Starting phenix.real_space_refine on Sat Jun 14 20:53:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sp3_40673/06_2025/8sp3_40673_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sp3_40673/06_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_40673/06_2025/8sp3_40673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sp3_40673/06_2025/8sp3_40673.map" model { file = "/net/cci-nas-00/data/ceres_data/8sp3_40673/06_2025/8sp3_40673_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sp3_40673/06_2025/8sp3_40673_neut.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.92, per 1000 atoms: 0.73 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: 4.06 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 5.59 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: 5.31 Time building geometry restraints manager: 4.78 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: 0.00 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: 4.580 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.570 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP E 319 HIS 0.007 0.001 HIS F 207 PHE 0.015 0.001 PHE B 313 TYR 0.014 0.001 TYR B 397 ARG 0.004 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.16216 ( 614) hydrogen bonds : angle 6.38401 ( 1858) covalent geometry : bond 0.00328 (16838) covalent geometry : angle 0.61562 (23128) *********************** 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 : 1.709 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: 0.7529 (mt-10) REVERT: B 138 VAL cc_start: 0.8560 (t) cc_final: 0.8273 (m) REVERT: B 254 TRP cc_start: 0.7502 (m100) cc_final: 0.7126 (m100) REVERT: B 309 ASP cc_start: 0.4368 (m-30) cc_final: 0.3691 (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: 0.4615 (m-40) REVERT: E 59 LYS cc_start: 0.7732 (tppt) cc_final: 0.7413 (tppt) REVERT: E 93 PHE cc_start: 0.6583 (t80) cc_final: 0.6217 (t80) REVERT: E 208 VAL cc_start: 0.7249 (t) cc_final: 0.6976 (t) REVERT: E 286 GLU cc_start: 0.5179 (tp30) cc_final: 0.4930 (tp30) REVERT: E 360 SER cc_start: 0.7501 (m) cc_final: 0.7201 (p) REVERT: F 16 HIS cc_start: 0.6018 (m-70) cc_final: 0.5724 (m-70) REVERT: F 37 TYR cc_start: 0.7710 (m-80) cc_final: 0.7382 (m-80) REVERT: F 56 TYR cc_start: 0.5739 (t80) cc_final: 0.5281 (t80) REVERT: F 91 ILE cc_start: 0.8396 (mt) cc_final: 0.8168 (tt) REVERT: F 94 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7083 (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: 0.7634 (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: 0.7533 (mtmm) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.3134 time to fit residues: 169.7016 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 : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 142 optimal weight: 0.0570 chunk 55 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN F 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.194181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160453 restraints weight = 24294.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.164749 restraints weight = 13855.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.167471 restraints weight = 9686.708| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16838 Z= 0.120 Angle : 0.560 12.379 23128 Z= 0.294 Chirality : 0.041 0.171 2538 Planarity : 0.004 0.046 2632 Dihedral : 18.047 177.329 3014 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.26 % Allowed : 7.48 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1764 helix: 1.77 (0.23), residues: 559 sheet: 0.06 (0.28), residues: 374 loop : -1.52 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 86 HIS 0.004 0.001 HIS E 340 PHE 0.023 0.001 PHE B 30 TYR 0.016 0.001 TYR B 6 ARG 0.006 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 