Starting phenix.real_space_refine on Fri Jul 3 22:04:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sp3_40673/07_2026/8sp3_40673_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sp3_40673/07_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_40673/07_2026/8sp3_40673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sp3_40673/07_2026/8sp3_40673.map" model { file = "/net/cci-nas-00/data/ceres_data/8sp3_40673/07_2026/8sp3_40673_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sp3_40673/07_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-dev-6108/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: 3.81, per 1000 atoms: 0.23 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: 1.42 Conformation dependent library (CDL) restraints added in 634.4 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: 1.80 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: 2.68 Time building geometry restraints manager: 1.80 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: 22425 1.67 - 3.34: 615 3.34 - 5.00: 64 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: 2174 0.061 - 0.121: 328 0.121 - 0.182: 30 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: 9.390 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.260 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- 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= 0.258 Angle : 0.634 8.341 23128 Z= 0.444 Chirality : 0.045 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 0.00356 / 0.26 (16838) covalent geometry : angle 0.63419 / 0.44 (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 : 0.405 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: 0.5984 (t70) REVERT: A 209 ARG cc_start: 0.6994 (mtp85) cc_final: 0.6741 (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: 0.6067 (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: 0.6822 (ttpp) REVERT: A 399 GLU cc_start: 0.7572 (mp0) cc_final: 0.7254 (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: 0.8274 (m) REVERT: B 254 TRP cc_start: 0.7502 (m100) cc_final: 0.7125 (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: 0.6443 (mtpp) REVERT: E 15 ASN cc_start: 0.5140 (m-40) cc_final: 0.4616 (m-40) REVERT: E 59 LYS cc_start: 0.7732 (tppt) cc_final: 0.7413 (tppt) REVERT: E 93 PHE cc_start: 0.6583 (t80) cc_final: 0.6217 (t80) REVERT: E 208 VAL cc_start: 0.7249 (t) cc_final: 0.6976 (t) REVERT: E 286 GLU cc_start: 0.5179 (tp30) cc_final: 0.4930 (tp30) REVERT: E 360 SER cc_start: 0.7501 (m) cc_final: 0.7201 (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: 0.5282 (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: 0.7082 (mmtm) REVERT: F 115 TYR cc_start: 0.7589 (t80) cc_final: 0.7384 (t80) REVERT: F 142 ILE cc_start: 0.7393 (mm) cc_final: 0.7036 (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: 0.6890 (m-80) REVERT: F 287 LYS cc_start: 0.7309 (mttm) cc_final: 0.7014 (mtmt) 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: 0.1283 time to fit residues: 70.3182 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 : 0.559 ------------------------------------------------------------------------------- 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 = 0.192605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158850 restraints weight = 24191.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.163186 restraints weight = 13870.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.165903 restraints weight = 9703.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.167635 restraints weight = 7764.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.168745 restraints weight = 6735.932| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16838 Z= 0.155 Angle : 0.589 14.186 23128 Z= 0.326 Chirality : 0.044 0.268 2538 Planarity : 0.004 0.048 2632 Dihedral : 18.198 179.970 3014 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.70 % Allowed : 7.23 % Favored : 91.07 % 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: -0.28 (0.20), residues: 1764 helix: 1.62 (0.23), residues: 556 sheet: 0.07 (0.28), residues: 384 loop : -1.63 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 186 TYR 0.019 0.001 TYR B 6 PHE 0.028 0.002 PHE B 30 TRP 0.014 0.001 TRP B 86 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16838) covalent geometry : angle 0.58916 / 0.33 (23128) hydrogen bonds : bond 0.05197 / 3.40 ( 614) hydrogen bonds : angle 5.01210 / 3.61 ( 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 341 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8140 (t) cc_final: 0.7747 (p) REVERT: A 35 ASP cc_start: 0.6046 (t70) cc_final: 0.5823 (t70) REVERT: A 209 ARG cc_start: 0.6955 (mtp85) cc_final: 0.6717 (mtp85) REVERT: A 210 TYR cc_start: 0.7124 (t80) cc_final: 0.6853 (t80) REVERT: A 213 TYR cc_start: 0.6458 (m-80) cc_final: 0.6075 (m-80) REVERT: A 240 ARG cc_start: 0.6678 (mtt180) cc_final: 0.6129 (mtt180) REVERT: A 241 ILE cc_start: 0.8090 (mp) cc_final: 0.7604 (pt) REVERT: A 255 PHE cc_start: 0.8431 (t80) cc_final: 0.8190 (t80) REVERT: A 263 ARG cc_start: 0.7399 (ttp80) cc_final: 0.6919 (ttp80) REVERT: A 267 GLN cc_start: 0.8237 (tt0) cc_final: 0.7916 (tt0) REVERT: A 291 THR cc_start: 0.7643 (m) cc_final: 0.7432 (p) REVERT: A 399 GLU cc_start: 0.7595 (mp0) cc_final: 0.7276 (mp0) REVERT: B 100 ASP cc_start: 0.6609 (m-30) cc_final: 0.6392 (m-30) REVERT: B 115 TYR cc_start: 0.7438 (t80) cc_final: 0.7075 (t80) REVERT: B 254 TRP cc_start: 0.7555 (m100) cc_final: 0.7046 (m100) REVERT: B 321 TYR cc_start: 0.7853 (m-80) cc_final: 0.7381 (m-10) REVERT: B 412 VAL cc_start: 0.8405 (t) cc_final: 0.8128 (p) REVERT: B 417 SER cc_start: 0.8100 (t) cc_final: 0.7672 (m) REVERT: B 444 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6732 (tm-30) REVERT: E 4 LYS cc_start: 0.6812 (mttm) cc_final: 0.6477 (mtpp) REVERT: E 15 ASN cc_start: 0.5204 (m-40) cc_final: 0.4662 (m-40) REVERT: E 59 LYS cc_start: 0.7745 (tppt) cc_final: 0.7401 (tppt) REVERT: E 93 PHE cc_start: 0.6544 (t80) cc_final: 0.6191 (t80) REVERT: E 193 MET cc_start: 0.5851 (mmm) cc_final: 0.5609 (mmm) REVERT: E 286 GLU cc_start: 0.5150 (tp30) cc_final: 0.4932 (tp30) REVERT: E 290 LYS cc_start: 0.8193 (pttt) cc_final: 0.7800 (ptpp) REVERT: F 14 PHE cc_start: 0.7480 (m-80) cc_final: 0.7073 (m-80) REVERT: F 16 HIS cc_start: 0.6001 (m-70) cc_final: 0.5735 (m-70) REVERT: F 37 TYR cc_start: 0.7674 (m-80) cc_final: 0.7433 (m-80) REVERT: F 40 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7435 (mptt) REVERT: F 56 TYR cc_start: 0.5615 (t80) cc_final: 0.5143 (t80) REVERT: F 91 ILE cc_start: 0.8417 (mt) cc_final: 0.8104 (tt) REVERT: F 93 PHE cc_start: 0.7421 (t80) cc_final: 0.7114 (t80) REVERT: F 94 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7407 (mmtm) REVERT: F 115 TYR cc_start: 0.7784 (t80) cc_final: 0.7422 (t80) REVERT: F 142 ILE cc_start: 0.7378 (mm) cc_final: 0.6922 (mt) REVERT: F 247 LYS cc_start: 0.7232 (mtpt) cc_final: 0.7017 (mtpp) REVERT: F 285 TYR cc_start: 0.7083 (m-80) cc_final: 0.6734 (m-80) REVERT: F 287 LYS cc_start: 0.7313 (mttm) cc_final: 0.6979 (mtmt) REVERT: F 306 ASP cc_start: 0.6224 (p0) cc_final: 0.5981 (p0) REVERT: F 311 THR cc_start: 0.8016 (t) cc_final: 0.7663 (p) REVERT: F 336 LYS cc_start: 0.8097 (mttp) cc_final: 0.7728 (mtmm) outliers start: 27 outliers final: 17 residues processed: 324 average time/residue: 0.1321 time to fit residues: 63.3311 Evaluate side-chains 319 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 302 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE 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 E residue 401 VAL Chi-restraints excluded: chain F residue 12 ILE 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: 0.3980 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 72 optimal weight: 0.0770 chunk 134 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 158 optimal weight: 0.0170 chunk 103 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 ASN ** B 209 GLN ** 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 = 0.4347 r_free = 0.4347 target = 0.193098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159198 restraints weight = 24565.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163528 restraints weight = 13951.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166290 restraints weight = 9731.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.168048 restraints weight = 7782.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.169042 restraints weight = 6742.403| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.1661 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= 0.130 Angle : 0.550 8.575 23128 Z= 0.305 Chirality : 0.043 0.270 2538 Planarity : 0.004 0.038 2632 Dihedral : 18.161 179.756 3014 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.01 % Allowed : 10.38 % Favored : 87.61 % 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: -0.26 (0.20), residues: 1764 helix: 1.57 (0.23), residues: 561 sheet: 0.03 (0.28), residues: 389 loop : -1.58 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 54 TYR 0.025 0.001 TYR A 251 PHE 0.030 0.002 PHE B 93 TRP 0.010 0.001 TRP E 319 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 0.55017 / 0.31 (23128) hydrogen bonds : bond 0.04447 / 2.92 ( 614) hydrogen bonds : angle 4.74014 / 3.42 ( 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 329 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8135 (t) cc_final: 0.7721 (p) REVERT: A 35 ASP cc_start: 0.5958 (t70) cc_final: 0.5742 (t70) REVERT: A 193 MET cc_start: 0.7030 (mmm) cc_final: 0.6722 (mmt) REVERT: A 209 ARG cc_start: 0.6979 (mtp85) cc_final: 0.6735 (mtp85) REVERT: A 210 TYR cc_start: 0.7136 (t80) cc_final: 0.6829 (t80) REVERT: A 213 TYR cc_start: 0.6479 (m-80) cc_final: 0.6094 (m-80) REVERT: A 255 PHE cc_start: 0.8431 (t80) cc_final: 0.8190 (t80) REVERT: A 263 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7081 (ttp80) REVERT: A 279 ASP cc_start: 0.7860 (t70) cc_final: 0.7638 (t0) REVERT: A 291 THR cc_start: 0.7623 (m) cc_final: 0.7419 (p) REVERT: A 348 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7402 (mttt) REVERT: A 399 GLU cc_start: 0.7650 (mp0) cc_final: 0.7270 (mp0) REVERT: B 115 TYR cc_start: 0.7419 (t80) cc_final: 0.7035 (t80) REVERT: B 214 LEU cc_start: 0.8306 (mp) cc_final: 0.7913 (mp) REVERT: B 226 GLU cc_start: 0.7468 (mp0) cc_final: 0.7206 (mp0) REVERT: B 254 TRP cc_start: 0.7557 (m100) cc_final: 0.7033 (m100) REVERT: B 321 TYR cc_start: 0.7847 (m-80) cc_final: 0.7308 (m-80) REVERT: B 412 VAL cc_start: 0.8376 (t) cc_final: 0.8092 (p) REVERT: B 417 SER cc_start: 0.8097 (t) cc_final: 0.7650 (m) REVERT: E 4 LYS cc_start: 0.6812 (mttm) cc_final: 0.6482 (mtpp) REVERT: E 15 ASN cc_start: 0.5223 (m-40) cc_final: 0.4672 (m-40) REVERT: E 59 LYS cc_start: 0.7743 (tppt) cc_final: 0.7395 (tppt) REVERT: E 93 PHE cc_start: 0.6547 (t80) cc_final: 0.6179 (t80) REVERT: E 286 GLU cc_start: 0.5127 (tp30) cc_final: 0.4911 (tp30) REVERT: E 364 GLN cc_start: 0.6470 (tt0) cc_final: 0.6107 (tm-30) REVERT: F 14 PHE cc_start: 0.7393 (m-80) cc_final: 0.7148 (m-80) REVERT: F 16 HIS cc_start: 0.6014 (m-70) cc_final: 0.5742 (m-70) REVERT: F 37 TYR cc_start: 0.7716 (m-80) cc_final: 0.7433 (m-80) REVERT: F 40 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7685 (mmmt) REVERT: F 56 TYR cc_start: 0.5569 (t80) cc_final: 0.5149 (t80) REVERT: F 115 TYR cc_start: 0.7768 (t80) cc_final: 0.7428 (t80) REVERT: F 142 ILE cc_start: 0.7336 (mm) cc_final: 0.6868 (mt) REVERT: F 247 LYS cc_start: 0.7214 (mtpt) cc_final: 0.6911 (mtpp) REVERT: F 278 VAL cc_start: 0.8494 (t) cc_final: 0.8197 (p) REVERT: F 287 LYS cc_start: 0.7291 (mttm) cc_final: 0.6809 (mtmm) REVERT: F 306 ASP cc_start: 0.6227 (p0) cc_final: 0.5946 (p0) REVERT: F 311 THR cc_start: 0.8072 (t) cc_final: 0.7756 (p) REVERT: F 336 LYS cc_start: 0.7950 (mttp) cc_final: 0.7636 (mtmm) outliers start: 32 outliers final: 17 residues processed: 306 average time/residue: 0.1232 time to fit residues: 55.3739 Evaluate side-chains 309 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 292 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 484 ASP Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 282 VAL 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: 1.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.186787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153250 restraints weight = 24651.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157191 restraints weight = 14425.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159730 restraints weight = 10265.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.161366 restraints weight = 8299.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.162189 restraints weight = 7232.004| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 16838 Z= 0.320 Angle : 0.742 8.249 23128 Z= 0.405 Chirality : 0.049 0.264 2538 Planarity : 0.005 0.076 2632 Dihedral : 18.407 179.986 3014 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.08 % Allowed : 12.58 % Favored : 84.34 % 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: -0.90 (0.20), residues: 1764 helix: 0.83 (0.22), residues: 565 sheet: -0.10 (0.28), residues: 385 loop : -1.92 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 362 TYR 0.032 0.003 TYR B 321 PHE 0.030 0.003 PHE B 93 TRP 0.027 0.003 TRP F 269 HIS 0.013 0.002 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.32 (16838) covalent geometry : angle 0.74173 / 0.40 (23128) hydrogen bonds : bond 0.06403 / 4.22 ( 614) hydrogen bonds : angle 5.24332 / 3.77 ( 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 351 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6371 (tpm170) cc_final: 0.6079 (tpm170) REVERT: A 174 ASN cc_start: 0.8114 (p0) cc_final: 0.7697 (p0) REVERT: A 209 ARG cc_start: 0.7101 (mtp85) cc_final: 0.6835 (mtp85) REVERT: A 210 TYR cc_start: 0.7109 (t80) cc_final: 0.6862 (t80) REVERT: A 213 TYR cc_start: 0.6680 (m-80) cc_final: 0.6136 (m-80) REVERT: A 222 ASP cc_start: 0.6434 (t0) cc_final: 0.6216 (t0) REVERT: A 263 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7185 (ttp80) REVERT: A 279 ASP cc_start: 0.8018 (t70) cc_final: 0.7756 (t0) REVERT: A 366 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7502 (ttpt) REVERT: A 399 GLU cc_start: 0.7680 (mp0) cc_final: 0.7293 (mp0) REVERT: A 400 LYS cc_start: 0.7475 (mttt) cc_final: 0.7101 (mttm) REVERT: B 21 THR cc_start: 0.5604 (OUTLIER) cc_final: 0.5205 (p) REVERT: B 226 GLU cc_start: 0.7643 (mp0) cc_final: 0.7290 (mp0) REVERT: B 412 VAL cc_start: 0.8357 (t) cc_final: 0.8080 (p) REVERT: B 417 SER cc_start: 0.8090 (t) cc_final: 0.7642 (m) REVERT: E 4 LYS cc_start: 0.6881 (mttm) cc_final: 0.6570 (mtpp) REVERT: E 15 ASN cc_start: 0.5543 (m-40) cc_final: 0.4983 (m-40) REVERT: E 59 LYS cc_start: 0.7806 (tppt) cc_final: 0.7471 (tppt) REVERT: E 93 PHE cc_start: 0.6715 (t80) cc_final: 0.6245 (t80) REVERT: E 119 ASP cc_start: 0.7980 (t0) cc_final: 0.7650 (t70) REVERT: E 290 LYS cc_start: 0.8259 (pttt) cc_final: 0.8001 (mtmm) REVERT: E 364 GLN cc_start: 0.6652 (tt0) cc_final: 0.6284 (tm-30) REVERT: F 16 HIS cc_start: 0.6216 (m-70) cc_final: 0.5943 (m-70) REVERT: F 74 MET cc_start: 0.3504 (ptm) cc_final: 0.3219 (ptm) REVERT: F 115 TYR cc_start: 0.7990 (t80) cc_final: 0.7622 (t80) REVERT: F 142 ILE cc_start: 0.7452 (mm) cc_final: 0.7091 (mm) REVERT: F 219 ILE cc_start: 0.8009 (mt) cc_final: 0.7806 (pt) REVERT: F 287 LYS cc_start: 0.7478 (mttm) cc_final: 0.6863 (mtmm) REVERT: F 306 ASP cc_start: 0.6452 (p0) cc_final: 0.6197 (p0) REVERT: F 316 GLU cc_start: 0.6946 (tp30) cc_final: 0.6678 (tp30) REVERT: F 336 LYS cc_start: 0.8164 (mttp) cc_final: 0.7903 (mtmm) REVERT: F 409 ASN cc_start: 0.7874 (m-40) cc_final: 0.7668 (m-40) outliers start: 49 outliers final: 36 residues processed: 321 average time/residue: 0.1339 time to fit residues: 63.3057 Evaluate side-chains 327 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS 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 33 LEU 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 227 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 437 VAL 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 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 336 MET 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 5 ILE 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 459 ILE 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: 0.7980 chunk 63 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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** ** 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 = 0.4310 r_free = 0.4310 target = 0.189485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156285 restraints weight = 24334.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160233 restraints weight = 14274.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.162840 restraints weight = 10193.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164211 restraints weight = 8212.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.165421 restraints weight = 7248.022| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16838 Z= 0.158 Angle : 0.604 8.439 23128 Z= 0.331 Chirality : 0.044 0.268 2538 Planarity : 0.004 0.048 2632 Dihedral : 18.336 179.789 3014 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.89 % Allowed : 15.22 % Favored : 81.89 % 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: -0.59 (0.20), residues: 1764 helix: 1.38 (0.23), residues: 541 sheet: -0.13 (0.28), residues: 385 loop : -1.77 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 54 TYR 0.024 0.002 TYR A 251 PHE 0.041 0.002 PHE E 223 TRP 0.015 0.001 TRP E 319 HIS 0.004 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (16838) covalent geometry : angle 0.60375 / 0.33 (23128) hydrogen bonds : bond 0.04769 / 3.13 ( 614) hydrogen bonds : angle 4.84020 / 3.48 ( 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 343 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6308 (tpm170) cc_final: 0.6008 (tpm170) REVERT: A 174 ASN cc_start: 0.7912 (p0) cc_final: 0.7621 (p0) REVERT: A 183 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6878 (mt-10) REVERT: A 209 ARG cc_start: 0.7000 (mtp85) cc_final: 0.6752 (mtp85) REVERT: A 210 TYR cc_start: 0.7124 (t80) cc_final: 0.6910 (t80) REVERT: A 213 TYR cc_start: 0.6597 (m-80) cc_final: 0.6208 (m-80) REVERT: A 222 ASP cc_start: 0.6289 (t0) cc_final: 0.6086 (t0) REVERT: A 263 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7046 (ttp80) REVERT: A 279 ASP cc_start: 0.8009 (t70) cc_final: 0.7744 (t0) REVERT: A 366 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7479 (ttpt) REVERT: A 399 GLU cc_start: 0.7681 (mp0) cc_final: 0.7267 (mp0) REVERT: B 9 GLU cc_start: 0.7681 (mp0) cc_final: 0.7404 (mp0) REVERT: B 115 TYR cc_start: 0.7527 (t80) cc_final: 0.7050 (t80) REVERT: B 226 GLU cc_start: 0.7507 (mp0) cc_final: 0.7263 (mp0) REVERT: B 254 TRP cc_start: 0.7468 (m100) cc_final: 0.7115 (m100) REVERT: B 321 TYR cc_start: 0.8032 (m-80) cc_final: 0.7597 (m-80) REVERT: B 412 VAL cc_start: 0.8288 (t) cc_final: 0.8024 (p) REVERT: B 417 SER cc_start: 0.8049 (t) cc_final: 0.7666 (m) REVERT: E 4 LYS cc_start: 0.6875 (mttm) cc_final: 0.6542 (mtpp) REVERT: E 59 LYS cc_start: 0.7835 (tppt) cc_final: 0.7495 (tppt) REVERT: E 93 PHE cc_start: 0.6560 (t80) cc_final: 0.6148 (t80) REVERT: E 119 ASP cc_start: 0.7961 (t0) cc_final: 0.7633 (t70) REVERT: E 222 ASP cc_start: 0.5794 (p0) cc_final: 0.5088 (t0) REVERT: E 341 ILE cc_start: 0.5043 (OUTLIER) cc_final: 0.4767 (mt) REVERT: E 364 GLN cc_start: 0.6459 (tt0) cc_final: 0.6214 (tm-30) REVERT: F 16 HIS cc_start: 0.6200 (m-70) cc_final: 0.5915 (m-70) REVERT: F 40 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7523 (mmmt) REVERT: F 142 ILE cc_start: 0.7364 (mm) cc_final: 0.6985 (mm) REVERT: F 287 LYS cc_start: 0.7440 (mttm) cc_final: 0.6842 (mtmm) REVERT: F 306 ASP cc_start: 0.6351 (p0) cc_final: 0.6011 (p0) REVERT: F 311 THR cc_start: 0.8170 (t) cc_final: 0.7924 (p) REVERT: F 316 GLU cc_start: 0.6856 (tp30) cc_final: 0.6565 (tp30) outliers start: 46 outliers final: 29 residues processed: 317 average time/residue: 0.1322 time to fit residues: 61.7831 Evaluate side-chains 319 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 ASP 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 227 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 322 ASN 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 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 341 ILE Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 12 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 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 160 optimal weight: 0.0040 chunk 30 optimal weight: 0.0970 chunk 163 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 135 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4320 r_free = 0.4320 target = 0.190612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157123 restraints weight = 24576.