Starting phenix.real_space_refine on Sun Aug 24 03:05:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sp3_40673/08_2025/8sp3_40673_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sp3_40673/08_2025/8sp3_40673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sp3_40673/08_2025/8sp3_40673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sp3_40673/08_2025/8sp3_40673.map" model { file = "/net/cci-nas-00/data/ceres_data/8sp3_40673/08_2025/8sp3_40673_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sp3_40673/08_2025/8sp3_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.79, 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: 1.45 Conformation dependent library (CDL) restraints added in 385.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.99 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: 2.82 Time building geometry restraints manager: 1.90 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: 22494 1.67 - 3.34: 550 3.34 - 5.00: 60 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=" N GLU A 260 " pdb=" CA GLU A 260 " pdb=" C GLU A 260 " ideal model delta sigma weight residual 112.38 106.80 5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" CA LEU A 185 " pdb=" C LEU A 185 " pdb=" O LEU A 185 " ideal model delta sigma weight residual 121.11 116.26 4.85 1.13e+00 7.83e-01 1.84e+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: 2207 0.061 - 0.121: 302 0.121 - 0.182: 23 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: 6.610 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.140 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 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 : 0.003 0.047 16838 Z= 0.189 Angle : 0.616 8.341 23128 Z= 0.368 Chirality : 0.043 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 aren 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 covalent geometry : bond 0.00328 (16838) covalent geometry : angle 0.61562 (23128) hydrogen bonds : bond 0.16216 ( 614) hydrogen bonds : angle 6.38401 ( 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 : 0.505 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: 0.3624 (m-30) REVERT: B 321 TYR cc_start: 0.7834 (m-80) cc_final: 0.7325 (m-10) REVERT: B 417 SER cc_start: 0.8107 (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: 0.7200 (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: 0.7836 (t) cc_final: 0.7635 (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: 0.1302 time to fit residues: 70.5346 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 : 0.540 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: F 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.192682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158837 restraints weight = 24151.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.163119 restraints weight = 13875.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.165870 restraints weight = 9739.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.167602 restraints weight = 7773.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.168678 restraints weight = 6747.058| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16838 Z= 0.143 Angle : 0.577 12.992 23128 Z= 0.303 Chirality : 0.042 0.173 2538 Planarity : 0.004 0.049 2632 Dihedral : 18.101 177.452 3014 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.57 % Allowed : 7.55 % Favored : 90.88 % 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 aren not related in a simple way. whole: -0.22 (0.20), residues: 1764 helix: 1.66 (0.23), residues: 559 sheet: -0.01 (0.28), residues: 379 loop : -1.54 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 407 TYR 0.016 0.001 TYR B 6 PHE 0.023 0.002 PHE B 30 TRP 0.019 0.001 TRP B 86 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00316 (16838) covalent geometry : angle 0.57680 (23128) hydrogen bonds : bond 0.04468 ( 614) hydrogen bonds : angle 4.76935 ( 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 339 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 314 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6666 (mp) cc_final: 0.6353 (mp) REVERT: A 8 SER cc_start: 0.8099 (t) cc_final: 0.7681 (p) REVERT: A 209 ARG cc_start: 0.6981 (mtp85) cc_final: 0.6711 (mtp85) REVERT: A 210 TYR cc_start: 0.7153 (t80) cc_final: 0.6837 (t80) REVERT: A 213 TYR cc_start: 0.6526 (m-80) cc_final: 0.6097 (m-80) REVERT: A 246 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8207 (tp) REVERT: A 255 PHE cc_start: 0.8423 (t80) cc_final: 0.8173 (t80) REVERT: A 263 ARG cc_start: 0.7425 (ttp80) cc_final: 0.7041 (ttp80) REVERT: A 279 ASP cc_start: 0.7926 (t70) cc_final: 0.7680 (t0) REVERT: A 399 GLU cc_start: 0.7606 (mp0) cc_final: 0.7262 (mp0) REVERT: B 132 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 254 TRP cc_start: 0.7533 (m100) cc_final: 0.7024 (m100) REVERT: B 321 TYR cc_start: 0.7867 (m-80) cc_final: 0.7298 (m-80) REVERT: B 412 VAL cc_start: 0.8339 (t) cc_final: 0.8073 (p) REVERT: B 417 SER cc_start: 0.8127 (t) cc_final: 0.7719 (m) REVERT: E 4 LYS cc_start: 0.6806 (mttm) cc_final: 0.6541 (mtpp) REVERT: E 15 ASN cc_start: 0.5294 (m-40) cc_final: 0.4726 (m-40) REVERT: E 59 LYS cc_start: 0.7737 (tppt) cc_final: 0.7392 (tppt) REVERT: E 93 PHE cc_start: 0.6553 (t80) cc_final: 0.6173 (t80) REVERT: E 119 ASP cc_start: 0.7881 (t0) cc_final: 0.7599 (t0) REVERT: E 128 LEU cc_start: 0.7174 (tp) cc_final: 0.6947 (tp) REVERT: E 246 ILE cc_start: 0.7181 (pt) cc_final: 0.6975 (mt) REVERT: E 286 GLU cc_start: 0.5154 (tp30) cc_final: 0.4945 (tp30) REVERT: E 290 LYS cc_start: 0.8207 (pttt) cc_final: 0.7826 (ptpp) REVERT: E 364 GLN cc_start: 0.6448 (tt0) cc_final: 0.6136 (tm-30) REVERT: F 5 ILE cc_start: 0.8015 (pt) cc_final: 0.7774 (pt) REVERT: F 16 HIS cc_start: 0.6088 (m-70) cc_final: 0.5833 (m-70) REVERT: F 37 TYR cc_start: 0.7685 (m-80) cc_final: 0.7435 (m-80) REVERT: F 40 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7643 (mmmt) REVERT: F 56 TYR cc_start: 0.5543 (t80) cc_final: 0.5056 (t80) REVERT: F 115 TYR cc_start: 0.7783 (t80) cc_final: 0.7434 (t80) REVERT: F 243 ARG cc_start: 0.6807 (mtm180) cc_final: 0.6466 (mtt180) REVERT: F 247 LYS cc_start: 0.7293 (mtpt) cc_final: 0.7022 (mtpp) REVERT: F 278 VAL cc_start: 0.8507 (t) cc_final: 0.8215 (p) REVERT: F 287 LYS cc_start: 0.7294 (mttm) cc_final: 0.6785 (mtmm) REVERT: F 311 THR cc_start: 0.8140 (t) cc_final: 0.7767 (p) REVERT: F 316 GLU cc_start: 0.6819 (tp30) cc_final: 0.6404 (tp30) REVERT: F 336 LYS cc_start: 0.8052 (mttp) cc_final: 0.7727 (mtmm) REVERT: F 342 SER cc_start: 0.8366 (m) cc_final: 0.8112 (t) outliers start: 25 outliers final: 15 residues processed: 323 average time/residue: 0.1410 time to fit residues: 65.3234 Evaluate side-chains 319 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 303 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 504 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 72 optimal weight: 0.0010 chunk 134 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 158 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.191166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.157351 restraints weight = 24723.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161627 restraints weight = 14071.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164407 restraints weight = 9838.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.166162 restraints weight = 7828.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.167231 restraints weight = 6777.575| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.2047 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= 0.151 Angle : 0.571 6.632 23128 Z= 0.302 Chirality : 0.042 0.169 2538 Planarity : 0.004 0.045 2632 Dihedral : 18.130 178.327 3014 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.39 % Allowed : 10.88 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.20), residues: 1764 helix: 1.58 (0.23), residues: 571 sheet: -0.04 (0.28), residues: 392 loop : -1.60 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 295 TYR 0.020 0.001 TYR A 251 PHE 0.027 0.002 PHE B 93 TRP 0.013 0.001 TRP F 269 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00339 (16838) covalent geometry : angle 0.57061 (23128) hydrogen bonds : bond 0.04405 ( 614) hydrogen bonds : angle 4.62100 ( 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 334 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6682 (mp) cc_final: 0.6356 (mp) REVERT: A 126 ARG cc_start: 0.6149 (tpm170) cc_final: 0.5871 (tpm170) REVERT: A 209 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6798 (mtp85) REVERT: A 210 TYR cc_start: 0.7154 (t80) cc_final: 0.6896 (t80) REVERT: A 213 TYR cc_start: 0.6521 (m-80) cc_final: 0.6160 (m-80) REVERT: A 246 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 263 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7059 (ttp80) REVERT: A 279 ASP cc_start: 0.8038 (t70) cc_final: 0.7787 (t0) REVERT: A 399 GLU cc_start: 0.7669 (mp0) cc_final: 0.7248 (mp0) REVERT: B 254 TRP cc_start: 0.7565 (m100) cc_final: 0.7170 (m100) REVERT: B 321 TYR cc_start: 0.7949 (m-80) cc_final: 0.7469 (m-80) REVERT: B 417 SER cc_start: 0.8033 (t) cc_final: 0.7689 (m) REVERT: E 4 LYS cc_start: 0.6827 (mttm) cc_final: 0.6513 (mtpp) REVERT: E 15 ASN cc_start: 0.5428 (m-40) cc_final: 0.4857 (m-40) REVERT: E 59 LYS cc_start: 0.7773 (tppt) cc_final: 0.7414 (tppt) REVERT: E 93 PHE cc_start: 0.6546 (t80) cc_final: 0.6157 (t80) REVERT: E 119 ASP cc_start: 0.7948 (t0) cc_final: 0.7624 (t70) REVERT: E 193 MET cc_start: 0.5646 (mmm) cc_final: 0.5442 (mmm) REVERT: E 360 SER cc_start: 0.7524 (m) cc_final: 0.7291 (p) REVERT: F 16 HIS cc_start: 0.6170 (m-70) cc_final: 0.5888 (m-70) REVERT: F 56 TYR cc_start: 0.5547 (t80) cc_final: 0.4990 (t80) REVERT: F 142 ILE cc_start: 0.7370 (mm) cc_final: 0.6994 (mm) REVERT: F 278 VAL cc_start: 0.8483 (t) cc_final: 0.8242 (p) REVERT: F 287 LYS cc_start: 0.7403 (mttm) cc_final: 0.6821 (mtmm) REVERT: F 311 THR cc_start: 0.8207 (t) cc_final: 0.7908 (p) REVERT: F 316 GLU cc_start: 0.6740 (tp30) cc_final: 0.6325 (tp30) REVERT: F 336 LYS cc_start: 0.8045 (mttp) cc_final: 0.7723 (mtmm) REVERT: F 342 SER cc_start: 0.8397 (m) cc_final: 0.8184 (t) REVERT: F 362 LYS cc_start: 0.7689 (mptt) cc_final: 0.7462 (mptt) outliers start: 38 outliers final: 27 residues processed: 307 average time/residue: 0.1363 time to fit residues: 60.9910 Evaluate side-chains 314 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 88 SER 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 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: 2.