outliers start: 12 outliers final: 1 residues processed: 147 average time/residue: 0.1891 time to fit residues: 33.5861 Evaluate side-chains 124 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.174 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0160 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0151 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0133 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: 0.0110 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: 0.9980 chunk 121 optimal weight: 0.0870 chunk 178 optimal weight: 0.9980 chunk 105 optimal weight: 0.0470 chunk 197 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 469 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 = 0.4475 r_free = 0.4475 target = 0.170706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.140402 restraints weight = 38658.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.147155 restraints weight = 21630.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.151837 restraints weight = 13660.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.155119 restraints weight = 9388.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.157616 restraints weight = 6899.686| |-----------------------------------------------------------------------------| r_work (final): 0.4324 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.218678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.216420 restraints weight = 8744.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.217581 restraints weight = 3241.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.218229 restraints weight = 1590.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.218554 restraints weight = 722.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.218779 restraints weight = 359.364| |-----------------------------------------------------------------------------| r_work (final): 0.4732 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.219209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.183308 restraints weight = 10800.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.183199 restraints weight = 4651.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.183986 restraints weight = 3220.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.183986 restraints weight = 3052.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.183986 restraints weight = 3052.659| |-----------------------------------------------------------------------------| r_work (final): 0.4353 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.186909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.178055 restraints weight = 8124.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.179393 restraints weight = 3393.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.180019 restraints weight = 1860.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.180212 restraints weight = 1393.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.180212 restraints weight = 1278.286| |-----------------------------------------------------------------------------| r_work (final): 0.4549 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.200021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.192060 restraints weight = 7527.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.193846 restraints weight = 2982.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.194611 restraints weight = 1914.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.195199 restraints weight = 1432.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.195199 restraints weight = 1256.097| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4264 moved from start: 10.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.189 23032 Z= 1.041 Angle : 1.992 62.293 31990 Z= 1.101 Chirality : 0.091 0.758 3552 Planarity : 0.014 0.155 3300 Dihedral : 26.323 174.076 4984 Min Nonbonded Distance : 1.391 Molprobity Statistics. All-atom Clashscore : 91.30 Ramachandran Plot: Outliers : 1.50 % Allowed : 12.76 % Favored : 85.74 % Rotamer: Outliers : 0.61 % Allowed : 5.51 % Favored : 93.88 % Cbeta Deviations : 0.98 % 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: -2.79 (0.18), residues: 2132 helix: -0.95 (0.15), residues: 1108 sheet: -2.21 (0.32), residues: 228 loop : -2.96 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG I 115 TYR 0.119 0.005 TYR I 237 PHE 0.042 0.004 PHE K 138 TRP 0.011 0.003 TRP A 167 HIS 0.020 0.005 HIS C 489 Details of bonding type rmsd/Z covalent geometry : bond 0.02025 / 1.04 (23016) covalent geometry : angle 1.98635 / 1.10 (31966) hydrogen bonds : bond 0.20593 / 14.00 ( 1281) hydrogen bonds : angle 8.60087 / 6.15 ( 3491) metal coordination : bond 0.01576 / 1.07 ( 16) metal coordination : angle 5.89549 / 3.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 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: symmetry clash revert: symmetry clash REVERT: I 112 GLN cc_start: 0.8475 (tp40) cc_final: 0.8136 (tp40) REVERT: I 134 ARG cc_start: 0.8655 (ttt180) cc_final: 0.8315 (mtm110) REVERT: I 135 GLN cc_start: 0.9055 (mm110) cc_final: 0.8837 (mm110) REVERT: I 141 PHE cc_start: 0.8363 (t80) cc_final: 0.7950 (t80) REVERT: I 202 PHE cc_start: 0.8304 (t80) cc_final: 0.8023 (t80) REVERT: I 224 GLN cc_start: 0.9007 (mt0) cc_final: 0.8791 (tm-30) REVERT: I 270 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7907 (pm20) REVERT: I 367 GLU cc_start: 0.8557 (pt0) cc_final: 0.8198 (pt0) REVERT: I 428 PHE cc_start: 0.6671 (m-10) cc_final: 0.6358 (m-10) outliers start: 3 outliers final: 1 residues processed: 121 average time/residue: 0.1738 time to fit residues: 25.9977 Evaluate side-chains 113 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.231 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: 0.0095 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 : 0.020 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0156 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 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: 0.0115 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 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: 0.0115 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 226 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 140 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 203 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 5 ASN I 40 GLN ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN I 368 ASN ** I 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.171767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.142346 restraints weight = 36753.