614) hydrogen bonds : angle 4.67832 ( 1858) covalent geometry : bond 0.00262 (16838) covalent geometry : angle 0.55970 (23128) *********************** 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 326 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 306 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6548 (mp) cc_final: 0.6245 (mp) REVERT: A 8 SER cc_start: 0.8103 (t) cc_final: 0.7672 (p) REVERT: A 209 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6704 (mtp85) REVERT: A 210 TYR cc_start: 0.7154 (t80) cc_final: 0.6794 (t80) REVERT: A 213 TYR cc_start: 0.6490 (m-80) cc_final: 0.6062 (m-80) REVERT: A 246 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8202 (tp) REVERT: A 255 PHE cc_start: 0.8431 (t80) cc_final: 0.8148 (t80) REVERT: A 263 ARG cc_start: 0.7379 (ttp80) cc_final: 0.6985 (ttp80) REVERT: A 279 ASP cc_start: 0.7903 (t70) cc_final: 0.7658 (t0) REVERT: A 399 GLU cc_start: 0.7608 (mp0) cc_final: 0.7257 (mp0) REVERT: B 115 TYR cc_start: 0.7429 (t80) cc_final: 0.7011 (t80) REVERT: B 132 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 254 TRP cc_start: 0.7503 (m100) cc_final: 0.7068 (m100) REVERT: B 321 TYR cc_start: 0.7814 (m-80) cc_final: 0.7314 (m-80) REVERT: B 417 SER cc_start: 0.8113 (t) cc_final: 0.7725 (m) REVERT: E 4 LYS cc_start: 0.6828 (mttm) cc_final: 0.6549 (mtpp) REVERT: E 15 ASN cc_start: 0.5309 (m-40) cc_final: 0.4749 (m-40) REVERT: E 59 LYS cc_start: 0.7742 (tppt) cc_final: 0.7407 (tppt) REVERT: E 93 PHE cc_start: 0.6565 (t80) cc_final: 0.6229 (t80) REVERT: E 128 LEU cc_start: 0.7207 (tp) cc_final: 0.6993 (tp) REVERT: E 286 GLU cc_start: 0.5169 (tp30) cc_final: 0.4948 (tp30) REVERT: E 290 LYS cc_start: 0.8186 (pttt) cc_final: 0.7809 (ptpp) REVERT: E 364 GLN cc_start: 0.6477 (tt0) cc_final: 0.6157 (tm-30) REVERT: F 5 ILE cc_start: 0.7925 (pt) cc_final: 0.7691 (pt) REVERT: F 16 HIS cc_start: 0.6045 (m-70) cc_final: 0.5790 (m-70) REVERT: F 19 LYS cc_start: 0.7776 (mttp) cc_final: 0.7560 (mttt) REVERT: F 37 TYR cc_start: 0.7684 (m-80) cc_final: 0.7431 (m-80) REVERT: F 56 TYR cc_start: 0.5642 (t80) cc_final: 0.5153 (t80) REVERT: F 115 TYR cc_start: 0.7690 (t80) cc_final: 0.7354 (t80) REVERT: F 142 ILE cc_start: 0.7375 (mm) cc_final: 0.6895 (mt) REVERT: F 247 LYS cc_start: 0.7191 (mtpt) cc_final: 0.6932 (mtpp) REVERT: F 278 VAL cc_start: 0.8472 (t) cc_final: 0.8224 (p) REVERT: F 287 LYS cc_start: 0.7263 (mttm) cc_final: 0.6751 (mtmm) REVERT: F 311 THR cc_start: 0.8102 (t) cc_final: 0.7716 (p) REVERT: F 316 GLU cc_start: 0.6763 (tp30) cc_final: 0.6365 (tp30) REVERT: F 336 LYS cc_start: 0.8030 (mttp) cc_final: 0.7716 (mtmm) REVERT: F 342 SER cc_start: 0.8348 (m) cc_final: 0.8113 (t) outliers start: 20 outliers final: 10 residues processed: 311 average time/residue: 0.3043 time to fit residues: 137.8120 Evaluate side-chains 308 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 297 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain B residue 298 CYS 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 391 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 161 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN E 188 HIS F 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.188485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154493 restraints weight = 24284.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.158678 restraints weight = 14047.