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.187537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154096 restraints weight = 24524.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158142 restraints weight = 14264.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.160710 restraints weight = 10122.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162359 restraints weight = 8178.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.163285 restraints weight = 7147.357| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 16838 Z= 0.264 Angle : 0.688 8.252 23128 Z= 0.366 Chirality : 0.046 0.169 2538 Planarity : 0.005 0.070 2632 Dihedral : 18.390 176.336 3014 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.96 % Allowed : 13.90 % Favored : 83.14 % 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 aren not related in a simple way. whole: -0.70 (0.20), residues: 1764 helix: 1.13 (0.22), residues: 555 sheet: -0.10 (0.28), residues: 373 loop : -1.80 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 213 TYR 0.030 0.002 TYR B 321 PHE 0.033 0.003 PHE B 30 TRP 0.019 0.002 TRP F 254 HIS 0.008 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00594 (16838) covalent geometry : angle 0.68812 (23128) hydrogen bonds : bond 0.05849 ( 614) hydrogen bonds : angle 5.02036 ( 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 342 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6679 (mp) cc_final: 0.6365 (mp) REVERT: A 126 ARG cc_start: 0.6223 (tpm170) cc_final: 0.5886 (tpm170) REVERT: A 209 ARG cc_start: 0.7099 (mtp85) cc_final: 0.6818 (mtp85) REVERT: A 210 TYR cc_start: 0.7178 (t80) cc_final: 0.6970 (t80) REVERT: A 213 TYR cc_start: 0.6636 (m-80) cc_final: 0.6011 (m-80) REVERT: A 246 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8422 (tp) REVERT: A 263 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7145 (ttp80) REVERT: A 279 ASP cc_start: 0.8053 (t70) cc_final: 0.7741 (t0) REVERT: A 399 GLU cc_start: 0.7715 (mp0) cc_final: 0.7308 (mp0) REVERT: A 411 LYS cc_start: 0.5550 (tttp) cc_final: 0.5256 (ttpp) REVERT: A 415 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8313 (m) REVERT: B 3 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6182 (mm-30) REVERT: B 9 GLU cc_start: 0.7699 (mp0) cc_final: 0.7346 (mt-10) REVERT: B 254 TRP cc_start: 0.7683 (m100) cc_final: 0.7413 (m100) REVERT: B 412 VAL cc_start: 0.8255 (t) cc_final: 0.7997 (p) REVERT: B 417 SER cc_start: 0.8067 (t) cc_final: 0.7653 (m) REVERT: E 4 LYS cc_start: 0.6881 (mttm) cc_final: 0.6533 (mtpp) REVERT: E 59 LYS cc_start: 0.7909 (tppt) cc_final: 0.7468 (tppt) REVERT: E 93 PHE cc_start: 0.6643 (t80) cc_final: 0.5995 (t80) REVERT: F 16 HIS cc_start: 0.6277 (m-70) cc_final: 0.5973 (m-70) REVERT: F 40 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7513 (mptt) REVERT: F 54 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.5915 (mpp80) REVERT: F 93 PHE cc_start: 0.7126 (t80) cc_final: 0.6841 (t80) REVERT: F 142 ILE cc_start: 0.7414 (mm) cc_final: 0.7137 (mm) REVERT: F 247 LYS cc_start: 0.7095 (mtpp) cc_final: 0.6828 (mtpp) REVERT: F 287 LYS cc_start: 0.7474 (mttm) cc_final: 0.7231 (ttmt) REVERT: F 306 ASP cc_start: 0.6401 (p0) cc_final: 0.6117 (p0) REVERT: F 311 THR cc_start: 0.8238 (t) cc_final: 0.7961 (p) REVERT: F 316 GLU cc_start: 0.6840 (tp30) cc_final: 0.6519 (tp30) REVERT: F 336 LYS cc_start: 0.8088 (mttp) cc_final: 0.7856 (mtmm) REVERT: F 342 SER cc_start: 0.8434 (m) cc_final: 0.8118 (t) REVERT: F 409 ASN cc_start: 0.7961 (m-40) cc_final: 0.7675 (m-40) outliers start: 47 outliers final: 34 residues processed: 315 average time/residue: 0.1256 time to fit residues: 58.3113 Evaluate side-chains 321 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 245 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 316 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 A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER 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 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 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 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 278 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 135 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 258 ASN B 61 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.187445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154155 restraints weight = 24311.