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.148952 restraints weight = 20952.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.153622 restraints weight = 13337.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.156923 restraints weight = 9167.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.159273 restraints weight = 6682.749| |-----------------------------------------------------------------------------| r_work (final): 0.4338 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.217649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.163547 restraints weight = 7233.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.169059 restraints weight = 3268.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.171205 restraints weight = 2463.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.176657 restraints weight = 2290.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.176862 restraints weight = 1947.325| |-----------------------------------------------------------------------------| r_work (final): 0.4310 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.218737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.184033 restraints weight = 10454.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.184013 restraints weight = 4399.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.184477 restraints weight = 3175.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.184802 restraints weight = 3022.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.184802 restraints weight = 2952.302| |-----------------------------------------------------------------------------| r_work (final): 0.4343 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.187940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.179427 restraints weight = 7834.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.180637 restraints weight = 3366.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.181317 restraints weight = 1945.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.181580 restraints weight = 1413.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.181580 restraints weight = 1252.513| |-----------------------------------------------------------------------------| r_work (final): 0.4546 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.203009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.193750 restraints weight = 7299.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.195525 restraints weight = 2592.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.196388 restraints weight = 1672.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.196592 restraints weight = 1409.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.196969 restraints weight = 1327.887| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4377 moved from start: 10.7423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.082 23032 Z= 0.978 Angle : 1.521 24.577 31990 Z= 0.900 Chirality : 0.080 0.444 3552 Planarity : 0.012 0.159 3300 Dihedral : 26.524 173.340 4984 Min Nonbonded Distance : 1.411 Molprobity Statistics. All-atom Clashscore : 75.39 Ramachandran Plot: Outliers : 0.75 % Allowed : 11.63 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Cbeta Deviations : 0.98 % 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: -0.74 (0.16), residues: 1124 sheet: -2.56 (0.30), residues: 228 loop : -2.51 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG K 115 TYR 0.114 0.005 TYR K 237 PHE 0.013 0.002 PHE C 532 TRP 0.009 0.002 TRP I 167 HIS 0.005 0.001 HIS I 489 Details of bonding type rmsd/Z covalent geometry : bond 0.02020 / 0.98 (23016) covalent geometry : angle 1.51573 / 0.90 (31966) hydrogen bonds : bond 0.17898 / 12.33 ( 1281) hydrogen bonds : angle 8.15911 / 5.85 ( 3491) metal coordination : bond 0.02019 / 1.39 ( 16) metal coordination : angle 4.67603 / 2.75 ( 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 123 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 6 ILE cc_start: 0.9117 (mt) cc_final: 0.8869 (mm) REVERT: I 74 LYS cc_start: 0.9168 (mttt) cc_final: 0.8766 (mttt) REVERT: I 112 GLN cc_start: 0.8318 (tp40) cc_final: 0.8068 (tp40) REVERT: I 123 LYS cc_start: 0.8205 (tptm) cc_final: 0.7889 (tttp) REVERT: I 224 GLN cc_start: 0.9092 (mt0) cc_final: 0.8806 (tm-30) REVERT: I 270 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7885 (pm20) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1716 time to fit residues: 25.7598 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 : 0.234 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: 0.0149 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 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: 0.0150 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0082 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: 0.0117 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 74 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 149 optimal weight: 0.1980 chunk 206 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 61 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 196 optimal weight: 0.0970 chunk 81 optimal weight: 0.5980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 5 ASN ** I 177 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 = 0.4512 r_free = 0.4512 target = 0.175444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.145998 restraints weight = 37499.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.152618 restraints weight = 21195.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.157283 restraints weight = 13569.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.160532 restraints weight = 9366.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.162956 restraints weight = 6859.795| |-----------------------------------------------------------------------------| r_work (final): 0.4382 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.220101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.215162 restraints weight = 7570.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.217087 restraints weight = 2739.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.218408 restraints weight = 1152.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.218868 restraints weight = 518.