Starting phenix.real_space_refine on Thu Aug 6 17:38:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sp3_40673/08_2026/8sp3_40673_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sp3_40673/08_2026/8sp3_40673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sp3_40673/08_2026/8sp3_40673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sp3_40673/08_2026/8sp3_40673.map" model { file = "/net/cci-nas-00/data/ceres_data/8sp3_40673/08_2026/8sp3_40673_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sp3_40673/08_2026/8sp3_40673_neut.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 6 Type Number sf(0) Gaussians P 82 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 10228 2.51 5 N 2708 2.21 5 O 3206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16270 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.26, per 1000 atoms: 0.20 Number of scatterers: 16270 At special positions: 0 Unit cell: (106.4, 171, 131.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 82 15.00 Mg 2 11.99 O 3206 8.00 N 2708 7.00 C 10228 6.00 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: 1.07 Conformation dependent library (CDL) restraints added in 762.2 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 21 sheets defined 35.5% alpha, 21.9% beta 18 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.559A pdb=" N ASP A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.804A pdb=" N ILE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.564A pdb=" N LEU A 203 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.982A pdb=" N VAL A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 109 through 131 removed outlier: 3.930A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.584A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 149' Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.686A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.663A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 478 through 491 removed outlier: 3.731A pdb=" N ALA B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 489 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 28 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 104 through 108 removed outlier: 4.044A pdb=" N ILE E 108 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.660A pdb=" N VAL E 113 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 146 through 158 removed outlier: 4.419A pdb=" N SER E 150 " --> pdb=" O ASP E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 369 through 385 removed outlier: 3.599A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 385 " --> pdb=" O ILE E 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 30 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 105 removed outlier: 3.555A pdb=" N ILE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 131 removed outlier: 4.272A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 151 removed outlier: 4.055A pdb=" N TYR F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS F 151 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 213 Processing helix chain 'F' and resid 214 through 218 removed outlier: 3.526A pdb=" N HIS F 217 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR F 218 " --> pdb=" O LEU F 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 214 through 218' Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 331 through 350 Processing helix chain 'F' and resid 366 through 376 removed outlier: 3.625A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 478 through 488 removed outlier: 3.855A pdb=" N ALA F 483 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.608A pdb=" N TYR F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 5.901A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 310 through 316 removed outlier: 3.671A pdb=" N GLY B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG B 295 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU B 305 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 278 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 413 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL B 412 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU B 3 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN A 413 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR B 6 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N SER A 415 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 414 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LYS A 167 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.785A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.593A pdb=" N ARG A 186 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 241 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 394 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.760A pdb=" N CYS B 20 " --> pdb=" O ILE B 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.755A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 425 through 426 Processing sheet with id=AB1, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.070A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE E 6 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL E 63 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER E 8 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE E 118 " --> pdb=" O ILE E 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 2 through 3 removed outlier: 3.993A pdb=" N GLY E 412 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 175 through 177 removed outlier: 4.054A pdb=" N LEU E 176 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 323 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E 293 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLY E 325 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR E 291 " --> pdb=" O GLY E 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 175 through 177 removed outlier: 4.054A pdb=" N LEU E 176 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 208 through 210 removed outlier: 4.174A pdb=" N ILE E 239 