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161356 restraints weight = 9912.448| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16838 Z= 0.218 Angle : 0.634 7.144 23128 Z= 0.337 Chirality : 0.044 0.174 2538 Planarity : 0.004 0.053 2632 Dihedral : 18.278 179.080 3014 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.39 % Allowed : 11.01 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1764 helix: 1.32 (0.23), residues: 566 sheet: -0.04 (0.28), residues: 383 loop : -1.67 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 269 HIS 0.008 0.001 HIS E 358 PHE 0.025 0.002 PHE B 93 TYR 0.025 0.002 TYR B 321 ARG 0.006 0.001 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.05342 ( 614) hydrogen bonds : angle 4.89008 ( 1858) covalent geometry : bond 0.00489 (16838) covalent geometry : angle 0.63381 (23128) *********************** 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 345 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6692 (mp) cc_final: 0.6371 (mp) REVERT: A 126 ARG cc_start: 0.6219 (tpm170) cc_final: 0.5909 (tpm170) REVERT: A 209 ARG cc_start: 0.7072 (mtp85) cc_final: 0.6807 (mtp85) REVERT: A 210 TYR cc_start: 0.7110 (t80) cc_final: 0.6879 (t80) REVERT: A 213 TYR cc_start: 0.6621 (m-80) cc_final: 0.6160 (m-80) REVERT: A 222 ASP cc_start: 0.6135 (m-30) cc_final: 0.5893 (m-30) REVERT: A 246 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8345 (tp) REVERT: A 263 ARG cc_start: 0.7546 (ttp80) cc_final: 0.7107 (ttp80) REVERT: A 279 ASP cc_start: 0.8018 (t70) cc_final: 0.7730 (t0) REVERT: A 399 GLU cc_start: 0.7723 (mp0) cc_final: 0.7291 (mp0) REVERT: A 400 LYS cc_start: 0.7483 (mttt) cc_final: 0.7206 (mttp) REVERT: B 226 GLU cc_start: 0.7597 (mp0) cc_final: 0.7252 (mp0) REVERT: B 270 LYS cc_start: 0.5897 (ttpt) cc_final: 0.5496 (tttm) REVERT: B 321 TYR cc_start: 0.8016 (m-80) cc_final: 0.7727 (m-80) REVERT: B 412 VAL cc_start: 0.8301 (t) cc_final: 0.8034 (p) REVERT: B 417 SER cc_start: 0.8040 (t) cc_final: 0.7673 (m) REVERT: E 4 LYS cc_start: 0.6844 (mttm) cc_final: 0.6509 (mtpp) REVERT: E 15 ASN cc_start: 0.5472 (m-40) cc_final: 0.4886 (m-40) REVERT: E 59 LYS cc_start: 0.7827 (tppt) cc_final: 0.7448 (tppt) REVERT: E 93 PHE cc_start: 0.6632 (t80) cc_final: 0.6215 (t80) REVERT: E 119 ASP cc_start: 0.7981 (t0) cc_final: 0.7635 (t70) REVERT: E 128 LEU cc_start: 0.7138 (tp) cc_final: 0.6873 (tp) REVERT: F 16 HIS cc_start: 0.6177 (m-70) cc_final: 0.5880 (m-70) REVERT: F 54 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5924 (mpp80) REVERT: F 74 MET cc_start: 0.3458 (ptm) cc_final: 0.3203 (ptm) REVERT: F 115 TYR cc_start: 0.7956 (t80) cc_final: 0.7615 (t80) REVERT: F 142 ILE cc_start: 0.7443 (mm) cc_final: 0.7089 (mm) REVERT: F 247 LYS cc_start: 0.7333 (mtpt) cc_final: 0.7118 (mtpp) REVERT: F 287 LYS cc_start: 0.7453 (mttm) cc_final: 0.6871 (mtmm) REVERT: F 306 ASP cc_start: 0.6350 (p0) cc_final: 0.6133 (p0) REVERT: F 311 THR cc_start: 0.8202 (t) cc_final: 0.7920 (p) REVERT: F 316 GLU cc_start: 0.6875 (tp30) cc_final: 0.6571 (tp30) REVERT: F 336 LYS cc_start: 0.8183 (mttp) cc_final: 0.7896 (mttp) REVERT: F 342 SER cc_start: 0.8422 (m) cc_final: 0.8113 (t) outliers start: 38 outliers final: 28 residues processed: 317 average time/residue: 0.2939 time to fit residues: 135.3255 Evaluate side-chains 322 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 394 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 228 THR 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 459 ILE 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 86 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 169 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 164 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 61 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.190102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156269 restraints weight = 24322.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.160401 restraints weight = 14011.