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.219223 restraints weight = 320.726| |-----------------------------------------------------------------------------| r_work (final): 0.4666 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.219637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.183836 restraints weight = 10904.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.185339 restraints weight = 4342.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.185709 restraints weight = 3186.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.187917 restraints weight = 2962.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.187946 restraints weight = 2822.758| |-----------------------------------------------------------------------------| r_work (final): 0.4352 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.193846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.184790 restraints weight = 7908.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.186151 restraints weight = 2869.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.186824 restraints weight = 1666.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.186908 restraints weight = 1322.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.186908 restraints weight = 1260.624| |-----------------------------------------------------------------------------| r_work (final): 0.4601 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.203257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.190379 restraints weight = 2938.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.196121 restraints weight = 888.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.199943 restraints weight = 399.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.200897 restraints weight = 163.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.201825 restraints weight = 84.945| |-----------------------------------------------------------------------------| r_work (final): 0.4729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4294 moved from start: 10.7782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.861 23032 Z= 0.875 Angle : 1.507 33.070 31990 Z= 0.881 Chirality : 0.078 0.427 3552 Planarity : 0.012 0.197 3300 Dihedral : 26.450 173.450 4984 Min Nonbonded Distance : 1.431 Molprobity Statistics. All-atom Clashscore : 67.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.51 % Favored : 89.31 % Rotamer: Outliers : 0.41 % Allowed : 3.88 % Favored : 95.71 % Cbeta Deviations : 0.78 % 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: -2.46 (0.18), residues: 2132 helix: -0.71 (0.15), residues: 1116 sheet: -2.57 (0.30), residues: 228 loop : -2.58 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.002 ARG K 128 TYR 0.080 0.005 TYR K 237 PHE 0.037 0.004 PHE K 138 TRP 0.019 0.006 TRP I 167 HIS 0.004 0.001 HIS I 489 Details of bonding type rmsd/Z covalent geometry : bond 0.01670 / 0.88 (23016) covalent geometry : angle 1.50130 / 0.88 (31966) hydrogen bonds : bond 0.16802 / 11.60 ( 1281) hydrogen bonds : angle 7.78633 / 5.59 ( 3491) metal coordination : bond 0.01647 / 1.18 ( 16) metal coordination : angle 4.81532 / 2.93 ( 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 125 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 6 ILE cc_start: 0.9098 (mt) cc_final: 0.8883 (mm) REVERT: I 27 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8122 (mp0) REVERT: I 123 LYS cc_start: 0.8390 (tptm) cc_final: 0.8131 (tttm) REVERT: I 134 ARG cc_start: 0.8530 (ttt180) cc_final: 0.8227 (mtm110) REVERT: I 146 GLU cc_start: 0.8720 (pt0) cc_final: 0.8237 (mp0) REVERT: I 224 GLN cc_start: 0.9031 (mt0) cc_final: 0.8831 (tm-30) REVERT: I 268 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7212 (mmp80) REVERT: I 270 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7836 (pm20) REVERT: I 273 GLN cc_start: 0.8277 (mt0) cc_final: 0.7823 (mt0) REVERT: I 484 ILE cc_start: 0.8702 (mm) cc_final: 0.8492 (mm) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1741 time to fit residues: 26.4657 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 : 0.226 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 : 0.012 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 : 0.014 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 : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0170 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: 0.0134 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: 0.0125 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- 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: 0.0020 chunk 9 optimal weight: 0.0970 chunk 129 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 212 optimal weight: 0.0980 chunk 3 optimal weight: 0.0020 chunk 131 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 172 optimal weight: 0.0010 chunk 24 optimal weight: 0.6980 overall best weight: 0.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 177 GLN ** 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 = 0.4530 r_free = 0.4530 target = 0.179522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.149942 restraints weight = 36472.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.156616 restraints weight = 21063.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.161279 restraints weight = 13531.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.164550 restraints weight = 9366.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.166927 restraints weight = 6863.420| |-----------------------------------------------------------------------------| r_work (final): 0.4400 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.221499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.159613 restraints weight = 9814.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.163128 restraints weight = 4690.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.164608 restraints weight = 3305.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.167719 restraints weight = 2937.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.167765 restraints weight = 2756.806| |-----------------------------------------------------------------------------| r_work (final): 0.4360 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.219964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.183005 restraints weight = 10519.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.184680 restraints weight = 4354.