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AB7, first strand: chain 'E' and resid 390 through 394 Processing sheet with id=AB8, first strand: chain 'F' and resid 5 through 6 removed outlier: 5.617A pdb=" N ILE F 443 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER F 389 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE F 445 " --> pdb=" O THR F 387 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR F 387 " --> pdb=" O ILE F 445 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 5 through 6 removed outlier: 5.617A pdb=" N ILE F 443 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER F 389 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE F 445 " --> pdb=" O THR F 387 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR F 387 " --> pdb=" O ILE F 445 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.739A pdb=" N CYS F 20 " --> pdb=" O ILE F 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.755A pdb=" N SER F 41 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LYS F 94 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 43 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TRP F 139 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE F 224 " --> pdb=" O TRP F 139 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL F 141 " --> pdb=" O PHE F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.849A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3862 1.33 - 1.45: 3970 1.45 - 1.57: 8780 1.57 - 1.70: 160 1.70 - 1.82: 66 Bond restraints: 16838 Sorted by residual: bond pdb=" N ASN F 293 " pdb=" CA ASN F 293 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.59e+01 bond pdb=" N PRO F 10 " pdb=" CA PRO F 10 " ideal model delta sigma weight residual 1.466 1.419 0.047 1.19e-02 7.06e+03 1.53e+01 bond pdb=" N ARG A 186 " pdb=" CA ARG A 186 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.48e+00 bond pdb=" N LYS B 11 " pdb=" CA LYS B 11 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.37e-02 5.33e+03 8.33e+00 ... (remaining 16833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 22314 1.67 - 3.34: 725 3.34 - 5.00: 65 5.00 - 6.67: 19 6.67 - 8.34: 5 Bond angle restraints: 23128 Sorted by residual: angle pdb=" N THR F 491 " pdb=" CA THR F 491 " pdb=" C THR F 491 " ideal model delta sigma weight residual 114.56 107.31 7.25 1.27e+00 6.20e-01 3.26e+01 angle pdb=" C PRO F 10 " pdb=" CA PRO F 10 " pdb=" CB PRO F 10 " ideal model delta sigma weight residual 110.98 103.64 7.34 1.31e+00 5.83e-01 3.14e+01 angle pdb=" N LEU A 185 " pdb=" CA LEU A 185 " pdb=" C LEU A 185 " ideal model delta sigma weight residual 109.72 101.38 8.34 1.60e+00 3.91e-01 2.72e+01 angle pdb=" C1' U G 17 " pdb=" N1 U G 17 " pdb=" C2 U G 17 " ideal model delta sigma weight residual 117.70 123.45 -5.75 1.20e+00 6.94e-01 2.30e+01 angle pdb=" C1' U C 17 " pdb=" N1 U C 17 " pdb=" C2 U C 17 " ideal model delta sigma weight residual 117.70 123.36 -5.66 1.20e+00 6.94e-01 2.23e+01 ... (remaining 23123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 9706 35.61 - 71.22: 286 71.22 - 106.83: 20 106.83 - 142.44: 1 142.44 - 178.05: 11 Dihedral angle restraints: 10024 sinusoidal: 4786 harmonic: 5238 Sorted by residual: dihedral pdb=" O4' U C 17 " pdb=" C1' U C 17 " pdb=" N1 U C 17 " pdb=" C2 U C 17 " ideal model delta sinusoidal sigma weight residual -160.00 18.05 -178.05 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U G 17 " pdb=" C1' U G 17 " pdb=" N1 U G 17 " pdb=" C2 U G 17 " ideal model delta sinusoidal sigma weight residual -160.00 16.42 -176.42 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U G 13 " pdb=" C1' U G 13 " pdb=" N1 U G 13 " pdb=" C2 U G 13 " ideal model delta sinusoidal sigma weight residual -160.00 14.27 -174.27 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 10021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2130 0.061 - 0.121: 339 0.121 - 0.182: 63 0.182 - 0.243: 4 0.243 - 0.303: 2 Chirality restraints: 2538 Sorted by residual: chirality pdb=" CA LEU A 185 " pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CB LEU A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA PRO F 10 " pdb=" N PRO F 10 " pdb=" C PRO F 10 " pdb=" CB PRO F 10 " both_signs ideal model delta sigma weight residual False 2.72 3.01 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA LEU E 185 " pdb=" N LEU E 185 " pdb=" C LEU E 185 " pdb=" CB LEU E 185 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2535 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 186 " 0.479 9.50e-02 1.11e+02 2.15e-01 2.82e+01 pdb=" NE ARG E 186 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG E 186 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG E 186 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 186 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 11 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.93e+00 pdb=" N9 A C 11 " -0.034 2.00e-02 2.50e+03 pdb=" C8 A C 11 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 11 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A C 11 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A C 11 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A C 11 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A C 11 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C 11 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A C 11 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A C 11 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A G 11 " -0.027 2.00e-02 2.50e+03 1.34e-02 4.93e+00 pdb=" N9 A G 11 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A G 11 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A G 11 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A G 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A G 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A G 11 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A G 11 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A G 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A G 11 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A G 11 " -0.001 2.00e-02 2.50e+03 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 15 2.29 - 2.94: 6763 2.94 - 3.59: 22375 3.59 - 4.25: 36407 4.25 - 4.90: 60991 Nonbonded interactions: 126551 Sorted by model distance: nonbonded pdb=" CE LYS B 11 " pdb=" CG2 THR B 21 " model vdw 1.632 3.860 nonbonded pdb=" CD2 LEU A 185 " pdb=" CE1 PHE A 217 " model vdw 1.829 3.760 nonbonded pdb=" CG2 ILE B 12 " pdb=" O LYS B 270 " model vdw 1.914 3.460 nonbonded pdb=" CD2 LEU A 185 " pdb=" CZ PHE A 217 " model vdw 1.944 3.760 nonbonded pdb=" OP2 U G 1 " pdb="MG MG F 601 " model vdw 1.950 2.170 ... (remaining 126546 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.240 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.360 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 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 : 0.004 0.047 16838 Z= 0.260 Angle : 0.657 8.341 23128 Z= 0.469 Chirality : 0.048 0.303 2538 Planarity : 0.006 0.215 2632 Dihedral : 17.323 178.055 6640 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1764 helix: 1.54 (0.23), residues: 553 sheet: 0.03 (0.29), residues: 355 loop : -1.65 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 362 TYR 0.014 0.001 TYR B 397 PHE 0.015 0.001 PHE B 313 TRP 0.014 0.001 TRP E 319 HIS 0.007 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.26 (16838) covalent geometry : angle 0.65735 / 0.47 (23128) hydrogen bonds : bond 0.16216 / 10.63 ( 614) hydrogen bonds : angle 6.38401 / 4.63 ( 1858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6623 (mp) cc_final: 0.6341 (mp) REVERT: A 35 ASP cc_start: 0.6205 (t70) cc_final: 0.5985 (t70) REVERT: A 209 ARG cc_start: 0.6994 (mtp85) cc_final: 0.6742 (mtp85) REVERT: A 210 TYR cc_start: 0.7093 (t80) cc_final: 0.6824 (t80) REVERT: A 213 TYR cc_start: 0.6375 (m-80) cc_final: 0.6066 (m-80) REVERT: A 255 PHE cc_start: 0.8377 (t80) cc_final: 0.8163 (t80) REVERT: A 263 ARG cc_start: 0.7372 (ttp80) cc_final: 0.6908 (ttp80) REVERT: A 267 GLN cc_start: 0.8156 (tt0) cc_final: 0.7802 (tt0) REVERT: A 349 LYS cc_start: 0.7219 (ttpp) cc_final: 0.6821 (ttpp) REVERT: A 399 GLU cc_start: 0.7572 (mp0) cc_final: 0.7255 (mp0) REVERT: B 115 TYR cc_start: 0.7436 (t80) cc_final: 0.7102 (t80) REVERT: B 132 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7525 (mt-10) REVERT: B 138 VAL cc_start: 0.8560 (t) cc_final: 0.8273 (m) REVERT: B 254 TRP cc_start: 0.7502 (m100) cc_final: 0.7126 (m100) REVERT: B 309 ASP cc_start: 0.4368 (m-30) cc_final: 0.3625 (m-30) REVERT: B 321 TYR cc_start: 0.7834 (m-80) cc_final: 0.7325 (m-10) REVERT: B 417 SER cc_start: 0.8108 (t) cc_final: 0.7668 (m) REVERT: E 4 LYS cc_start: 0.6764 (mttm) cc_final: 0.6441 (mtpp) REVERT: E 15 ASN cc_start: 0.5140 (m-40) cc_final: 0.4617 (m-40) REVERT: E 59 LYS cc_start: 0.7732 (tppt) cc_final: 0.7414 (tppt) REVERT: E 93 PHE cc_start: 0.6583 (t80) cc_final: 0.6218 (t80) REVERT: E 208 VAL cc_start: 0.7249 (t) cc_final: 0.6971 (t) REVERT: E 286 GLU cc_start: 0.5179 (tp30) cc_final: 0.4932 (tp30) REVERT: E 360 SER cc_start: 0.7501 (m) cc_final: 0.7199 (p) REVERT: F 16 HIS cc_start: 0.6018 (m-70) cc_final: 0.5724 (m-70) REVERT: F 37 TYR cc_start: 0.7710 (m-80) cc_final: 0.7384 (m-80) REVERT: F 56 TYR cc_start: 0.5739 (t80) cc_final: 0.5285 (t80) REVERT: F 91 ILE cc_start: 0.8396 (mt) cc_final: 0.8167 (tt) REVERT: F 94 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7081 (mmtm) REVERT: F 115 TYR cc_start: 0.7589 (t80) cc_final: 0.7383 (t80) REVERT: F 142 ILE cc_start: 0.7393 (mm) cc_final: 0.7035 (mt) REVERT: F 272 SER cc_start: 0.7837 (t) cc_final: 0.7636 (p) REVERT: F 285 TYR cc_start: 0.7145 (m-80) cc_final: 0.6875 (m-80) REVERT: F 287 LYS cc_start: 0.7309 (mttm) cc_final: 0.7101 (ttmt) REVERT: F 336 LYS cc_start: 0.7855 (mttp) cc_final: 0.7534 (mtmm) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.1147 time to fit residues: 63.1709 Evaluate side-chains 295 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN F 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.192734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159048 restraints weight = 24200.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163335 restraints weight = 13827.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.166069 restraints weight = 9673.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.167783 restraints weight = 7731.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.168663 restraints weight = 6718.234| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16838 Z= 0.150 Angle : 0.592 15.171 23128 Z= 0.326 Chirality : 0.044 0.293 2538 Planarity : 0.004 0.045 2632 Dihedral : 18.164 179.080 3014 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.64 % Allowed : 7.61 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1764 helix: 1.61 (0.23), residues: 556 sheet: 0.05 (0.28), residues: 384 loop : -1.63 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 186 TYR 0.020 0.001 TYR B 6 PHE 0.027 0.002 PHE B 30 TRP 0.020 0.001 TRP B 86 HIS 0.006 0.001 HIS E 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (16838) covalent geometry : angle 0.59218 / 0.33 (23128) hydrogen bonds : bond 0.05180 / 3.40 ( 614) hydrogen bonds : angle 4.99337 / 3.60 ( 1858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 312 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8137 (t) cc_final: 0.7745 (p) REVERT: A 209 ARG cc_start: 0.6971 (mtp85) cc_final: 0.6728 (mtp85) REVERT: A 210 TYR cc_start: 0.7117 (t80) cc_final: 0.6845 (t80) REVERT: A 213 TYR cc_start: 0.6464 (m-80) cc_final: 0.6078 (m-80) REVERT: A 240 ARG cc_start: 0.6675 (mtt180) cc_final: 0.6111 (mtt180) REVERT: A 255 PHE cc_start: 0.8418 (t80) cc_final: 0.8176 (t80) REVERT: A 263 ARG cc_start: 0.7400 (ttp80) cc_final: 0.6916 (ttp80) REVERT: A 267 GLN cc_start: 0.8246 (tt0) cc_final: 0.7919 (tt0) REVERT: A 291 THR cc_start: 0.7643 (m) cc_final: 0.7424 (p) REVERT: A 399 GLU cc_start: 0.7602 (mp0) cc_final: 0.7244 (mp0) REVERT: B 115 TYR cc_start: 0.7438 (t80) cc_final: 0.7063 (t80) REVERT: B 254 TRP cc_start: 0.7562 (m100) cc_final: 0.7053 (m100) REVERT: B 321 TYR cc_start: 0.7856 (m-80) cc_final: 0.7382 (m-10) REVERT: B 412 VAL cc_start: 0.8401 (t) cc_final: 0.8123 (p) REVERT: B 417 SER cc_start: 0.8099 (t) cc_final: 0.7673 (m) REVERT: B 444 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6716 (tm-30) REVERT: E 4 LYS cc_start: 0.6810 (mttm) cc_final: 0.6473 (mtpp) REVERT: E 15 ASN cc_start: 0.5243 (m-40) cc_final: 0.4686 (m-40) REVERT: E 59 LYS cc_start: 0.7745 (tppt) cc_final: 0.7400 (tppt) REVERT: E 93 PHE cc_start: 0.6552 (t80) cc_final: 0.6191 (t80) REVERT: E 286 GLU cc_start: 0.5171 (tp30) cc_final: 0.4950 (tp30) REVERT: E 290 LYS cc_start: 0.8192 (pttt) cc_final: 0.7798 (ptpp) REVERT: F 5 ILE cc_start: 0.8000 (pt) cc_final: 0.7617 (pt) REVERT: F 14 PHE cc_start: 0.7452 (m-80) cc_final: 0.7175 (m-80) REVERT: F 16 HIS cc_start: 0.6011 (m-70) cc_final: 0.5740 (m-70) REVERT: F 37 TYR cc_start: 0.7672 (m-80) cc_final: 0.7429 (m-80) REVERT: F 40 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7500 (mptt) REVERT: F 56 TYR cc_start: 0.5640 (t80) cc_final: 0.5170 (t80) REVERT: F 93 PHE cc_start: 0.7418 (t80) cc_final: 0.7092 (t80) REVERT: F 94 LYS cc_start: 0.7755 (mmmm) cc_final: 0.7456 (mmtm) REVERT: F 115 TYR cc_start: 0.7780 (t80) cc_final: 0.7410 (t80) REVERT: F 285 TYR cc_start: 0.7078 (m-80) cc_final: 0.6704 (m-80) REVERT: F 287 LYS cc_start: 0.7320 (mttm) cc_final: 0.6867 (mtmm) REVERT: F 306 ASP cc_start: 0.6219 (p0) cc_final: 0.5967 (p0) REVERT: F 311 THR cc_start: 0.8032 (t) cc_final: 0.7679 (p) REVERT: F 336 LYS cc_start: 0.8099 (mttp) cc_final: 0.7760 (mtmm) outliers start: 26 outliers final: 14 residues processed: 322 average time/residue: 0.1290 time to fit residues: 61.3424 Evaluate side-chains 312 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 298 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 48 optimal weight: 0.0030 chunk 62 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.191418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157554 restraints weight = 24576.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161813 restraints weight = 14003.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164565 restraints weight = 9792.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166327 restraints weight = 7811.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.167227 restraints weight = 6771.502| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16838 Z= 0.171 Angle : 0.582 7.628 23128 Z= 0.322 Chirality : 0.044 0.291 2538 Planarity : 0.004 0.039 2632 Dihedral : 18.182 179.572 3014 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.08 % Allowed : 11.19 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1764 helix: 1.51 (0.23), residues: 556 sheet: 0.11 (0.28), residues: 378 loop : -1.61 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 54 TYR 0.024 0.002 TYR A 251 PHE 0.028 0.002 PHE B 93 TRP 0.017 0.002 TRP F 269 HIS 0.007 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (16838) covalent geometry : angle 0.58217 / 0.32 (23128) hydrogen bonds : bond 0.04915 / 3.24 ( 614) hydrogen bonds : angle 4.83018 / 3.48 ( 1858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8102 (t) cc_final: 0.7695 (p) REVERT: A 193 MET cc_start: 0.7058 (mmm) cc_final: 0.6802 (mmt) REVERT: A 209 ARG cc_start: 0.7010 (mtp85) cc_final: 0.6750 (mtp85) REVERT: A 210 TYR cc_start: 0.7123 (t80) cc_final: 0.6837 (t80) REVERT: A 213 TYR cc_start: 0.6502 (m-80) cc_final: 0.6133 (m-80) REVERT: A 255 PHE cc_start: 0.8445 (t80) cc_final: 0.8218 (t80) REVERT: A 263 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7020 (ttp80) REVERT: A 279 ASP cc_start: 0.7923 (t70) cc_final: 0.7711 (t0) REVERT: A 291 THR cc_start: 0.7713 (m) cc_final: 0.7447 (p) REVERT: A 348 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7449 (mttt) REVERT: A 399 GLU cc_start: 0.7652 (mp0) cc_final: 0.7282 (mp0) REVERT: B 226 GLU cc_start: 0.7525 (mp0) cc_final: 0.7278 (mp0) REVERT: B 254 TRP cc_start: 0.7603 (m100) cc_final: 0.7226 (m100) REVERT: B 321 TYR cc_start: 0.7928 (m-80) cc_final: 0.7284 (m-10) REVERT: B 412 VAL cc_start: 0.8346 (t) cc_final: 0.8070 (p) REVERT: B 417 SER cc_start: 0.8111 (t) cc_final: 0.7653 (m) REVERT: E 4 LYS cc_start: 0.6819 (mttm) cc_final: 0.6478 (mtpp) REVERT: E 15 ASN cc_start: 0.5340 (m-40) cc_final: 0.4792 (m-40) REVERT: E 59 LYS cc_start: 0.7771 (tppt) cc_final: 0.7408 (tppt) REVERT: E 93 PHE cc_start: 0.6589 (t80) cc_final: 0.6188 (t80) REVERT: E 119 ASP cc_start: 0.7917 (t0) cc_final: 0.7622 (t0) REVERT: F 12 ILE cc_start: 0.6829 (mt) cc_final: 0.6618 (mm) REVERT: F 16 HIS cc_start: 0.6090 (m-70) cc_final: 0.5820 (m-70) REVERT: F 40 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7637 (mmmt) REVERT: F 56 TYR cc_start: 0.5585 (t80) cc_final: 0.5055 (t80) REVERT: F 142 ILE cc_start: 0.7385 (mm) cc_final: 0.6900 (mt) REVERT: F 278 VAL cc_start: 0.8494 (t) cc_final: 0.8219 (p) REVERT: F 287 LYS cc_start: 0.7341 (mttm) cc_final: 0.6889 (mtmm) REVERT: F 306 ASP cc_start: 0.6304 (p0) cc_final: 0.6039 (p0) REVERT: F 311 THR cc_start: 0.8112 (t) cc_final: 0.7802 (p) REVERT: F 336 LYS cc_start: 0.7973 (mttp) cc_final: 0.7672 (mtmm) outliers start: 33 outliers final: 20 residues processed: 296 average time/residue: 0.1266 time to fit residues: 55.3814 Evaluate side-chains 305 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 285 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 129 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 38 optimal weight: 0.0060 chunk 67 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.190737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156705 restraints weight = 24589.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.160928 restraints weight = 14061.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163644 restraints weight = 9843.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165366 restraints weight = 7882.