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163090 restraints weight = 9885.052| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2491 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= 0.162 Angle : 0.581 7.356 23128 Z= 0.308 Chirality : 0.042 0.171 2538 Planarity : 0.004 0.055 2632 Dihedral : 18.186 179.746 3014 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.77 % Allowed : 13.84 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1764 helix: 1.53 (0.23), residues: 556 sheet: -0.06 (0.28), residues: 373 loop : -1.70 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 319 HIS 0.005 0.001 HIS F 207 PHE 0.034 0.002 PHE B 30 TYR 0.019 0.001 TYR A 251 ARG 0.006 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 614) hydrogen bonds : angle 4.64061 ( 1858) covalent geometry : bond 0.00363 (16838) covalent geometry : angle 0.58131 (23128) *********************** 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 343 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6513 (mp) cc_final: 0.6173 (mp) REVERT: A 126 ARG cc_start: 0.6241 (tpm170) cc_final: 0.5889 (tpm170) REVERT: A 174 ASN cc_start: 0.7916 (p0) cc_final: 0.7515 (p0) REVERT: A 209 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6793 (mtp85) REVERT: A 210 TYR cc_start: 0.7166 (t80) cc_final: 0.6862 (t80) REVERT: A 213 TYR cc_start: 0.6608 (m-80) cc_final: 0.6200 (m-80) REVERT: A 246 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8374 (tp) REVERT: A 255 PHE cc_start: 0.8664 (t80) cc_final: 0.8452 (t80) REVERT: A 263 ARG cc_start: 0.7482 (ttp80) cc_final: 0.6970 (ttp80) REVERT: A 279 ASP cc_start: 0.8042 (t70) cc_final: 0.7739 (t0) REVERT: A 399 GLU cc_start: 0.7705 (mp0) cc_final: 0.7261 (mp0) REVERT: A 400 LYS cc_start: 0.7476 (mttt) cc_final: 0.7274 (mttm) REVERT: A 416 TYR cc_start: 0.6900 (p90) cc_final: 0.6649 (p90) REVERT: B 254 TRP cc_start: 0.7451 (m100) cc_final: 0.6973 (m100) REVERT: B 417 SER cc_start: 0.8048 (t) cc_final: 0.7640 (m) REVERT: E 4 LYS cc_start: 0.6883 (mttm) cc_final: 0.6535 (mtpp) REVERT: E 15 ASN cc_start: 0.5439 (m-40) cc_final: 0.4879 (m-40) REVERT: E 59 LYS cc_start: 0.7850 (tppt) cc_final: 0.7490 (tppt) REVERT: E 93 PHE cc_start: 0.6610 (t80) cc_final: 0.6227 (t80) REVERT: E 119 ASP cc_start: 0.7993 (t0) cc_final: 0.7629 (t0) REVERT: E 128 LEU cc_start: 0.7188 (tp) cc_final: 0.6900 (tp) REVERT: E 171 TYR cc_start: 0.6453 (m-80) cc_final: 0.6244 (m-80) REVERT: E 210 TYR cc_start: 0.7207 (t80) cc_final: 0.6938 (t80) REVERT: F 5 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7857 (pt) REVERT: F 16 HIS cc_start: 0.6175 (m-70) cc_final: 0.5881 (m-70) REVERT: F 56 TYR cc_start: 0.5445 (t80) cc_final: 0.4922 (t80) REVERT: F 74 MET cc_start: 0.3391 (ptm) cc_final: 0.3138 (ptm) REVERT: F 115 TYR cc_start: 0.7987 (t80) cc_final: 0.7702 (t80) REVERT: F 142 ILE cc_start: 0.7416 (mm) cc_final: 0.7060 (mm) REVERT: F 247 LYS cc_start: 0.7345 (mtpt) cc_final: 0.7109 (mtpp) REVERT: F 278 VAL cc_start: 0.8549 (t) cc_final: 0.8276 (p) REVERT: F 287 LYS cc_start: 0.7430 (mttm) cc_final: 0.6881 (mtmm) REVERT: F 311 THR cc_start: 0.8224 (t) cc_final: 0.7891 (p) REVERT: F 316 GLU cc_start: 0.6765 (tp30) cc_final: 0.6497 (tp30) REVERT: F 336 LYS cc_start: 0.7954 (mttp) cc_final: 0.7726 (mtmm) REVERT: F 342 SER cc_start: 0.8422 (m) cc_final: 0.8147 (t) outliers start: 44 outliers final: 32 residues processed: 318 average time/residue: 0.2919 time to fit residues: 135.8103 Evaluate side-chains 325 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 291 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain 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 41 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 298 CYS 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 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 5 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 88 SER 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 Chi-restraints excluded: chain F residue 465 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.188331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154900 restraints weight = 24697.