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.185097 restraints weight = 3205.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.185097 restraints weight = 2978.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.185097 restraints weight = 2978.305| |-----------------------------------------------------------------------------| r_work (final): 0.4355 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.196273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.187000 restraints weight = 7997.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.188525 restraints weight = 2897.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.189163 restraints weight = 1627.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.189166 restraints weight = 1374.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.189213 restraints weight = 1370.690| |-----------------------------------------------------------------------------| r_work (final): 0.4599 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.206799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.199348 restraints weight = 7064.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.200263 restraints weight = 3220.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.200940 restraints weight = 2460.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.200997 restraints weight = 2243.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.201073 restraints weight = 2057.102| |-----------------------------------------------------------------------------| r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 moved from start: 10.8140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.453 23032 Z= 0.821 Angle : 1.353 21.150 31990 Z= 0.807 Chirality : 0.076 0.419 3552 Planarity : 0.011 0.131 3300 Dihedral : 26.493 179.971 4984 Min Nonbonded Distance : 1.434 Molprobity Statistics. All-atom Clashscore : 66.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.69 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.78 % 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: -2.41 (0.18), residues: 2132 helix: -0.76 (0.15), residues: 1128 sheet: -2.51 (0.30), residues: 228 loop : -2.42 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG C 531 TYR 0.121 0.004 TYR A 237 PHE 0.041 0.003 PHE K 202 TRP 0.008 0.002 TRP C 167 HIS 0.004 0.001 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01144 / 0.82 (23016) covalent geometry : angle 1.34779 / 0.81 (31966) hydrogen bonds : bond 0.16701 / 11.44 ( 1281) hydrogen bonds : angle 7.81088 / 5.59 ( 3491) metal coordination : bond 0.01743 / 1.22 ( 16) metal coordination : angle 4.64831 / 2.82 ( 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 121 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.238 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 6 ILE cc_start: 0.9103 (mt) cc_final: 0.8861 (mm) REVERT: I 74 LYS cc_start: 0.9099 (mttt) cc_final: 0.8663 (mttp) REVERT: I 112 GLN cc_start: 0.8338 (tp-100) cc_final: 0.7904 (tp-100) REVERT: I 180 LYS cc_start: 0.8999 (ptpp) cc_final: 0.8488 (mmtt) REVERT: I 232 LYS cc_start: 0.7747 (mmtm) cc_final: 0.7360 (mmtt) REVERT: I 268 ARG cc_start: 0.7558 (mmm160) cc_final: 0.7254 (mmp80) REVERT: I 270 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7823 (pm20) REVERT: I 273 GLN cc_start: 0.8188 (mt0) cc_final: 0.7741 (mt0) REVERT: I 290 GLN cc_start: 0.9123 (mt0) cc_final: 0.8871 (mt0) REVERT: I 291 GLN cc_start: 0.8557 (pt0) cc_final: 0.7846 (pp30) REVERT: I 366 VAL cc_start: 0.8842 (m) cc_final: 0.8604 (m) REVERT: I 498 ASN cc_start: 0.7271 (t0) cc_final: 0.6225 (t0) REVERT: I 502 ARG cc_start: 0.8495 (mtp-110) cc_final: 0.7834 (tpp-160) REVERT: I 515 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8010 (pttt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1695 time to fit residues: 25.3140 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 : 0.167 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0093 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 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 : 0.007 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 : 0.009 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: 0.0110 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: 0.9980 chunk 26 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 135 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 203 optimal weight: 0.0870 chunk 161 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4542 r_free = 0.4542 target = 0.182551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.152979 restraints weight = 36066.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.159569 restraints weight = 21007.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.164183 restraints weight = 13577.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.167490 restraints weight = 9444.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.169686 restraints weight = 6932.427| |-----------------------------------------------------------------------------| r_work (final): 0.4408 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.220862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.216933 restraints weight = 8537.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.218576 restraints weight = 2935.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.219325 restraints weight = 1121.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.219822 restraints weight = 529.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.219937 restraints weight = 251.480| |-----------------------------------------------------------------------------| r_work (final): 0.4724 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.219250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.181036 restraints weight = 10350.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.182529 restraints weight = 4602.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.184949 restraints weight = 3431.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.185097 restraints weight = 3103.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.186740 restraints weight = 3034.938| |-----------------------------------------------------------------------------| r_work (final): 0.4352 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.198412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.189174 restraints weight = 7736.