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.158204 restraints weight = 14250.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.160813 restraints weight = 10155.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.162471 restraints weight = 8177.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.163393 restraints weight = 7124.704| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.2971 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= 0.193 Angle : 0.615 8.903 23128 Z= 0.328 Chirality : 0.043 0.171 2538 Planarity : 0.004 0.051 2632 Dihedral : 18.305 177.957 3014 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.08 % Allowed : 16.16 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1764 helix: 1.45 (0.23), residues: 542 sheet: -0.09 (0.28), residues: 367 loop : -1.77 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 213 TYR 0.021 0.002 TYR A 251 PHE 0.028 0.002 PHE B 93 TRP 0.017 0.002 TRP E 319 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00435 (16838) covalent geometry : angle 0.61523 (23128) hydrogen bonds : bond 0.04927 ( 614) hydrogen bonds : angle 4.77541 ( 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 349 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 300 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6613 (mp) cc_final: 0.6301 (mp) REVERT: A 94 ILE cc_start: 0.8402 (mt) cc_final: 0.8083 (mm) REVERT: A 126 ARG cc_start: 0.6171 (tpm170) cc_final: 0.5750 (tpm170) REVERT: A 174 ASN cc_start: 0.8045 (p0) cc_final: 0.7640 (p0) REVERT: A 189 GLU cc_start: 0.6408 (tm-30) cc_final: 0.5663 (tp30) REVERT: A 209 ARG cc_start: 0.7093 (mtp85) cc_final: 0.6822 (mtp180) REVERT: A 210 TYR cc_start: 0.7173 (t80) cc_final: 0.6952 (t80) REVERT: A 213 TYR cc_start: 0.6554 (m-80) cc_final: 0.6044 (m-80) REVERT: A 246 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 279 ASP cc_start: 0.8083 (t70) cc_final: 0.7791 (t0) REVERT: A 366 LYS cc_start: 0.7996 (tttm) cc_final: 0.7498 (ttpt) REVERT: A 399 GLU cc_start: 0.7698 (mp0) cc_final: 0.7263 (mp0) REVERT: A 411 LYS cc_start: 0.5574 (tttp) cc_final: 0.5215 (ttpp) REVERT: B 3 GLU cc_start: 0.6475 (mm-30) cc_final: 0.6214 (mm-30) REVERT: B 412 VAL cc_start: 0.8232 (t) cc_final: 0.7969 (p) REVERT: B 417 SER cc_start: 0.8074 (t) cc_final: 0.7688 (m) REVERT: E 4 LYS cc_start: 0.6902 (mttm) cc_final: 0.6647 (mtpp) REVERT: E 59 LYS cc_start: 0.7934 (tppt) cc_final: 0.7553 (tppt) REVERT: E 63 VAL cc_start: 0.7363 (t) cc_final: 0.7155 (p) REVERT: E 93 PHE cc_start: 0.6634 (t80) cc_final: 0.6152 (t80) REVERT: E 128 LEU cc_start: 0.7181 (tp) cc_final: 0.6934 (tt) REVERT: E 208 VAL cc_start: 0.7202 (t) cc_final: 0.6653 (m) REVERT: E 364 GLN cc_start: 0.6522 (tt0) cc_final: 0.6104 (tm-30) REVERT: F 16 HIS cc_start: 0.6210 (m-70) cc_final: 0.5911 (m-70) REVERT: F 40 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7542 (mptt) REVERT: F 54 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.5645 (mpp80) REVERT: F 94 LYS cc_start: 0.7836 (mmtm) cc_final: 0.7498 (mmtm) REVERT: F 142 ILE cc_start: 0.7438 (mm) cc_final: 0.7076 (mm) REVERT: F 287 LYS cc_start: 0.7447 (mttm) cc_final: 0.7213 (ttmt) REVERT: F 311 THR cc_start: 0.8240 (t) cc_final: 0.7942 (p) REVERT: F 316 GLU cc_start: 0.6733 (tp30) cc_final: 0.6454 (tp30) REVERT: F 336 LYS cc_start: 0.7959 (mttp) cc_final: 0.7759 (mtmm) REVERT: F 342 SER cc_start: 0.8424 (m) cc_final: 0.8146 (t) REVERT: F 409 ASN cc_start: 0.7911 (m-40) cc_final: 0.7674 (m-40) outliers start: 49 outliers final: 35 residues processed: 322 average time/residue: 0.1393 time to fit residues: 65.1263 Evaluate side-chains 327 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 200 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 THR 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 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 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 224 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 219 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 435 MET 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: 1.9990 chunk 60 optimal weight: 0.8980 chunk 160 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.189378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.155998 restraints weight = 24485.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.160144 restraints weight = 14313.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.162682 restraints weight = 10139.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.164342 restraints weight = 8195.