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161248 restraints weight = 14359.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.163864 restraints weight = 10166.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.165519 restraints weight = 8182.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166492 restraints weight = 7129.841| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16838 Z= 0.139 Angle : 0.580 9.836 23128 Z= 0.319 Chirality : 0.043 0.269 2538 Planarity : 0.004 0.042 2632 Dihedral : 18.284 179.992 3014 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.70 % Allowed : 16.35 % Favored : 80.94 % 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: -0.46 (0.20), residues: 1764 helix: 1.58 (0.23), residues: 544 sheet: -0.07 (0.28), residues: 385 loop : -1.76 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 209 TYR 0.025 0.001 TYR A 251 PHE 0.042 0.002 PHE F 358 TRP 0.012 0.001 TRP F 370 HIS 0.004 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (16838) covalent geometry : angle 0.58020 / 0.32 (23128) hydrogen bonds : bond 0.04460 / 2.93 ( 614) hydrogen bonds : angle 4.71869 / 3.39 ( 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 330 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6316 (tpm170) cc_final: 0.5980 (tpm170) REVERT: A 174 ASN cc_start: 0.7916 (p0) cc_final: 0.7555 (p0) REVERT: A 209 ARG cc_start: 0.7013 (mtp85) cc_final: 0.6781 (mtp85) REVERT: A 210 TYR cc_start: 0.7109 (t80) cc_final: 0.6879 (t80) REVERT: A 213 TYR cc_start: 0.6584 (m-80) cc_final: 0.6213 (m-80) REVERT: A 222 ASP cc_start: 0.6281 (t0) cc_final: 0.6079 (t0) REVERT: A 263 ARG cc_start: 0.7437 (ttp80) cc_final: 0.6994 (ttp80) REVERT: A 279 ASP cc_start: 0.8048 (t70) cc_final: 0.7789 (t0) REVERT: A 366 LYS cc_start: 0.7953 (tttm) cc_final: 0.7482 (ttpt) REVERT: A 399 GLU cc_start: 0.7696 (mp0) cc_final: 0.7242 (mp0) REVERT: B 9 GLU cc_start: 0.7688 (mp0) cc_final: 0.7439 (mt-10) REVERT: B 226 GLU cc_start: 0.7452 (mp0) cc_final: 0.7153 (mp0) REVERT: B 254 TRP cc_start: 0.7481 (m100) cc_final: 0.7130 (m100) REVERT: B 321 TYR cc_start: 0.8045 (m-80) cc_final: 0.7586 (m-80) REVERT: B 417 SER cc_start: 0.8050 (t) cc_final: 0.7666 (m) REVERT: E 4 LYS cc_start: 0.6881 (mttm) cc_final: 0.6550 (mtpp) REVERT: E 59 LYS cc_start: 0.7839 (tppt) cc_final: 0.7485 (tppt) REVERT: E 93 PHE cc_start: 0.6576 (t80) cc_final: 0.6158 (t80) REVERT: E 119 ASP cc_start: 0.7943 (t0) cc_final: 0.7630 (t70) REVERT: E 171 TYR cc_start: 0.6414 (m-80) cc_final: 0.6195 (m-80) REVERT: E 222 ASP cc_start: 0.5628 (p0) cc_final: 0.5148 (t0) REVERT: E 341 ILE cc_start: 0.5024 (OUTLIER) cc_final: 0.4722 (mt) REVERT: E 364 GLN cc_start: 0.6461 (tt0) cc_final: 0.6190 (tm-30) REVERT: F 16 HIS cc_start: 0.6166 (m-70) cc_final: 0.5875 (m-70) REVERT: F 40 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7526 (mptt) REVERT: F 142 ILE cc_start: 0.7374 (mm) cc_final: 0.6997 (mm) REVERT: F 287 LYS cc_start: 0.7402 (mttm) cc_final: 0.6840 (mtmm) REVERT: F 311 THR cc_start: 0.8181 (t) cc_final: 0.7962 (p) REVERT: F 316 GLU cc_start: 0.6757 (tp30) cc_final: 0.6495 (tp30) REVERT: F 395 LYS cc_start: 0.6805 (mttt) cc_final: 0.6604 (mttm) outliers start: 43 outliers final: 34 residues processed: 306 average time/residue: 0.1195 time to fit residues: 54.0301 Evaluate side-chains 315 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 303 ASP 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 384 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU 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 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 341 ILE 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 12 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 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: 0.6980 chunk 150 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 125 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 chunk 63 optimal weight: 0.0070 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN B 209 GLN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.191659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.157842 restraints weight = 24419.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162051 restraints weight = 14065.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.164753 restraints weight = 9903.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166449 restraints weight = 7920.