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.190851 restraints weight = 2907.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.191552 restraints weight = 1659.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.191750 restraints weight = 1340.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 12)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.191749 restraints weight = 1269.446| |-----------------------------------------------------------------------------| r_work (final): 0.4620 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.207216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.200282 restraints weight = 7086.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.201066 restraints weight = 3126.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.201674 restraints weight = 2440.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.201676 restraints weight = 2166.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.201676 restraints weight = 2160.065| |-----------------------------------------------------------------------------| r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4249 moved from start: 10.8383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.454 23032 Z= 0.807 Angle : 1.293 21.248 31990 Z= 0.774 Chirality : 0.074 0.440 3552 Planarity : 0.011 0.150 3300 Dihedral : 26.500 172.629 4984 Min Nonbonded Distance : 1.428 Molprobity Statistics. All-atom Clashscore : 64.11 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.63 % Favored : 87.99 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: -2.26 (0.18), residues: 2132 helix: -0.63 (0.15), residues: 1120 sheet: -2.40 (0.32), residues: 228 loop : -2.38 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG K 128 TYR 0.114 0.004 TYR A 237 PHE 0.030 0.002 PHE K 202 TRP 0.007 0.002 TRP I 167 HIS 0.009 0.002 HIS C 489 Details of bonding type rmsd/Z covalent geometry : bond 0.01095 / 0.81 (23016) covalent geometry : angle 1.28579 / 0.77 (31966) hydrogen bonds : bond 0.16603 / 11.32 ( 1281) hydrogen bonds : angle 7.58359 / 5.42 ( 3491) metal coordination : bond 0.01529 / 1.11 ( 16) metal coordination : angle 4.98923 / 3.02 ( 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 112 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 6 ILE cc_start: 0.9112 (mt) cc_final: 0.8592 (mp) REVERT: I 112 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8033 (tp-100) REVERT: I 133 MET cc_start: 0.8737 (ttp) cc_final: 0.8175 (tmm) REVERT: I 134 ARG cc_start: 0.8331 (ptt180) cc_final: 0.8059 (ptt-90) REVERT: I 151 ARG cc_start: 0.8543 (mmp80) cc_final: 0.8136 (mmp80) REVERT: I 159 TYR cc_start: 0.8794 (m-10) cc_final: 0.8588 (m-10) REVERT: I 180 LYS cc_start: 0.9005 (ptpp) cc_final: 0.8502 (mmtt) REVERT: I 268 ARG cc_start: 0.7558 (mmm160) cc_final: 0.7277 (mmp80) REVERT: I 270 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7876 (pm20) REVERT: I 273 GLN cc_start: 0.8180 (mt0) cc_final: 0.7765 (mt0) REVERT: I 366 VAL cc_start: 0.8862 (m) cc_final: 0.8621 (m) REVERT: I 428 PHE cc_start: 0.6895 (m-10) cc_final: 0.6683 (m-10) REVERT: I 498 ASN cc_start: 0.7304 (t0) cc_final: 0.6364 (t0) REVERT: I 502 ARG cc_start: 0.8520 (mtp-110) cc_final: 0.7916 (tpp80) REVERT: I 515 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8002 (pttt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1726 time to fit residues: 23.9501 Evaluate side-chains 107 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.152 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: 0.0095 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 : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0091 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0115 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0111 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 155 optimal weight: 0.0050 chunk 46 optimal weight: 0.9980 chunk 202 optimal weight: 50.0000 chunk 87 optimal weight: 0.0570 chunk 172 optimal weight: 0.0370 chunk 86 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.0060 chunk 210 optimal weight: 30.0000 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.181696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.151337 restraints weight = 36278.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.157918 restraints weight = 21389.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.162533 restraints weight = 13949.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.165897 restraints weight = 9791.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.168425 restraints weight = 7258.858| |-----------------------------------------------------------------------------| r_work (final): 0.4409 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.221901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.174017 restraints weight = 8305.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.170999 restraints weight = 5916.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.172765 restraints weight = 5305.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.172993 restraints weight = 4111.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.172991 restraints weight = 3625.605| |-----------------------------------------------------------------------------| r_work (final): 0.4326 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.219476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.181870 restraints weight = 10376.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.182688 restraints weight = 4577.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.185907 restraints weight = 3376.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.185915 restraints weight = 3134.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.185915 restraints weight = 3123.286| |-----------------------------------------------------------------------------| r_work (final): 0.4363 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.190865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.182850 restraints weight = 3013.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.185374 restraints weight = 619.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.187123 restraints weight = 261.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.188174 restraints weight = 145.