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.165183 restraints weight = 7148.923| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16838 Z= 0.157 Angle : 0.589 9.893 23128 Z= 0.314 Chirality : 0.042 0.169 2538 Planarity : 0.004 0.044 2632 Dihedral : 18.249 178.055 3014 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.27 % Allowed : 16.73 % Favored : 80.00 % 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 aren not related in a simple way. whole: -0.53 (0.20), residues: 1764 helix: 1.49 (0.23), residues: 547 sheet: -0.14 (0.28), residues: 371 loop : -1.75 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 364 TYR 0.019 0.001 TYR E 330 PHE 0.038 0.002 PHE F 93 TRP 0.018 0.001 TRP E 319 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00353 (16838) covalent geometry : angle 0.58915 (23128) hydrogen bonds : bond 0.04464 ( 614) hydrogen bonds : angle 4.64810 ( 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 348 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6556 (mp) cc_final: 0.6238 (mp) REVERT: A 94 ILE cc_start: 0.8398 (mt) cc_final: 0.8094 (mm) REVERT: A 126 ARG cc_start: 0.6189 (tpm170) cc_final: 0.5746 (tpm170) REVERT: A 189 GLU cc_start: 0.6451 (tm-30) cc_final: 0.5520 (tm-30) REVERT: A 209 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6816 (mtp180) REVERT: A 210 TYR cc_start: 0.7175 (t80) cc_final: 0.6961 (t80) REVERT: A 213 TYR cc_start: 0.6584 (m-80) cc_final: 0.6362 (m-80) REVERT: A 279 ASP cc_start: 0.8097 (t70) cc_final: 0.7803 (t0) REVERT: A 366 LYS cc_start: 0.7967 (tttm) cc_final: 0.7449 (ttpt) REVERT: A 399 GLU cc_start: 0.7679 (mp0) cc_final: 0.7229 (mp0) REVERT: A 411 LYS cc_start: 0.5557 (tttp) cc_final: 0.5194 (ttpp) REVERT: A 415 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 254 TRP cc_start: 0.7452 (m100) cc_final: 0.7101 (m100) REVERT: B 417 SER cc_start: 0.8015 (t) cc_final: 0.7642 (m) REVERT: E 4 LYS cc_start: 0.6894 (mttm) cc_final: 0.6477 (mtpp) REVERT: E 59 LYS cc_start: 0.7935 (tppt) cc_final: 0.7537 (tppt) REVERT: E 63 VAL cc_start: 0.7453 (t) cc_final: 0.7228 (p) REVERT: E 93 PHE cc_start: 0.6621 (t80) cc_final: 0.5906 (t80) REVERT: E 119 ASP cc_start: 0.8076 (t0) cc_final: 0.7715 (t0) REVERT: E 128 LEU cc_start: 0.7056 (tp) cc_final: 0.6797 (tt) REVERT: E 171 TYR cc_start: 0.6357 (m-80) cc_final: 0.6135 (m-80) REVERT: F 16 HIS cc_start: 0.6253 (m-70) cc_final: 0.5931 (m-70) REVERT: F 40 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7553 (mptt) REVERT: F 142 ILE cc_start: 0.7418 (mm) cc_final: 0.7072 (mm) REVERT: F 311 THR cc_start: 0.8293 (t) cc_final: 0.7973 (p) REVERT: F 316 GLU cc_start: 0.6699 (tp30) cc_final: 0.6434 (tp30) REVERT: F 342 SER cc_start: 0.8420 (m) cc_final: 0.8137 (t) REVERT: F 409 ASN cc_start: 0.7873 (m-40) cc_final: 0.7638 (m-40) REVERT: F 436 GLU cc_start: 0.4957 (mt-10) cc_final: 0.4553 (mt-10) outliers start: 52 outliers final: 42 residues processed: 317 average time/residue: 0.1346 time to fit residues: 62.4251 Evaluate side-chains 327 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 197 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 SER 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER 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 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 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 164 VAL 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 339 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 219 ILE 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 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: 0.9980 chunk 139 optimal weight: 0.0770 chunk 150 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 52 optimal weight: 0.4980 chunk 125 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.187088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153440 restraints weight = 24389.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.157507 restraints weight = 14393.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.160072 restraints weight = 10276.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161675 restraints weight = 8310.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.162727 restraints weight = 7266.844| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16838 Z= 0.163 Angle : 0.602 9.674 23128 Z= 0.318 Chirality : 0.043 0.199 2538 Planarity : 0.004 0.041 2632 Dihedral : 18.225 177.172 3014 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.70 % Allowed : 17.55 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.20), residues: 1764 helix: 1.46 (0.23), residues: 550 sheet: -0.13 (0.28), residues: 373 loop : -1.71 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 364 TYR 0.021 0.001 TYR A 251 PHE 0.038 0.002 PHE F 93 TRP 0.017 0.001 TRP E 319 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00369 (16838) covalent geometry : angle 0.60196 (23128) hydrogen bonds : bond 0.04556 ( 614) hydrogen bonds : angle 4.64520 ( 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 328 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6581 (mp) cc_final: 0.6256 (mp) REVERT: A 60 PHE cc_start: 0.7449 (t80) cc_final: 0.7097 (t80) REVERT: A 94 ILE cc_start: 0.8433 (mt) cc_final: 0.8134 (mm) REVERT: A 174 ASN cc_start: 0.7994 (p0) cc_final: 0.7610 (p0) REVERT: A 183 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 189 GLU cc_start: 0.6569 (tm-30) cc_final: 0.6322 (tp30) REVERT: A 209 ARG cc_start: 0.7037 (mtp85) cc_final: 0.6798 (mtp180) REVERT: A 210 TYR cc_start: 0.7194 (t80) cc_final: 0.6960 (t80) REVERT: A 213 TYR cc_start: 0.6565 (m-80) cc_final: 0.6281 (m-80) REVERT: A 279 ASP cc_start: 0.8055 (t70) cc_final: 0.7766 (t0) REVERT: A 399 GLU cc_start: 0.7670 (mp0) cc_final: 0.7232 (mp0) REVERT: A 411 LYS cc_start: 0.5586 (tttp) cc_final: 0.5339 (ttpp) REVERT: A 415 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8304 (m) REVERT: B 138 VAL cc_start: 0.8440 (t) cc_final: 0.8162 (m) REVERT: B 254 TRP cc_start: 0.7510 (m100) cc_final: 0.7159 (m100) REVERT: B 417 SER cc_start: 0.7980 (t) cc_final: 0.7549 (m) REVERT: E 4 LYS cc_start: 0.6907 (mttm) cc_final: 0.6483 (mtpp) REVERT: E 59 LYS cc_start: 0.7946 (tppt) cc_final: 0.7568 (tppt) REVERT: E 93 PHE cc_start: 0.6642 (t80) cc_final: 0.5909 (t80) REVERT: E 119 ASP cc_start: 0.8132 (t0) cc_final: 0.7769 (t0) REVERT: E 171 TYR cc_start: 0.6324 (m-80) cc_final: 0.6093 (m-80) REVERT: E 372 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.7000 (t) REVERT: F 16 HIS cc_start: 0.6236 (m-70) cc_final: 0.5942 (m-70) REVERT: F 40 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7520 (mptt) REVERT: F 94 LYS cc_start: 0.7673 (mmtm) cc_final: 0.7359 (mmtm) REVERT: F 142 ILE cc_start: 0.7416 (mm) cc_final: 0.7069 (mm) REVERT: F 311 THR cc_start: 0.8294 (t) cc_final: 0.7980 (p) REVERT: F 316 GLU cc_start: 0.6687 (tp30) cc_final: 0.6422 (tp30) REVERT: F 342 SER cc_start: 0.8420 (m) cc_final: 0.8148 (t) REVERT: F 409 ASN cc_start: 0.7854 (m-40) cc_final: 0.7610 (m-40) outliers start: 43 outliers final: 37 residues processed: 303 average time/residue: 0.1321 time to fit residues: 59.1807 Evaluate side-chains 318 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 197 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 SER 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 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 122 MET Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 219 ILE 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 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: 0.0980 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 155 optimal weight: 0.0370 chunk 130 optimal weight: 0.0870 chunk 181 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 40 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.193551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.160358 restraints weight = 24438.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164538 restraints weight = 13891.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167206 restraints weight = 9704.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.168879 restraints weight = 7773.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.169894 restraints weight = 6755.314| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16838 Z= 0.111 Angle : 0.557 11.630 23128 Z= 0.294 Chirality : 0.041 0.167 2538 Planarity : 0.004 0.041 2632 Dihedral : 18.096 179.908 3014 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.45 % Allowed : 18.18 % Favored : 79.37 % 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 aren not related in a simple way. whole: -0.37 (0.21), residues: 1764 helix: 1.54 (0.23), residues: 567 sheet: -0.14 (0.28), residues: 382 loop : -1.63 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 364 TYR 0.020 0.001 TYR A 251 PHE 0.034 0.001 PHE F 93 TRP 0.013 0.001 TRP E 175 HIS 0.004 0.001 HIS E 234 Details of bonding type rmsd covalent geometry : bond 0.00246 (16838) covalent geometry : angle 0.55750 (23128) hydrogen bonds : bond 0.03571 ( 614) hydrogen bonds : angle 4.33821 ( 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 324 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6483 (mp) cc_final: 0.6157 (mp) REVERT: A 94 ILE cc_start: 0.8448 (mt) cc_final: 0.8191 (mm) REVERT: A 183 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 209 ARG cc_start: 0.6945 (mtp85) cc_final: 0.6732 (mtp85) REVERT: A 210 TYR cc_start: 0.7216 (t80) cc_final: 0.6994 (t80) REVERT: A 213 TYR cc_start: 0.6462 (m-80) cc_final: 0.6245 (m-80) REVERT: A 240 ARG cc_start: 0.6379 (mtt180) cc_final: 0.5922 (mtt-85) REVERT: A 279 ASP cc_start: 0.8081 (t70) cc_final: 0.7776 (t0) REVERT: A 366 LYS cc_start: 0.7960 (tttm) cc_final: 0.7431 (ttpt) REVERT: B 254 TRP cc_start: 0.7524 (m100) cc_final: 0.6949 (m100) REVERT: B 285 TYR cc_start: 0.7458 (m-80) cc_final: 0.7211 (m-80) REVERT: B 346 TYR cc_start: 0.4751 (t80) cc_final: 0.4509 (t80) REVERT: B 417 SER cc_start: 0.8063 (t) cc_final: 0.7757 (m) REVERT: E 4 LYS cc_start: 0.6879 (mttm) cc_final: 0.6577 (mtpp) REVERT: E 15 ASN cc_start: 0.5515 (m-40) cc_final: 0.4924 (m-40) REVERT: E 59 LYS cc_start: 0.7917 (tppt) cc_final: 0.7558 (tppt) REVERT: E 63 VAL cc_start: 0.7467 (t) cc_final: 0.7261 (p) REVERT: E 93 PHE