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158900 restraints weight = 14404.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161465 restraints weight = 10259.961| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16838 Z= 0.206 Angle : 0.633 12.035 23128 Z= 0.334 Chirality : 0.044 0.167 2538 Planarity : 0.004 0.043 2632 Dihedral : 18.297 176.971 3014 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.27 % Allowed : 16.04 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1764 helix: 1.47 (0.23), residues: 542 sheet: -0.01 (0.28), residues: 369 loop : -1.74 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 254 HIS 0.007 0.001 HIS F 207 PHE 0.028 0.002 PHE B 93 TYR 0.021 0.002 TYR A 171 ARG 0.005 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 614) hydrogen bonds : angle 4.81184 ( 1858) covalent geometry : bond 0.00467 (16838) covalent geometry : angle 0.63342 (23128) *********************** 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 340 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6561 (mp) cc_final: 0.6241 (mp) REVERT: A 126 ARG cc_start: 0.6220 (tpm170) cc_final: 0.5817 (tpm170) REVERT: A 174 ASN cc_start: 0.8032 (p0) cc_final: 0.7629 (p0) REVERT: A 209 ARG cc_start: 0.7090 (mtp85) cc_final: 0.6815 (mtp180) REVERT: A 210 TYR cc_start: 0.7191 (t80) cc_final: 0.6928 (t80) REVERT: A 213 TYR cc_start: 0.6665 (m-80) cc_final: 0.6092 (m-80) REVERT: A 246 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8418 (tp) REVERT: A 263 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7085 (ttp80) REVERT: A 279 ASP cc_start: 0.8070 (t70) cc_final: 0.7785 (t0) REVERT: A 399 GLU cc_start: 0.7721 (mp0) cc_final: 0.7265 (mp0) REVERT: A 411 LYS cc_start: 0.5529 (tttp) cc_final: 0.5175 (ttpt) REVERT: B 3 GLU cc_start: 0.6479 (mm-30) cc_final: 0.6211 (mm-30) REVERT: B 37 TYR cc_start: 0.6195 (m-80) cc_final: 0.5985 (m-80) REVERT: B 254 TRP cc_start: 0.7523 (m100) cc_final: 0.7148 (m100) REVERT: B 417 SER cc_start: 0.8055 (t) cc_final: 0.7653 (m) REVERT: E 4 LYS cc_start: 0.6904 (mttm) cc_final: 0.6647 (mtpp) REVERT: E 15 ASN cc_start: 0.5444 (m-40) cc_final: 0.4878 (m-40) REVERT: E 59 LYS cc_start: 0.7932 (tppt) cc_final: 0.7519 (tppt) REVERT: E 63 VAL cc_start: 0.7424 (t) cc_final: 0.7189 (p) REVERT: E 93 PHE cc_start: 0.6634 (t80) cc_final: 0.5941 (t80) REVERT: E 128 LEU cc_start: 0.7172 (tp) cc_final: 0.6856 (tp) REVERT: E 208 VAL cc_start: 0.7200 (t) cc_final: 0.6692 (m) REVERT: E 210 TYR cc_start: 0.7158 (t80) cc_final: 0.6819 (t80) REVERT: E 364 GLN cc_start: 0.6772 (tt0) cc_final: 0.6298 (tm-30) REVERT: F 16 HIS cc_start: 0.6184 (m-70) cc_final: 0.5877 (m-70) REVERT: F 74 MET cc_start: 0.3561 (ptm) cc_final: 0.3343 (ptm) REVERT: F 115 TYR cc_start: 0.8057 (t80) cc_final: 0.7760 (t80) REVERT: F 142 ILE cc_start: 0.7465 (mm) cc_final: 0.7087 (mm) REVERT: F 247 LYS cc_start: 0.7398 (mtpt) cc_final: 0.7098 (mtpp) REVERT: F 287 LYS cc_start: 0.7471 (mttm) cc_final: 0.7220 (ttmt) REVERT: F 316 GLU cc_start: 0.6766 (tp30) cc_final: 0.6506 (tp30) REVERT: F 342 SER cc_start: 0.8442 (m) cc_final: 0.8125 (t) REVERT: F 409 ASN cc_start: 0.7838 (m-40) cc_final: 0.7612 (m-40) outliers start: 52 outliers final: 41 residues processed: 308 average time/residue: 0.2958 time to fit residues: 134.4392 Evaluate side-chains 322 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 291 THR 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 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 41 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 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 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 5 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 126 ILE 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 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.186589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153127 restraints weight = 24590.