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.188792 restraints weight = 92.812| |-----------------------------------------------------------------------------| r_work (final): 0.4762 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.209003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.202311 restraints weight = 6658.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.203213 restraints weight = 2951.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.203213 restraints weight = 2256.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.203213 restraints weight = 2199.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.203213 restraints weight = 2199.139| |-----------------------------------------------------------------------------| r_work (final): 0.4678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4310 moved from start: 10.8710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.452 23032 Z= 0.791 Angle : 1.223 21.015 31990 Z= 0.737 Chirality : 0.072 0.406 3552 Planarity : 0.009 0.114 3300 Dihedral : 26.487 172.588 4984 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 57.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.63 % Favored : 87.99 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -2.15 (0.18), residues: 2132 helix: -0.52 (0.15), residues: 1124 sheet: -2.33 (0.33), residues: 228 loop : -2.36 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 128 TYR 0.105 0.004 TYR I 237 PHE 0.034 0.003 PHE A 202 TRP 0.008 0.002 TRP I 167 HIS 0.003 0.001 HIS C 489 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.79 (23016) covalent geometry : angle 1.21672 / 0.74 (31966) hydrogen bonds : bond 0.15615 / 10.71 ( 1281) hydrogen bonds : angle 7.48496 / 5.34 ( 3491) metal coordination : bond 0.01616 / 1.15 ( 16) metal coordination : angle 4.73779 / 2.89 ( 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 120 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 27 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7145 (tt0) REVERT: I 74 LYS cc_start: 0.9083 (mttt) cc_final: 0.8725 (mttt) REVERT: I 151 ARG cc_start: 0.8530 (mmp80) cc_final: 0.8038 (mmp80) REVERT: I 232 LYS cc_start: 0.7458 (mmtm) cc_final: 0.7042 (mmtt) REVERT: I 270 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7869 (pm20) REVERT: I 273 GLN cc_start: 0.8135 (mt0) cc_final: 0.7774 (mt0) REVERT: I 290 GLN cc_start: 0.9008 (mt0) cc_final: 0.8625 (mp10) REVERT: I 366 VAL cc_start: 0.8860 (m) cc_final: 0.8623 (m) REVERT: I 502 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.7747 (tpp80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1903 time to fit residues: 27.9578 Evaluate side-chains 115 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.168 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: 0.0168 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0159 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 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 : 0.012 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 ------------------------------------------------------------------------------- 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: 0.0970 chunk 180 optimal weight: 0.0020 chunk 93 optimal weight: 50.0000 chunk 197 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.0870 chunk 34 optimal weight: 0.0870 chunk 203 optimal weight: 0.1980 chunk 229 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.179542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.148479 restraints weight = 36369.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.155225 restraints weight = 21422.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.159928 restraints weight = 14027.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.163348 restraints weight = 9901.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.165632 restraints weight = 7344.580| |-----------------------------------------------------------------------------| r_work (final): 0.4406 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.222005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.161246 restraints weight = 9648.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.164690 restraints weight = 4658.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.168602 restraints weight = 3392.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.175086 restraints weight = 2855.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.175138 restraints weight = 2600.394| |-----------------------------------------------------------------------------| r_work (final): 0.4279 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.219846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.183298 restraints weight = 10655.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.185069 restraints weight = 4458.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.185779 restraints weight = 3215.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.185779 restraints weight = 2910.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.185779 restraints weight = 2910.447| |-----------------------------------------------------------------------------| r_work (final): 0.4360 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.200804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.192705 restraints weight = 8223.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.194367 restraints weight = 3051.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.194927 restraints weight = 1786.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.195276 restraints weight = 1539.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.195277 restraints weight = 1356.050| |-----------------------------------------------------------------------------| r_work (final): 0.4662 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.197678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.177237 restraints weight = 3159.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.182569 restraints weight = 957.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.185757 restraints weight = 441.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.187764 restraints weight = 260.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.188867 restraints weight = 182.485| |-----------------------------------------------------------------------------| r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4229 moved from start: 10.8927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.464 23032 Z= 0.792 Angle : 1.220 20.887 31990 Z= 0.736 Chirality : 0.073 0.409 3552 Planarity : 0.009 0.119 3300 Dihedral : 26.583 172.470 4984 Min Nonbonded Distance : 1.269 Molprobity Statistics. All-atom Clashscore : 54.