cc_start: 0.6555 (t80) cc_final: 0.5865 (t80) REVERT: E 119 ASP cc_start: 0.8074 (t0) cc_final: 0.7719 (t0) REVERT: E 171 TYR cc_start: 0.6302 (m-80) cc_final: 0.6043 (m-80) REVERT: E 233 TYR cc_start: 0.6665 (t80) cc_final: 0.6362 (t80) REVERT: E 277 MET cc_start: 0.6627 (tpp) cc_final: 0.6400 (tpt) REVERT: F 16 HIS cc_start: 0.6258 (m-70) cc_final: 0.5948 (m-70) REVERT: F 94 LYS cc_start: 0.7624 (mmtm) cc_final: 0.7307 (mmtm) REVERT: F 142 ILE cc_start: 0.7390 (mm) cc_final: 0.7104 (mm) REVERT: F 243 ARG cc_start: 0.6731 (mtm180) cc_final: 0.6209 (mtm180) REVERT: F 311 THR cc_start: 0.8284 (t) cc_final: 0.8018 (p) outliers start: 39 outliers final: 29 residues processed: 301 average time/residue: 0.1341 time to fit residues: 59.7130 Evaluate side-chains 309 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 170 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 245 GLU 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 394 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 143 optimal weight: 0.0870 chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 163 optimal weight: 0.3980 chunk 109 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN B 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.190419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.157544 restraints weight = 24387.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.161591 restraints weight = 14181.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.164182 restraints weight = 10062.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.165797 restraints weight = 8110.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166731 restraints weight = 7081.830| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16838 Z= 0.152 Angle : 0.587 9.906 23128 Z= 0.310 Chirality : 0.042 0.168 2538 Planarity : 0.004 0.038 2632 Dihedral : 18.153 177.740 3014 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.26 % Allowed : 18.68 % Favored : 79.06 % 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 aren not related in a simple way. whole: -0.37 (0.21), residues: 1764 helix: 1.49 (0.23), residues: 567 sheet: -0.00 (0.28), residues: 373 loop : -1.66 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.018 0.001 TYR A 251 PHE 0.032 0.002 PHE F 93 TRP 0.018 0.001 TRP E 319 HIS 0.005 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00344 (16838) covalent geometry : angle 0.58713 (23128) hydrogen bonds : bond 0.04310 ( 614) hydrogen bonds : angle 4.47864 ( 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 312 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6493 (mp) cc_final: 0.6177 (mp) REVERT: A 94 ILE cc_start: 0.8405 (mt) cc_final: 0.8109 (mm) REVERT: A 183 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 210 TYR cc_start: 0.7189 (t80) cc_final: 0.6965 (t80) REVERT: A 213 TYR cc_start: 0.6362 (m-80) cc_final: 0.6162 (m-80) REVERT: A 279 ASP cc_start: 0.8074 (t70) cc_final: 0.7779 (t0) REVERT: A 400 LYS cc_start: 0.7338 (mttt) cc_final: 0.6974 (mmtp) REVERT: A 411 LYS cc_start: 0.5517 (tttp) cc_final: 0.5215 (ttpp) REVERT: A 415 SER cc_start: 0.8487 (p) cc_final: 0.8260 (m) REVERT: B 254 TRP cc_start: 0.7530 (m100) cc_final: 0.7198 (m100) REVERT: B 417 SER cc_start: 0.7978 (t) cc_final: 0.7580 (m) REVERT: E 4 LYS cc_start: 0.6907 (mttm) cc_final: 0.6578 (mtpp) REVERT: E 59 LYS cc_start: 0.7916 (tppt) cc_final: 0.7562 (tppt) REVERT: E 63 VAL cc_start: 0.7595 (t) cc_final: 0.7334 (p) REVERT: E 93 PHE cc_start: 0.6639 (t80) cc_final: 0.5915 (t80) REVERT: E 119 ASP cc_start: 0.8098 (t0) cc_final: 0.7729 (t0) REVERT: E 171 TYR cc_start: 0.6412 (m-80) cc_final: 0.6145 (m-80) REVERT: E 233 TYR cc_start: 0.6755 (t80) cc_final: 0.6443 (t80) REVERT: E 411 LYS cc_start: 0.7625 (ttmt) cc_final: 0.7386 (tppt) REVERT: F 14 PHE cc_start: 0.7476 (m-80) cc_final: 0.7214 (m-80) REVERT: F 16 HIS cc_start: 0.6316 (m-70) cc_final: 0.6012 (m-70) REVERT: F 40 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7548 (mptt) REVERT: F 94 LYS cc_start: 0.7553 (mmtm) cc_final: 0.7225 (mmtm) REVERT: F 142 ILE cc_start: 0.7427 (mm) cc_final: 0.7115 (mm) REVERT: F 311 THR cc_start: 0.8290 (t) cc_final: 0.8002 (p) outliers start: 36 outliers final: 33 residues processed: 290 average time/residue: 0.1336 time to fit residues: 57.1310 Evaluate side-chains 305 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 197 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 SER 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 386 ASP Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 369 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 265 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 435 MET 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: 4.9990 chunk 144 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.189207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.156105 restraints weight = 24303.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.160138 restraints weight = 14198.