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157195 restraints weight = 14483.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159800 restraints weight = 10294.029| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16838 Z= 0.219 Angle : 0.638 11.271 23128 Z= 0.338 Chirality : 0.044 0.169 2538 Planarity : 0.004 0.049 2632 Dihedral : 18.323 176.498 3014 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.58 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1764 helix: 1.33 (0.23), residues: 542 sheet: -0.18 (0.28), residues: 375 loop : -1.78 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 254 HIS 0.007 0.001 HIS F 207 PHE 0.027 0.002 PHE B 93 TYR 0.021 0.002 TYR A 171 ARG 0.005 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 614) hydrogen bonds : angle 4.83984 ( 1858) covalent geometry : bond 0.00497 (16838) covalent geometry : angle 0.63832 (23128) *********************** 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 339 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6553 (mp) cc_final: 0.6232 (mp) REVERT: A 126 ARG cc_start: 0.6229 (tpm170) cc_final: 0.5754 (tpm170) REVERT: A 189 GLU cc_start: 0.6549 (tm-30) cc_final: 0.5261 (tm-30) REVERT: A 209 ARG cc_start: 0.7100 (mtp85) cc_final: 0.6845 (mtp180) REVERT: A 210 TYR cc_start: 0.7182 (t80) cc_final: 0.6949 (t80) REVERT: A 213 TYR cc_start: 0.6586 (m-80) cc_final: 0.6182 (m-80) REVERT: A 222 ASP cc_start: 0.6075 (m-30) cc_final: 0.5854 (m-30) REVERT: A 246 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8441 (tp) REVERT: A 279 ASP cc_start: 0.8081 (t70) cc_final: 0.7793 (t0) REVERT: A 303 ASP cc_start: 0.5703 (m-30) cc_final: 0.5503 (m-30) REVERT: A 399 GLU cc_start: 0.7739 (mp0) cc_final: 0.7257 (mp0) REVERT: A 411 LYS cc_start: 0.5704 (tttp) cc_final: 0.5181 (ttpt) REVERT: B 3 GLU cc_start: 0.6458 (mm-30) cc_final: 0.6212 (mm-30) REVERT: B 254 TRP cc_start: 0.7587 (m100) cc_final: 0.7143 (m100) REVERT: B 334 GLU cc_start: 0.7583 (mp0) cc_final: 0.7331 (mp0) REVERT: B 417 SER cc_start: 0.8017 (t) cc_final: 0.7626 (m) REVERT: E 4 LYS cc_start: 0.6924 (mttm) cc_final: 0.6575 (mtpp) REVERT: E 15 ASN cc_start: 0.5494 (m-40) cc_final: 0.4994 (m-40) REVERT: E 59 LYS cc_start: 0.7972 (tppt) cc_final: 0.7628 (tppt) REVERT: E 63 VAL cc_start: 0.7583 (t) cc_final: 0.7318 (p) REVERT: E 93 PHE cc_start: 0.6658 (t80) cc_final: 0.6252 (t80) REVERT: E 128 LEU cc_start: 0.7153 (tp) cc_final: 0.6821 (tp) REVERT: E 210 TYR cc_start: 0.7148 (t80) cc_final: 0.6845 (t80) REVERT: E 364 GLN cc_start: 0.6795 (tt0) cc_final: 0.6396 (tm-30) REVERT: F 16 HIS cc_start: 0.6278 (m-70) cc_final: 0.5970 (m-70) REVERT: F 44 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7516 (mp) REVERT: F 74 MET cc_start: 0.3681 (ptm) cc_final: 0.3480 (ptm) REVERT: F 85 LYS cc_start: 0.6846 (mttm) cc_final: 0.6498 (mttm) REVERT: F 115 TYR cc_start: 0.8077 (t80) cc_final: 0.7817 (t80) REVERT: F 142 ILE cc_start: 0.7468 (mm) cc_final: 0.7090 (mm) REVERT: F 287 LYS cc_start: 0.7442 (mttm) cc_final: 0.7226 (mtmt) REVERT: F 311 THR cc_start: 0.8169 (t) cc_final: 0.7928 (p) REVERT: F 316 GLU cc_start: 0.6798 (tp30) cc_final: 0.6528 (tp30) REVERT: F 342 SER cc_start: 0.8446 (m) cc_final: 0.8130 (t) REVERT: F 356 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7159 (tm-30) REVERT: F 362 LYS cc_start: 