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166430 restraints weight = 6843.442| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16838 Z= 0.166 Angle : 0.579 8.436 23128 Z= 0.319 Chirality : 0.044 0.291 2538 Planarity : 0.004 0.064 2632 Dihedral : 18.210 179.829 3014 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.64 % Allowed : 12.64 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1764 helix: 1.49 (0.23), residues: 560 sheet: 0.04 (0.28), residues: 381 loop : -1.68 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 126 TYR 0.022 0.001 TYR A 251 PHE 0.032 0.002 PHE B 30 TRP 0.013 0.001 TRP F 254 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (16838) covalent geometry : angle 0.57921 / 0.32 (23128) hydrogen bonds : bond 0.04732 / 3.11 ( 614) hydrogen bonds : angle 4.76696 / 3.44 ( 1858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8046 (t) cc_final: 0.7583 (p) REVERT: A 126 ARG cc_start: 0.6225 (tpm170) cc_final: 0.5998 (tpm170) REVERT: A 209 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6785 (mtp85) REVERT: A 210 TYR cc_start: 0.7139 (t80) cc_final: 0.6880 (t80) REVERT: A 213 TYR cc_start: 0.6541 (m-80) cc_final: 0.6167 (m-80) REVERT: A 263 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7036 (ttp80) REVERT: A 279 ASP cc_start: 0.8025 (t70) cc_final: 0.7767 (t0) REVERT: A 291 THR cc_start: 0.7737 (m) cc_final: 0.7462 (p) REVERT: A 366 LYS cc_start: 0.7869 (tttm) cc_final: 0.7415 (ttpt) REVERT: A 399 GLU cc_start: 0.7670 (mp0) cc_final: 0.7256 (mp0) REVERT: B 9 GLU cc_start: 0.7530 (mp0) cc_final: 0.7115 (mp0) REVERT: B 21 THR cc_start: 0.5340 (OUTLIER) cc_final: 0.5073 (p) REVERT: B 115 TYR cc_start: 0.7380 (t80) cc_final: 0.7135 (t80) REVERT: B 226 GLU cc_start: 0.7526 (mp0) cc_final: 0.7249 (mp0) REVERT: B 254 TRP cc_start: 0.7638 (m100) cc_final: 0.7184 (m100) REVERT: B 321 TYR cc_start: 0.7944 (m-80) cc_final: 0.7212 (m-80) REVERT: B 412 VAL cc_start: 0.8326 (t) cc_final: 0.8046 (p) REVERT: B 417 SER cc_start: 0.8085 (t) cc_final: 0.7635 (m) REVERT: E 4 LYS cc_start: 0.6807 (mttm) cc_final: 0.6487 (mtpp) REVERT: E 15 ASN cc_start: 0.5337 (m-40) cc_final: 0.4785 (m-40) REVERT: E 59 LYS cc_start: 0.7785 (tppt) cc_final: 0.7424 (tppt) REVERT: E 93 PHE cc_start: 0.6582 (t80) cc_final: 0.6182 (t80) REVERT: E 119 ASP cc_start: 0.7928 (t0) cc_final: 0.7659 (t0) REVERT: E 193 MET cc_start: 0.5807 (mmm) cc_final: 0.5530 (mmm) REVERT: E 360 SER cc_start: 0.7456 (m) cc_final: 0.7218 (p) REVERT: F 16 HIS cc_start: 0.6148 (m-70) cc_final: 0.5869 (m-70) REVERT: F 40 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7688 (mmmt) REVERT: F 142 ILE cc_start: 0.7396 (mm) cc_final: 0.7037 (mm) REVERT: F 278 VAL cc_start: 0.8498 (t) cc_final: 0.8256 (p) REVERT: F 287 LYS cc_start: 0.7355 (mttm) cc_final: 0.6852 (mtmm) REVERT: F 306 ASP cc_start: 0.6319 (p0) cc_final: 0.6026 (p0) REVERT: F 311 THR cc_start: 0.8190 (t) cc_final: 0.7884 (p) REVERT: F 316 GLU cc_start: 0.6822 (tp30) cc_final: 0.6416 (tp30) REVERT: F 336 LYS cc_start: 0.7932 (mttp) cc_final: 0.7697 (mtmm) outliers start: 42 outliers final: 27 residues processed: 300 average time/residue: 0.1310 time to fit residues: 57.5085 Evaluate side-chains 310 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 135 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.191279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157387 restraints weight = 24416.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161563 restraints weight = 14057.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.164281 restraints weight = 9917.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.165995 restraints weight = 7945.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.167005 restraints weight = 6912.000| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16838 Z= 0.145 Angle : 0.572 8.483 23128 Z= 0.313 Chirality : 0.043 0.295 2538 Planarity : 0.004 0.075 2632 Dihedral : 18.209 179.963 3014 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.26 % Allowed : 13.58 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1764 helix: 1.56 (0.23), residues: 561 sheet: 0.05 (0.28), residues: 381 loop : -1.73 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 213 TYR 0.023 0.001 TYR A 251 PHE 0.041 0.002 PHE F 93 TRP 0.012 0.001 TRP F 254 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16838) covalent geometry : angle 0.57152 / 0.31 (23128) hydrogen bonds : bond 0.04399 / 2.89 ( 614) hydrogen bonds : angle 4.67661 / 3.37 ( 1858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8034 (t) cc_final: 0.7581 (p) REVERT: A 126 ARG cc_start: 0.6241 (tpm170) cc_final: 0.5991 (tpm170) REVERT: A 209 ARG cc_start: 0.7035 (mtp85) cc_final: 0.6785 (mtp85) REVERT: A 210 TYR cc_start: 0.7151 (t80) cc_final: 0.6934 (t80) REVERT: A 213 TYR cc_start: 0.6542 (m-80) cc_final: 0.6185 (m-80) REVERT: A 263 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7060 (ttp80) REVERT: A 279 ASP cc_start: 0.8043 (t70) cc_final: 0.7797 (t0) REVERT: A 291 THR cc_start: 0.7724 (m) cc_final: 0.7469 (p) REVERT: A 366 LYS cc_start: 0.7887 (tttm) cc_final: 0.7425 (ttpt) REVERT: A 399 GLU cc_start: 0.7664 (mp0) cc_final: 0.7237 (mp0) REVERT: A 400 LYS cc_start: 0.7322 (mttt) cc_final: 0.6773 (mttm) REVERT: B 9 GLU cc_start: 0.7599 (mp0) cc_final: 0.7084 (mt-10) REVERT: B 115 TYR cc_start: 0.7407 (t80) cc_final: 0.7172 (t80) REVERT: B 226 GLU cc_start: 0.7528 (mp0) cc_final: 0.7220 (mp0) REVERT: B 254 TRP cc_start: 0.7657 (m100) cc_final: 0.7192 (m100) REVERT: B 321 TYR cc_start: 0.7948 (m-80) cc_final: 0.7643 (m-80) REVERT: B 417 SER cc_start: 0.8059 (t) cc_final: 0.7648 (m) REVERT: E 4 LYS cc_start: 0.6832 (mttm) cc_final: 0.6511 (mtpp) REVERT: E 15 ASN cc_start: 0.5358 (m-40) cc_final: 0.4794 (m-40) REVERT: E 59 LYS cc_start: 0.7758 (tppt) cc_final: 0.7417 (tppt) REVERT: E 93 PHE cc_start: 0.6579 (t80) cc_final: 0.6174 (t80) REVERT: E 119 ASP cc_start: 0.7938 (t0) cc_final: 0.7643 (t70) REVERT: E 360 SER cc_start: 0.7469 (m) cc_final: 0.7240 (p) REVERT: F 16 HIS cc_start: 0.6129 (m-70) cc_final: 0.5848 (m-70) REVERT: F 40 