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.162689 restraints weight = 10104.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.164324 restraints weight = 8177.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.165134 restraints weight = 7126.736| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16838 Z= 0.170 Angle : 0.612 9.283 23128 Z= 0.323 Chirality : 0.043 0.182 2538 Planarity : 0.004 0.043 2632 Dihedral : 18.219 177.389 3014 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.14 % Allowed : 19.12 % Favored : 78.74 % 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 aren not related in a simple way. whole: -0.40 (0.21), residues: 1764 helix: 1.55 (0.23), residues: 553 sheet: -0.04 (0.28), residues: 371 loop : -1.68 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.019 0.001 TYR B 280 PHE 0.032 0.002 PHE F 93 TRP 0.022 0.001 TRP E 319 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00386 (16838) covalent geometry : angle 0.61152 (23128) hydrogen bonds : bond 0.04591 ( 614) hydrogen bonds : angle 4.59262 ( 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 312 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6524 (mp) cc_final: 0.6216 (mp) REVERT: A 94 ILE cc_start: 0.8427 (mt) cc_final: 0.8120 (mm) REVERT: A 174 ASN cc_start: 0.7983 (p0) cc_final: 0.7695 (p0) REVERT: A 183 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 210 TYR cc_start: 0.7201 (t80) cc_final: 0.6989 (t80) REVERT: A 213 TYR cc_start: 0.6401 (m-80) cc_final: 0.6064 (m-80) REVERT: A 245 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: A 279 ASP cc_start: 0.8081 (t70) cc_final: 0.7804 (t0) REVERT: A 400 LYS cc_start: 0.7382 (mttt) cc_final: 0.6648 (mttm) REVERT: A 411 LYS cc_start: 0.5648 (tttp) cc_final: 0.5349 (ttpp) REVERT: A 415 SER cc_start: 0.8501 (p) cc_final: 0.8285 (m) REVERT: B 254 TRP cc_start: 0.7538 (m100) cc_final: 0.7203 (m100) REVERT: B 417 SER cc_start: 0.8022 (t) cc_final: 0.7608 (m) REVERT: E 4 LYS cc_start: 0.6890 (mttm) cc_final: 0.6543 (mtpp) REVERT: E 59 LYS cc_start: 0.7942 (tppt) cc_final: 0.7574 (tppt) REVERT: E 63 VAL cc_start: 0.7610 (t) cc_final: 0.7343 (p) REVERT: E 93 PHE cc_start: 0.6654 (t80) cc_final: 0.5887 (t80) REVERT: E 119 ASP cc_start: 0.8148 (t0) cc_final: 0.7786 (t0) REVERT: E 233 TYR cc_start: 0.6753 (t80) cc_final: 0.6445 (t80) REVERT: E 411 LYS cc_start: 0.7647 (ttmt) cc_final: 0.7405 (tppt) REVERT: F 14 PHE cc_start: 0.7497 (m-80) cc_final: 0.7244 (m-80) REVERT: F 16 HIS cc_start: 0.6286 (m-70) cc_final: 0.6004 (m-70) REVERT: F 40 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7511 (mptt) REVERT: F 94 LYS cc_start: 0.7498 (mmtm) cc_final: 0.7268 (mmtt) REVERT: F 142 ILE cc_start: 0.7416 (mm) cc_final: 0.7093 (mm) REVERT: F 311 THR cc_start: 0.8315 (t) cc_final: 0.8029 (p) REVERT: F 316 GLU cc_start: 0.6721 (tp30) cc_final: 0.6454 (tp30) REVERT: F 362 LYS cc_start: 0.7536 (mmtp) cc_final: 0.7313 (mttt) outliers start: 34 outliers final: 33 residues processed: 288 average time/residue: 0.1325 time to fit residues: 56.4740 Evaluate side-chains 310 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 180 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 245 GLU 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS 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 265 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 435 MET 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: 0.9990 chunk 51 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 155 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.188858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155669 restraints weight = 24389.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159744 restraints weight = 14211.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.162324 restraints weight = 10106.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.163933 restraints weight = 8149.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.164968 restraints weight = 7113.821| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16838 Z= 0.176 Angle : 0.621 9.067 23128 Z= 0.329 Chirality : 0.043 0.178 2538 Planarity : 0.004 0.043 2632 Dihedral : 18.264 177.597 3014 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.14 % Allowed : 19.18 % Favored : 78.68 % 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 aren not related in a simple way. whole: -0.44 (0.21), residues: 1764 helix: 1.54 (0.23), residues: 552 sheet: -0.13 (0.28), residues: 373 loop : -1.68 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.022 0.001 TYR B 280 PHE 0.031 0.002 PHE F 93 TRP 0.020 0.001 TRP E 319 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00401 (16838) covalent geometry : angle 0.62146 (23128) hydrogen bonds : bond 0.04635 ( 614) hydrogen bonds : angle 4.61520 ( 1858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.69 seconds wall clock time: 53 minutes 21.32 seconds (3201.32 seconds total)