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.69 % Favored : 88.93 % 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 : 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: -2.04 (0.18), residues: 2132 helix: -0.43 (0.16), residues: 1128 sheet: -2.33 (0.33), residues: 220 loop : -2.32 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 153 TYR 0.115 0.004 TYR A 237 PHE 0.020 0.002 PHE A 138 TRP 0.008 0.002 TRP I 167 HIS 0.001 0.000 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01051 / 0.79 (23016) covalent geometry : angle 1.21329 / 0.74 (31966) hydrogen bonds : bond 0.15570 / 10.62 ( 1281) hydrogen bonds : angle 7.41018 / 5.27 ( 3491) metal coordination : bond 0.01540 / 1.10 ( 16) metal coordination : angle 4.74056 / 2.90 ( 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 117 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.241 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: I 74 LYS cc_start: 0.9117 (mttt) cc_final: 0.8754 (mttt) REVERT: I 151 ARG cc_start: 0.8315 (mmp80) cc_final: 0.7818 (mmp80) REVERT: I 161 TYR cc_start: 0.6217 (m-10) cc_final: 0.5630 (m-10) REVERT: I 180 LYS cc_start: 0.8794 (mppt) cc_final: 0.8523 (mmmt) REVERT: I 270 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7831 (pm20) REVERT: I 290 GLN cc_start: 0.8949 (mt0) cc_final: 0.8513 (mp10) REVERT: I 366 VAL cc_start: 0.8949 (m) cc_final: 0.8682 (m) REVERT: I 478 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7595 (ttt180) REVERT: I 502 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.7779 (tpp80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1701 time to fit residues: 24.7184 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 : 0.234 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0155 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 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: 0.0152 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 : 0.008 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 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: 0.0108 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 : 0.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 171 optimal weight: 0.9980 chunk 219 optimal weight: 0.5980 chunk 119 optimal weight: 0.0870 chunk 194 optimal weight: 0.0670 chunk 175 optimal weight: 0.0070 chunk 155 optimal weight: 0.0470 chunk 94 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 214 optimal weight: 50.0000 chunk 109 optimal weight: 2.9990 overall best weight: 0.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.185812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.155763 restraints weight = 35885.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.162338 restraints weight = 21636.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.167031 restraints weight = 14335.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.170313 restraints weight = 10142.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.172639 restraints weight = 7545.698| |-----------------------------------------------------------------------------| r_work (final): 0.4440 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.223010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.161202 restraints weight = 9708.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.164562 restraints weight = 4818.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.168935 restraints weight = 3467.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.169095 restraints weight = 2894.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.169091 restraints weight = 2813.823| |-----------------------------------------------------------------------------| r_work (final): 0.4353 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.220039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.191020 restraints weight = 10809.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.191178 restraints weight = 7593.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.191256 restraints weight = 5731.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.190745 restraints weight = 4518.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.191339 restraints weight = 4487.710| |-----------------------------------------------------------------------------| r_work (final): 0.4364 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.202744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.194395 restraints weight = 8257.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.196085 restraints weight = 3108.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.196723 restraints weight = 1903.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.197184 restraints weight = 1602.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.197274 restraints weight = 1386.565| |-----------------------------------------------------------------------------| r_work (final): 0.4671 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.197902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.179514 restraints weight = 2704.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.184579 restraints weight = 823.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.187697 restraints weight = 388.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.189448 restraints weight = 232.