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7527 (mmmt) REVERT: F 54 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5924 (mpp80) REVERT: F 56 TYR cc_start: 0.5404 (t80) cc_final: 0.4916 (t80) REVERT: F 142 ILE cc_start: 0.7394 (mm) cc_final: 0.7048 (mm) REVERT: F 287 LYS cc_start: 0.7404 (mttm) cc_final: 0.6843 (mtmm) REVERT: F 311 THR cc_start: 0.8212 (t) cc_final: 0.7889 (p) REVERT: F 356 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6843 (tm-30) outliers start: 36 outliers final: 24 residues processed: 308 average time/residue: 0.1347 time to fit residues: 60.9473 Evaluate side-chains 310 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 chunk 163 optimal weight: 0.7980 chunk 23 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 0.0570 chunk 135 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.190509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156701 restraints weight = 24621.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160865 restraints weight = 14106.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.163567 restraints weight = 9933.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.165310 restraints weight = 7944.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166424 restraints weight = 6890.957| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16838 Z= 0.129 Angle : 0.566 9.693 23128 Z= 0.307 Chirality : 0.043 0.299 2538 Planarity : 0.004 0.062 2632 Dihedral : 18.194 179.856 3014 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.14 % Allowed : 14.84 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1764 helix: 1.63 (0.23), residues: 561 sheet: 0.01 (0.28), residues: 390 loop : -1.74 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 209 TYR 0.026 0.001 TYR B 65 PHE 0.035 0.002 PHE F 93 TRP 0.011 0.001 TRP F 254 HIS 0.004 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (16838) covalent geometry : angle 0.56590 / 0.31 (23128) hydrogen bonds : bond 0.04136 / 2.70 ( 614) hydrogen bonds : angle 4.60808 / 3.33 ( 1858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6226 (tpm170) cc_final: 0.5937 (tpm170) REVERT: A 209 ARG cc_start: 0.7025 (mtp85) cc_final: 0.6787 (mtp180) REVERT: A 210 TYR cc_start: 0.7128 (t80) cc_final: 0.6919 (t80) REVERT: A 213 TYR cc_start: 0.6506 (m-80) cc_final: 0.6180 (m-80) REVERT: A 263 ARG cc_start: 0.7449 (ttp80) cc_final: 0.7044 (ttp80) REVERT: A 291 THR cc_start: 0.7715 (m) cc_final: 0.7467 (p) REVERT: A 321 PHE cc_start: 0.7095 (t80) cc_final: 0.6441 (t80) REVERT: A 386 ASP cc_start: 0.6642 (t0) cc_final: 0.6397 (m-30) REVERT: A 399 GLU cc_start: 0.7649 (mp0) cc_final: 0.7214 (mp0) REVERT: B 115 TYR cc_start: 0.7487 (t80) cc_final: 0.7177 (t80) REVERT: B 226 GLU cc_start: 0.7438 (mp0) cc_final: 0.7179 (mp0) REVERT: B 322 ASN cc_start: 0.7344 (p0) cc_final: 0.7123 (p0) REVERT: B 417 SER cc_start: 0.8051 (t) cc_final: 0.7670 (m) REVERT: E 4 LYS cc_start: 0.6841 (mttm) cc_final: 0.6518 (mtpp) REVERT: E 59 LYS cc_start: 0.7777 (tppt) cc_final: 0.7433 (tppt) REVERT: E 93 PHE cc_start: 0.6588 (t80) cc_final: 0.6207 (t80) REVERT: E 119 ASP cc_start: 0.7951 (t0) cc_final: 0.7649 (t70) REVERT: E 309 MET cc_start: 0.7091 (ttm) cc_final: 0.6837 (ttm) REVERT: E 360 SER cc_start: 0.7476 (m) cc_final: 0.7253 (p) REVERT: F 16 HIS cc_start: 0.6147 (m-70) cc_final: 0.5866 (m-70) REVERT: F 37 TYR cc_start: 0.7720 (m-80) cc_final: 0.7519 (m-80) REVERT: F 40 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7586 (mmmt) REVERT: F 56 TYR cc_start: 0.5308 (t80) cc_final: 0.4883 (t80) REVERT: F 142 ILE cc_start: 0.7379 (mm) cc_final: 0.7041 (mm) REVERT: F 278 VAL cc_start: 0.8521 (t) cc_final: 0.7943 (p) REVERT: F 287 LYS cc_start: 0.7384 (mttm) cc_final: 0.6839 (mtmm) REVERT: F 311 THR cc_start: 0.8256 (t) cc_final: 0.7911 (p) REVERT: F 356 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6811 (tm-30) outliers start: 34 outliers final: 28 residues processed: 293 average time/residue: 0.1281 time to fit residues: 55.2402 Evaluate side-chains 303 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 167 optimal weight: 0.1980 chunk 139 optimal weight: 0.0570 chunk 150 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.191570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157555 restraints weight = 24509.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161809 restraints weight = 14131.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164511 restraints weight = 9950.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166207 restraints weight = 7990.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.167119 restraints weight = 6953.887| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16838 Z= 0.142 Angle : 0.580 9.586 23128 Z= 0.313 Chirality : 0.043 0.297 2538 Planarity : 0.004 0.055 2632 Dihedral : 18.213 179.847 3014 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.64 % Allowed : 15.09 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1764 helix: 1.66 (0.23), residues: 559 sheet: 0.11 (0.29), residues: 371 loop : -1.75 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 209 TYR 0.023 0.001 TYR A 251 PHE 0.037 0.002 PHE B 93 TRP 0.012 0.001 TRP F 254 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16838) covalent geometry : angle 0.57984 / 0.31 (23128) hydrogen bonds : bond 0.04224 / 2.77 ( 614) hydrogen bonds : angle 4.64607 / 3.35 ( 1858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6321 (tpm170) cc_final: 0.5931 (tpm170) REVERT: A 209 ARG cc_start: 0.7046 (mtp85) cc_final: 0.6800 (mtp180) REVERT: A 210 TYR cc_start: 0.7135 (t80) cc_final: 0.6902 (t80) REVERT: A 213 TYR cc_start: 0.6561 (m-80) cc_final: 0.6201 (m-80) REVERT: A 263 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7025 (ttp80) REVERT: A 279 ASP cc_start: 0.8147 (t0) cc_final: 0.7650 (t0) REVERT: A 291 THR cc_start: 0.7725 (m) cc_final: 0.7485 (p) REVERT: A 366 LYS cc_start: 0.7939 (tttm) cc_final: 0.7442 (ttpt) REVERT: A 399 GLU cc_start: 0.7668 (mp0) cc_final: 0.7200 (mp0) REVERT: B 213 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.8031 (mtp180) REVERT: B 226 GLU cc_start: 0.7440 (mp0) cc_final: 0.7193 (mp0) REVERT: B 417 SER cc_start: 0.8040 (t) cc_final: 0.7703 (m) REVERT: E 4 LYS cc_start: 0.6889 (mttm) cc_final: 0.6574 (mtpp) REVERT: E 59 LYS cc_start: 0.7780 (tppt) cc_final: 0.7456 (tppt) REVERT: E 93 PHE cc_start: 0.6559 (t80) cc_final: 0.6167 (t80) REVERT: E 119 ASP cc_start: 0.7958 (t0) cc_final: 0.7657 (t70) REVERT: E 309 MET cc_start: 0.7098 (ttm) cc_final: 0.6843 (ttm) REVERT: E 411 LYS cc_start: 0.7580 (ttmt) cc_final: 0.7369 (tppt) REVERT: F 16 HIS cc_start: 0.6143 (m-70) cc_final: 0.5869 (m-70) REVERT: F 40 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7536 (mptt) REVERT: F 56 TYR cc_start: 0.5380 (t80) cc_final: 0.4932 (t80) REVERT: F 142 ILE cc_start: 0.7373 (mm) cc_final: 0.7027 (mm) REVERT: F 278 VAL cc_start: 0.8524 (t) cc_final: 0.7945 (p) REVERT: F 287 LYS cc_start: 0.7397 (mttm) cc_final: 0.6805 (mtmm) REVERT: F 311 THR cc_start: 0.8289 (t) cc_final: 0.7968 (p) REVERT: F 356 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6912 (tm-30) outliers start: 42 outliers final: 36 residues processed: 284 average time/residue: 0.1188 time to fit residues: 49.9778 Evaluate side-chains 299 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 160 optimal weight: 0.0000 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.0170 chunk 91 optimal weight: 4.9990 chunk 155 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.191878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158176 restraints weight = 24625.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.162340 restraints weight = 14116.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165010 restraints weight = 9948.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.166692 restraints weight = 7990.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.167768 restraints weight = 6960.269| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16838 Z= 0.121 Angle : 0.560 8.588 23128 Z= 0.303 Chirality : 0.042 0.303 2538 Planarity : 0.004 0.052 2632 Dihedral : 18.208 179.519 3014 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.39 % Allowed : 15.66 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1764 helix: 1.71 (0.23), residues: 559 sheet: 0.00 (0.28), residues: 392 loop : -1.72 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 209 TYR 0.020 0.001 TYR A 251 PHE 0.033 0.002 PHE F 93 TRP 0.010 0.001 TRP F 254 HIS 0.003 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (16838) covalent geometry : angle 0.56015 / 0.30 (23128) hydrogen bonds : bond 0.03957 / 2.58 ( 614) hydrogen bonds : angle 4.51391 / 3.24 ( 1858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6282 (tpm170) cc_final: 0.5894 (tpm170) REVERT: A 209 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6810 (mtp180) REVERT: A 210 TYR cc_start: 0.7149 (t80) cc_final: 0.6947 (t80) REVERT: A 213 TYR cc_start: 0.6517 (m-80) cc_final: 0.6192 (m-80) REVERT: A 263 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7018 (ttp80) REVERT: A 291 THR cc_start: 0.7687 (m) cc_final: 0.7471 (p) REVERT: A 399 GLU cc_start: 0.7625 (mp0) cc_final: 0.7190 (mp0) REVERT: B 138 VAL cc_start: 0.8471 (t) cc_final: 0.8200 (m) REVERT: B 226 GLU cc_start: 0.7392 (mp0) cc_final: 0.7175 (mp0) REVERT: B 417 SER cc_start: 0.8021 (t) cc_final: 0.7599 (m) REVERT: E 4 LYS cc_start: 0.6887 (mttm) cc_final: 0.6555 (mtpp) REVERT: E 59 LYS cc_start: 0.7783 (tppt) cc_final: 0.7453 (tppt) REVERT: E 93 PHE cc_start: 0.6551 (t80) cc_final: 0.6194 (t80) REVERT: E 119 ASP cc_start: 0.7983 (t0) cc_final: 0.7686 (t70) REVERT: E 309 MET cc_start: 0.7058 (ttm) cc_final: 0.6819 (ttm) REVERT: F 16 HIS cc_start: 0.6104 (m-70) cc_final: 0.5831 (m-70) REVERT: F 56 TYR cc_start: 0.5340 (t80) cc_final: 0.4902 (t80) REVERT: F 142 ILE cc_start: 0.7367 (mm) cc_final: 0.7026 (mm) REVERT: F 278 VAL cc_start: 0.8507 (t) cc_final: 0.7944 (p) REVERT: F 287 LYS cc_start: 0.7357 (mttm) cc_final: 0.6811 (mtmm) REVERT: F 311 THR cc_start: 0.8301 (t) cc_final: 0.7966 (p) REVERT: F 356 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6932 (tm-30) outliers start: 38 outliers final: 32 residues processed: 286 average time/residue: 0.1221 time to fit residues: 52.1877 Evaluate side-chains 300 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 143 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 163 optimal weight: 0.0670 chunk 109 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.189637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156337 restraints weight = 24534.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.160405 restraints weight = 14367.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.162980 restraints weight = 10195.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164599 restraints weight = 8215.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.165548 restraints weight = 7178.998| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16838 Z= 0.171 Angle : 0.604 10.578 23128 Z= 0.324 Chirality : 0.044 0.294 2538 Planarity : 0.004 0.051 2632 Dihedral : 18.244 179.690 3014 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.39 % Allowed : 16.16 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1764 helix: 1.56 (0.23), residues: 561 sheet: 0.06 (0.29), residues: 359 loop : -1.71 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 213 TYR 0.022 0.002 TYR A 251 PHE 0.030 0.002 PHE F 93 TRP 0.014 0.001 TRP F 254 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16838) covalent geometry : angle 0.60355 / 0.32 (23128) hydrogen bonds : bond 0.04524 / 2.96 ( 614) hydrogen bonds : angle 4.60595 / 3.31 ( 1858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6274 (tpm170) cc_final: 0.5870 (tpm170) REVERT: A 209 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6806 (mtp180) REVERT: A 213 TYR cc_start: 0.6537 (m-80) cc_final: 0.6186 (m-80) REVERT: A 263 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7039 (ttp80) REVERT: A 321 PHE cc_start: 0.7245 (t80) cc_final: 