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.167461 restraints weight = 6870.419| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2625 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= 0.132 Angle : 0.571 10.607 23128 Z= 0.312 Chirality : 0.043 0.272 2538 Planarity : 0.004 0.042 2632 Dihedral : 18.274 179.994 3014 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.77 % Allowed : 16.54 % Favored : 80.69 % 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: -0.45 (0.20), residues: 1764 helix: 1.57 (0.23), residues: 558 sheet: -0.06 (0.28), residues: 373 loop : -1.79 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 209 TYR 0.031 0.001 TYR B 65 PHE 0.033 0.002 PHE B 93 TRP 0.011 0.001 TRP A 319 HIS 0.004 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (16838) covalent geometry : angle 0.57140 / 0.31 (23128) hydrogen bonds : bond 0.04208 / 2.76 ( 614) hydrogen bonds : angle 4.62485 / 3.31 ( 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 325 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6336 (tpm170) cc_final: 0.5984 (tpm170) REVERT: A 209 ARG cc_start: 0.7020 (mtp85) cc_final: 0.6783 (mtp85) REVERT: A 210 TYR cc_start: 0.7103 (t80) cc_final: 0.6850 (t80) REVERT: A 213 TYR cc_start: 0.6570 (m-80) cc_final: 0.6205 (m-80) REVERT: A 222 ASP cc_start: 0.6291 (t0) cc_final: 0.6075 (t0) REVERT: A 263 ARG cc_start: 0.7451 (ttp80) cc_final: 0.6987 (ttp80) REVERT: A 274 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6725 (tp30) REVERT: A 279 ASP cc_start: 0.8070 (t70) cc_final: 0.7825 (t0) REVERT: A 321 PHE cc_start: 0.6982 (t80) cc_final: 0.6349 (t80) REVERT: A 366 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7486 (ttpt) REVERT: A 399 GLU cc_start: 0.7710 (mp0) cc_final: 0.7218 (mp0) REVERT: B 138 VAL cc_start: 0.8465 (t) cc_final: 0.8173 (m) REVERT: B 226 GLU cc_start: 0.7455 (mp0) cc_final: 0.7207 (mp0) REVERT: B 321 TYR cc_start: 0.8038 (m-80) cc_final: 0.7638 (m-80) REVERT: B 417 SER cc_start: 0.8081 (t) cc_final: 0.7731 (m) REVERT: E 4 LYS cc_start: 0.6879 (mttm) cc_final: 0.6460 (mtpp) REVERT: E 59 LYS cc_start: 0.7830 (tppt) cc_final: 0.7493 (tppt) REVERT: E 93 PHE cc_start: 0.6576 (t80) cc_final: 0.6149 (t80) REVERT: E 119 ASP cc_start: 0.7958 (t0) cc_final: 0.7641 (t70) REVERT: E 222 ASP cc_start: 0.5731 (p0) cc_final: 0.5260 (t0) REVERT: E 330 TYR cc_start: 0.7780 (t80) cc_final: 0.7519 (t80) REVERT: E 341 ILE cc_start: 0.5036 (OUTLIER) cc_final: 0.4782 (mt) REVERT: E 372 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6978 (t) REVERT: F 16 HIS cc_start: 0.6145 (m-70) cc_final: 0.5860 (m-70) REVERT: F 40 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7604 (mptt) REVERT: F 142 ILE cc_start: 0.7372 (mm) cc_final: 0.7011 (mm) REVERT: F 287 LYS cc_start: 0.7364 (mttm) cc_final: 0.6837 (mtmm) REVERT: F 311 THR cc_start: 0.8222 (t) cc_final: 0.7986 (p) outliers start: 44 outliers final: 31 residues processed: 299 average time/residue: 0.1156 time to fit residues: 51.5511 Evaluate side-chains 309 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS 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 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 44 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 463 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 160 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 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 = 0.4315 r_free = 0.4315 target = 0.190273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.156894 restraints weight = 24510.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.160958 restraints weight = 14297.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.163515 restraints weight = 10138.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165164 restraints weight = 8193.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166178 restraints weight = 7145.789| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16838 Z= 0.178 Angle : 0.604 10.006 23128 Z= 0.329 Chirality : 0.044 0.266 2538 Planarity : 0.004 0.076 2632 Dihedral : 18.306 179.961 3014 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.77 % Allowed : 16.86 % Favored : 80.38 % 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: -0.45 (0.20), residues: 1764 helix: 1.63 (0.23), residues: 544 sheet: -0.01 (0.28), residues: 371 loop : -1.80 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 209 TYR 0.028 0.002 TYR B 65 PHE 0.035 0.002 PHE F 358 TRP 0.016 0.001 TRP E 319 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (16838) covalent geometry : angle 0.60387 / 0.33 (23128) hydrogen bonds : bond 0.04606 / 3.05 ( 614) hydrogen bonds : angle 4.73365 / 3.39 ( 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 322 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6274 (tpm170) cc_final: 0.5945 (tpm170) REVERT: A 174 ASN cc_start: 0.7959 (p0) cc_final: 0.7576 (p0) REVERT: A 209 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6796 (mtp85) REVERT: A 210 TYR cc_start: 0.7137 (t80) cc_final: 0.6926 (t80) REVERT: A 213 TYR cc_start: 0.6619 (m-80) cc_final: 0.6227 (m-80) REVERT: A 222 ASP cc_start: 0.6309 (t0) cc_final: 0.6061 (t0) REVERT: A 263 ARG cc_start: 0.7433 (ttp80) cc_final: 0.6968 (ttp80) REVERT: A 274 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6668 (tp30) REVERT: A 279 ASP cc_start: 0.8060 (t70) cc_final: 0.7798 (t0) REVERT: A 321 PHE cc_start: 0.7308 (t80) cc_final: 0.6608 (t80) REVERT: A 366 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7428 (ttpt) REVERT: A 399 GLU cc_start: 0.7701 (mp0) cc_final: 0.7215 (mp0) REVERT: A 400 LYS cc_start: 0.7353 (mttt) cc_final: 0.6845 (mttm) REVERT: B 138 VAL cc_start: 0.8470 (t) cc_final: 0.8184 (m) REVERT: B 226 GLU cc_start: 0.7496 (mp0) cc_final: 0.7221 (mp0) REVERT: B 321 TYR cc_start: 0.8070 (m-80) cc_final: 0.7685 (m-80) REVERT: B 417 SER cc_start: 0.8055 (t) cc_final: 0.7692 (m) REVERT: E 4 LYS cc_start: 0.6907 (mttm) cc_final: 0.6504 (mtpp) REVERT: E 59 LYS cc_start: 0.7895 (tppt) cc_final: 0.7562 (tppt) REVERT: E 93 PHE cc_start: 0.6608 (t80) cc_final: 0.6182 (t80) REVERT: E 119 ASP cc_start: 0.7998 (t0) cc_final: 0.7686 (t70) REVERT: E 222 ASP cc_start: 0.5704 (p0) cc_final: 0.5143 (t0) REVERT: E 372 THR cc_start: 0.7249 (OUTLIER) cc_final: 0.7009 (t) REVERT: F 16 HIS cc_start: 0.6196 (m-70) cc_final: 0.5907 (m-70) REVERT: F 40 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7593 (mptt) REVERT: F 142 ILE cc_start: 0.7380 (mm) cc_final: 0.7007 (mm) REVERT: F 287 LYS cc_start: 0.7383 (mttm) cc_final: 0.6853 (mtmm) REVERT: F 311 THR cc_start: 0.8213 (t) cc_final: 0.8002 (p) outliers start: 44 outliers final: 38 residues processed: 294 average time/residue: 0.1219 time to fit residues: 53.0493 Evaluate side-chains 318 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS 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 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 339 SER Chi-restraints excluded: chain E residue 372 THR 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 44 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 143 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 chunk 109 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** 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 = 0.4304 r_free = 0.4304 target = 0.189168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155770 restraints weight = 24427.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.159787 restraints weight = 14346.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.162377 restraints weight = 10194.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.163868 restraints weight = 8230.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.164950 restraints weight = 7229.612| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16838 Z= 0.196 Angle : 0.626 10.405 23128 Z= 0.341 Chirality : 0.045 0.265 2538 Planarity : 0.004 0.061 2632 Dihedral : 18.342 179.829 3014 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.70 % Allowed : 17.42 % Favored : 79.87 % 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: -0.54 (0.20), residues: 1764 helix: 1.50 (0.23), residues: 543 sheet: -0.12 (0.29), residues: 361 loop : -1.76 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 213 TYR 0.027 0.002 TYR A 251 PHE 0.037 0.002 PHE B 93 TRP 0.015 0.002 TRP F 254 HIS 0.007 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (16838) covalent geometry : angle 0.62591 / 0.34 (23128) hydrogen bonds : bond 0.04940 / 3.26 ( 614) hydrogen bonds : angle 4.77495 / 3.42 ( 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 323 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6305 (tpm170) cc_final: 0.5905 (tpm170) REVERT: A 174 ASN cc_start: 0.7999 (p0) cc_final: 0.7620 (p0) REVERT: A 209 ARG cc_start: 0.7054 (mtp85) cc_final: 0.6817 (mtp85) REVERT: A 213 TYR cc_start: 0.6649 (m-80) cc_final: 0.6217 (m-80) REVERT: A 222 ASP cc_start: 0.6311 (t0) cc_final: 0.6069 (t0) REVERT: A 263 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7079 (ttp80) REVERT: A 269 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6468 (mp) REVERT: A 279 ASP cc_start: 0.8059 (t70) cc_final: 0.7772 (t0) REVERT: A 321 PHE cc_start: 0.7284 (t80) cc_final: 0.7070 (t80) REVERT: A 366 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7479 (ttpt) REVERT: A 399 GLU cc_start: 0.7717 (mp0) cc_final: 0.7234 (mp0) REVERT: A 400 LYS cc_start: 0.7399 (mttt) cc_final: 0.6789 (mttm) REVERT: B 138 VAL cc_start: 0.8481 (t) cc_final: 0.8180 (m) REVERT: B 226 GLU cc_start: 0.7522 (mp0) cc_final: 0.7174 (mp0) REVERT: B 321 TYR cc_start: 0.8098 (m-80) cc_final: 0.7733 (m-80) REVERT: B 417 SER cc_start: 0.8034 (t) cc_final: 0.7637 (m) REVERT: E 4 LYS cc_start: 0.6931 (mttm) cc_final: 0.6505 (mtpp) REVERT: E 59 LYS cc_start: 0.7902 (tppt) cc_final: 0.7590 (tppt) REVERT: E 93 PHE cc_start: 0.6667 (t80) cc_final: 0.6215 (t80) REVERT: E 119 ASP cc_start: 0.8032 (t0) cc_final: 0.7722 (t70) REVERT: E 222 ASP cc_start: 0.5739 (OUTLIER) cc_final: 0.5159 (t0) REVERT: E 372 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.7029 (t) REVERT: F 6 TYR cc_start: 0.7638 (t80) cc_final: 0.7316 (t80) REVERT: F 16 HIS cc_start: 0.6162 (m-70) cc_final: 0.5900 (m-70) REVERT: F 40 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7556 (mptt) REVERT: F 142 ILE cc_start: 0.7353 (mm) cc_final: 0.6962 (mm) REVERT: F 287 LYS cc_start: 0.7403 (mttm) cc_final: 0.6888 (mtmm) REVERT: F 311 THR cc_start: 0.8248 (t) cc_final: 0.8009 (p) outliers start: 43 outliers final: 37 residues processed: 298 average time/residue: 0.1196 time to fit residues: 53.0828 Evaluate side-chains 318 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS 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 317 VAL Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 437 VAL 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 222 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 372 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 27 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** 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 = 0.4319 r_free = 0.4319 target = 0.190483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157329 restraints weight = 24332.