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.190673 restraints weight = 158.923| |-----------------------------------------------------------------------------| r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4304 moved from start: 10.9184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.312 23032 Z= 0.655 Angle : 1.257 20.731 31990 Z= 0.769 Chirality : 0.073 0.526 3552 Planarity : 0.010 0.123 3300 Dihedral : 26.546 176.194 4984 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 54.18 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.51 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.98 % 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: -1.96 (0.18), residues: 2132 helix: -0.26 (0.16), residues: 1108 sheet: -2.45 (0.32), residues: 220 loop : -2.36 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG C 153 TYR 0.053 0.003 TYR K 237 PHE 0.058 0.002 PHE I 138 TRP 0.007 0.002 TRP C 234 HIS 0.001 0.000 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00938 / 0.65 (23016) covalent geometry : angle 1.25038 / 0.77 (31966) hydrogen bonds : bond 0.18373 / 12.52 ( 1281) hydrogen bonds : angle 7.36774 / 5.25 ( 3491) metal coordination : bond 0.01564 / 1.12 ( 16) metal coordination : angle 4.83445 / 2.96 ( 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 113 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.245 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: I 59 MET cc_start: 0.5297 (mmp) cc_final: 0.4721 (mmp) REVERT: I 74 LYS cc_start: 0.8946 (mttt) cc_final: 0.8637 (mttt) REVERT: I 133 MET cc_start: 0.8749 (ttp) cc_final: 0.8295 (tmm) REVERT: I 135 GLN cc_start: 0.8633 (mm110) cc_final: 0.8315 (mm-40) REVERT: I 138 PHE cc_start: 0.6148 (p90) cc_final: 0.5929 (m-80) REVERT: I 161 TYR cc_start: 0.6041 (m-10) cc_final: 0.5823 (m-10) REVERT: I 236 GLN cc_start: 0.8127 (tt0) cc_final: 0.7631 (tp40) REVERT: I 270 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7858 (pm20) REVERT: I 290 GLN cc_start: 0.8886 (mt0) cc_final: 0.8625 (mp10) REVERT: I 366 VAL cc_start: 0.8842 (m) cc_final: 0.8640 (m) REVERT: I 451 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7489 (pt0) REVERT: I 502 ARG cc_start: 0.8741 (mtp-110) cc_final: 0.7830 (tpp80) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1718 time to fit residues: 24.1575 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 : 0.239 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: 0.0160 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0153 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 : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0121 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: 0.0115 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- 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: 0.9980 chunk 224 optimal weight: 2.9990 chunk 161 optimal weight: 0.2980 chunk 227 optimal weight: 3.9990 chunk 185 optimal weight: 0.0030 chunk 113 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.0070 chunk 163 optimal weight: 0.1980 chunk 179 optimal weight: 0.9980 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.183825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.152439 restraints weight = 36119.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.159146 restraints weight = 21656.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.163876 restraints weight = 14326.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.167253 restraints weight = 10153.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.169754 restraints weight = 7597.962| |-----------------------------------------------------------------------------| r_work (final): 0.4546 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.223153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.161441 restraints weight = 9524.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.164708 restraints weight = 4756.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.168879 restraints weight = 3434.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.169008 restraints weight = 2886.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.176334 restraints weight = 2800.790| |-----------------------------------------------------------------------------| r_work (final): 0.4355 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.219875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.181232 restraints weight = 10566.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.182581 restraints weight = 4730.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.185421 restraints weight = 3422.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.185660 restraints weight = 3067.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.185794 restraints weight = 2874.215| |-----------------------------------------------------------------------------| r_work (final): 0.4358 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.199941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.185362 restraints weight = 2502.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.189224 restraints weight = 637.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.191961 restraints weight = 296.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.193857 restraints weight = 175.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.194817 restraints weight = 110.692| |-----------------------------------------------------------------------------| r_work (final): 0.4696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.215491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.208710 restraints weight = 7336.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.209413 restraints weight = 4316.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.209413 restraints weight = 3550.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.209413 restraints weight = 3550.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.209413 restraints weight = 3550.206| |-----------------------------------------------------------------------------| r_work (final): 0.4699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4057 moved from start: 10.9369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.313 23032 Z= 0.568 Angle : 1.183 20.544 31990 Z= 0.701 Chirality : 0.074 0.493 3552 Planarity : 0.009 0.087 3300 Dihedral : 26.498 172.422 4984 Min Nonbonded Distance : 1.422 Molprobity Statistics. All-atom Clashscore : 52.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.51 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.96 (0.18), residues: 2132 helix: -0.34 (0.16), residues: 1108 sheet: -2.52 (0.31), residues: 220 loop : -2.21 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 153 TYR 0.064 0.003 TYR C 237 PHE 0.023 0.002 PHE A 138 TRP 0.006 0.002 TRP A 167 HIS 0.002 0.000 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.57 (23016) covalent geometry : angle 1.17498 / 0.70 (31966) hydrogen bonds : bond 0.19389 / 13.69 ( 1281) hydrogen bonds : angle 7.39440 / 5.24 ( 3491) metal coordination : bond 0.01477 / 1.07 ( 16) metal coordination : angle 5.20676 / 3.18 ( 24) =============================================================================== Job complete usr+sys time: 4322.32 seconds wall clock time: 75 minutes 44.17 seconds (4544.17 seconds total)