0.6793 (t80) REVERT: A 399 GLU cc_start: 0.7633 (mp0) cc_final: 0.7216 (mp0) REVERT: B 213 ARG cc_start: 0.8308 (mtm180) cc_final: 0.8097 (mtp180) REVERT: B 226 GLU cc_start: 0.7470 (mp0) cc_final: 0.7185 (mp0) REVERT: B 417 SER cc_start: 0.8029 (t) cc_final: 0.7661 (m) REVERT: E 4 LYS cc_start: 0.6917 (mttm) cc_final: 0.6562 (mtpp) REVERT: E 59 LYS cc_start: 0.7792 (tppt) cc_final: 0.7503 (tppt) REVERT: E 93 PHE cc_start: 0.6592 (t80) cc_final: 0.6177 (t80) REVERT: E 119 ASP cc_start: 0.8014 (t0) cc_final: 0.7700 (t70) REVERT: E 309 MET cc_start: 0.7102 (ttm) cc_final: 0.6845 (ttm) REVERT: E 411 LYS cc_start: 0.7586 (ttmt) cc_final: 0.7370 (tppt) REVERT: F 16 HIS cc_start: 0.6204 (m-70) cc_final: 0.5920 (m-70) REVERT: F 40 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7577 (mptt) REVERT: F 142 ILE cc_start: 0.7403 (mm) cc_final: 0.7055 (mm) REVERT: F 287 LYS cc_start: 0.7402 (mttm) cc_final: 0.7178 (ttmt) REVERT: F 311 THR cc_start: 0.8309 (t) cc_final: 0.7971 (p) REVERT: F 347 LYS cc_start: 0.6975 (tppt) cc_final: 0.6761 (tppt) REVERT: F 356 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7037 (tm-30) outliers start: 38 outliers final: 34 residues processed: 282 average time/residue: 0.1171 time to fit residues: 49.2372 Evaluate side-chains 303 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 269 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 10 optimal weight: 0.0050 chunk 67 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.189334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.156181 restraints weight = 24566.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.160232 restraints weight = 14386.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162817 restraints weight = 10226.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.164417 restraints weight = 8262.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165530 restraints weight = 7215.191| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16838 Z= 0.157 Angle : 0.603 10.221 23128 Z= 0.324 Chirality : 0.043 0.298 2538 Planarity : 0.004 0.058 2632 Dihedral : 18.271 179.419 3014 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.39 % Allowed : 16.54 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1764 helix: 1.51 (0.23), residues: 561 sheet: 0.00 (0.28), residues: 375 loop : -1.70 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 213 TYR 0.020 0.002 TYR A 251 PHE 0.034 0.002 PHE F 93 TRP 0.012 0.001 TRP F 254 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (16838) covalent geometry : angle 0.60332 / 0.32 (23128) hydrogen bonds : bond 0.04433 / 2.91 ( 614) hydrogen bonds : angle 4.59128 / 3.30 ( 1858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6228 (tpm170) cc_final: 0.5885 (tpm170) REVERT: A 209 ARG cc_start: 0.7052 (mtp85) cc_final: 0.6825 (mtp180) REVERT: A 213 TYR cc_start: 0.6588 (m-80) cc_final: 0.6223 (m-80) REVERT: A 263 ARG cc_start: 0.7428 (ttp80) cc_final: 0.7042 (ttp80) REVERT: A 279 ASP cc_start: 0.8163 (t0) cc_final: 0.7681 (t0) REVERT: A 321 PHE cc_start: 0.7228 (t80) cc_final: 0.6813 (t80) REVERT: A 399 GLU cc_start: 0.7638 (mp0) cc_final: 0.7234 (mp0) REVERT: A 400 LYS cc_start: 0.7403 (mttt) cc_final: 0.6799 (mttm) REVERT: B 213 ARG cc_start: 0.8260 (mtm180) cc_final: 0.8023 (mtp180) REVERT: B 226 GLU cc_start: 0.7437 (mp0) cc_final: 0.7204 (mp0) REVERT: B 417 SER cc_start: 0.8016 (t) cc_final: 0.7641 (m) REVERT: E 4 LYS cc_start: 0.6921 (mttm) cc_final: 0.6567 (mtpp) REVERT: E 59 LYS cc_start: 0.7855 (tppt) cc_final: 0.7528 (tppt) REVERT: E 93 PHE cc_start: 0.6590 (t80) cc_final: 0.6181 (t80) REVERT: E 119 ASP cc_start: 0.8032 (t0) cc_final: 0.7729 (t70) REVERT: E 309 MET cc_start: 0.7083 (ttm) cc_final: 0.6827 (ttm) REVERT: E 411 LYS cc_start: 0.7575 (ttmt) cc_final: 0.7327 (tppt) REVERT: F 14 PHE cc_start: 0.7437 (m-80) cc_final: 0.7102 (m-80) REVERT: F 16 HIS cc_start: 0.6152 (m-70) cc_final: 0.5902 (m-70) REVERT: F 40 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7582 (mptt) REVERT: F 56 TYR cc_start: 0.5391 (t80) cc_final: 0.4930 (t80) REVERT: F 142 ILE cc_start: 0.7409 (mm) cc_final: 0.7065 (mm) REVERT: F 287 LYS cc_start: 0.7408 (mttm) cc_final: 0.7193 (ttmt) REVERT: F 311 THR cc_start: 0.8308 (t) cc_final: 0.7988 (p) REVERT: F 347 LYS cc_start: 0.6951 (tppt) cc_final: 0.6712 (tppt) REVERT: F 356 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7019 (tm-30) outliers start: 38 outliers final: 36 residues processed: 286 average time/residue: 0.1194 time to fit residues: 50.8488 Evaluate side-chains 307 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 164 optimal weight: 0.0050 chunk 149 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.189818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156646 restraints weight = 24645.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.160672 restraints weight = 14378.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.163311 restraints weight = 10205.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.164957 restraints weight = 8229.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165843 restraints weight = 7173.315| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16838 Z= 0.143 Angle : 0.594 9.988 23128 Z= 0.319 Chirality : 0.043 0.302 2538 Planarity : 0.004 0.052 2632 Dihedral : 18.265 179.486 3014 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.26 % Allowed : 16.98 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1764 helix: 1.55 (0.23), residues: 560 sheet: 0.02 (0.28), residues: 373 loop : -1.70 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 407 TYR 0.024 0.001 TYR A 251 PHE 0.033 0.002 PHE F 93 TRP 0.021 0.001 TRP E 319 HIS 0.005 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16838) covalent geometry : angle 0.59425 / 0.32 (23128) hydrogen bonds : bond 0.04267 / 2.79 ( 614) hydrogen bonds : angle 4.54523 / 3.27 ( 1858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.37 seconds wall clock time: 48 minutes 5.22 seconds (2885.22 seconds total)