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.161343 restraints weight = 14212.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163903 restraints weight = 10101.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.165426 restraints weight = 8159.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.166571 restraints weight = 7149.599| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16838 Z= 0.153 Angle : 0.599 9.706 23128 Z= 0.326 Chirality : 0.044 0.272 2538 Planarity : 0.004 0.057 2632 Dihedral : 18.331 179.601 3014 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.77 % Allowed : 17.67 % Favored : 79.56 % 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: -0.49 (0.20), residues: 1764 helix: 1.56 (0.23), residues: 544 sheet: -0.10 (0.28), residues: 373 loop : -1.76 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 213 TYR 0.025 0.001 TYR A 251 PHE 0.036 0.002 PHE B 93 TRP 0.012 0.001 TRP A 319 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16838) covalent geometry : angle 0.59918 / 0.33 (23128) hydrogen bonds : bond 0.04522 / 2.98 ( 614) hydrogen bonds : angle 4.65509 / 3.34 ( 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 327 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6244 (tpm170) cc_final: 0.5865 (tpm170) REVERT: A 174 ASN cc_start: 0.7969 (p0) cc_final: 0.7619 (p0) REVERT: A 209 ARG cc_start: 0.7022 (mtp85) cc_final: 0.6778 (mtp85) REVERT: A 213 TYR cc_start: 0.6585 (m-80) cc_final: 0.6205 (m-80) REVERT: A 222 ASP cc_start: 0.6280 (t0) cc_final: 0.6033 (t0) REVERT: A 245 GLU cc_start: 0.7282 (pt0) cc_final: 0.6683 (tm-30) REVERT: A 263 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7023 (ttp80) REVERT: A 269 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6434 (mt) REVERT: A 279 ASP cc_start: 0.8058 (t70) cc_final: 0.7766 (t0) REVERT: A 366 LYS cc_start: 0.7986 (tttm) cc_final: 0.7461 (ttpt) REVERT: A 400 LYS cc_start: 0.7314 (mttt) cc_final: 0.6936 (mttm) REVERT: B 138 VAL cc_start: 0.8466 (t) cc_final: 0.8185 (m) REVERT: B 226 GLU cc_start: 0.7457 (mp0) cc_final: 0.7184 (mp0) REVERT: B 321 TYR cc_start: 0.8084 (m-80) cc_final: 0.7693 (m-80) REVERT: B 417 SER cc_start: 0.8009 (t) cc_final: 0.7624 (m) REVERT: E 4 LYS cc_start: 0.6907 (mttm) cc_final: 0.6484 (mtpp) REVERT: E 59 LYS cc_start: 0.7909 (tppt) cc_final: 0.7620 (tppt) REVERT: E 93 PHE cc_start: 0.6627 (t80) cc_final: 0.6157 (t80) REVERT: E 119 ASP cc_start: 0.8024 (t0) cc_final: 0.7718 (t70) REVERT: E 222 ASP cc_start: 0.5666 (OUTLIER) cc_final: 0.5127 (t0) REVERT: E 372 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.6992 (t) REVERT: E 411 LYS cc_start: 0.7580 (ttmt) cc_final: 0.7334 (tppt) REVERT: F 6 TYR cc_start: 0.7609 (t80) cc_final: 0.7266 (t80) REVERT: F 16 HIS cc_start: 0.6186 (m-70) cc_final: 0.5911 (m-70) REVERT: F 40 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7543 (mptt) REVERT: F 142 ILE cc_start: 0.7351 (mm) cc_final: 0.6967 (mm) REVERT: F 311 THR cc_start: 0.8230 (t) cc_final: 0.7999 (p) outliers start: 44 outliers final: 37 residues processed: 304 average time/residue: 0.1089 time to fit residues: 49.4102 Evaluate side-chains 318 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 269 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 127 SER 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 322 ASN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 437 VAL 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 222 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 372 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 155 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 GLN F 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.189152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156051 restraints weight = 24476.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.160060 restraints weight = 14302.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162607 restraints weight = 10167.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164062 restraints weight = 8211.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165167 restraints weight = 7216.767| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16838 Z= 0.191 Angle : 0.633 10.484 23128 Z= 0.345 Chirality : 0.045 0.269 2538 Planarity : 0.004 0.053 2632 Dihedral : 18.334 179.786 3014 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.58 % Allowed : 18.18 % Favored : 79.25 % 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: -0.57 (0.20), residues: 1764 helix: 1.49 (0.23), residues: 536 sheet: -0.08 (0.28), residues: 371 loop : -1.82 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 213 TYR 0.023 0.002 TYR A 251 PHE 0.034 0.002 PHE B 93 TRP 0.015 0.002 TRP F 254 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (16838) covalent geometry : angle 0.63251 / 0.35 (23128) hydrogen bonds : bond 0.04953 / 3.27 ( 614) hydrogen bonds : angle 4.75293 / 3.42 ( 1858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.26 seconds wall clock time: 48 minutes 57.26 seconds (2937.26 seconds total)