0.7542 (mptt) cc_final: 0.7153 (mttt) REVERT: F 409 ASN cc_start: 0.7791 (m-40) cc_final: 0.7562 (m-40) REVERT: F 436 GLU cc_start: 0.5128 (mt-10) cc_final: 0.4358 (mt-10) outliers start: 57 outliers final: 44 residues processed: 301 average time/residue: 0.3061 time to fit residues: 136.4424 Evaluate side-chains 325 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 248 SER Chi-restraints excluded: chain A residue 291 THR 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 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 322 ASN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 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 392 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.1980 chunk 166 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 158 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.185186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.151670 restraints weight = 24458.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.155736 restraints weight = 14364.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.158332 restraints weight = 10223.792| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16838 Z= 0.139 Angle : 0.572 9.135 23128 Z= 0.302 Chirality : 0.041 0.168 2538 Planarity : 0.004 0.044 2632 Dihedral : 18.210 178.506 3014 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.14 % Allowed : 17.42 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1764 helix: 1.53 (0.23), residues: 549 sheet: -0.06 (0.28), residues: 371 loop : -1.73 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 254 HIS 0.004 0.001 HIS F 207 PHE 0.028 0.001 PHE B 93 TYR 0.021 0.001 TYR A 251 ARG 0.005 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 614) hydrogen bonds : angle 4.54868 ( 1858) covalent geometry : bond 0.00314 (16838) covalent geometry : angle 0.57206 (23128) *********************** 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 339 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6502 (mp) cc_final: 0.6179 (mp) REVERT: A 60 PHE cc_start: 0.7389 (t80) cc_final: 0.7028 (t80) REVERT: A 94 ILE cc_start: 0.8476 (mt) cc_final: 0.8200 (mm) REVERT: A 126 ARG cc_start: 0.6147 (tpm170) cc_final: 0.5754 (tpm170) REVERT: A 174 ASN cc_start: 0.7958 (p0) cc_final: 0.7566 (p0) REVERT: A 189 GLU cc_start: 0.6557 (tm-30) cc_final: 0.5327 (tm-30) REVERT: A 209 ARG cc_start: 0.7058 (mtp85) cc_final: 0.6809 (mtp180) REVERT: A 210 TYR cc_start: 0.7203 (t80) cc_final: 0.6959 (t80) REVERT: A 213 TYR cc_start: 0.6584 (m-80) cc_final: 0.6259 (m-80) REVERT: A 222 ASP cc_start: 0.6041 (m-30) cc_final: 0.5817 (m-30) REVERT: A 279 ASP cc_start: 0.8118 (t70) cc_final: 0.7809 (t0) REVERT: A 399 GLU cc_start: 0.7734 (mp0) cc_final: 0.7239 (mp0) REVERT: A 400 LYS cc_start: 0.7356 (mttt) cc_final: 0.7116 (mttm) REVERT: A 411 LYS cc_start: 0.5564 (tttp) cc_final: 0.5070 (ttpp) REVERT: A 415 SER cc_start: 0.8527 (p) cc_final: 0.8292 (m) REVERT: B 74 MET cc_start: 0.5077 (mmm) cc_final: 0.4689 (tpp) REVERT: B 213 ARG cc_start: 0.8257 (ttp-170) cc_final: 0.8050 (mtp180) REVERT: B 254 TRP cc_start: 0.7541 (m100) cc_final: 0.7125 (m100) REVERT: B 417 SER cc_start: 0.8011 (t) cc_final: 0.7688 (m) REVERT: E 4 LYS cc_start: 0.6895 (mttm) cc_final: 0.6537 (mtpp) REVERT: E 15 ASN cc_start: 0.5541 (m-40) cc_final: 0.5023 (m-40) REVERT: E 59 LYS cc_start: 0.7956 (tppt) cc_final: 0.7612 (tppt) REVERT: E 93 PHE cc_start: 0.6631 (t80) cc_final: 0.6200 (t80) REVERT: E 119 ASP cc_start: 0.8133 (t0) cc_final: 0.7771 (t0) REVERT: E 171 TYR cc_start: 0.6322 (m-80) cc_final: 0.6073 (m-80) REVERT: E 210 TYR cc_start: 0.7091 (t80) cc_final: 0.6725 (t80) REVERT: E 364 GLN cc_start: 0.6630 (tt0) cc_final: 0.6130 (tm-30) REVERT: E 411 LYS cc_start: 0.7572 (ttmt) cc_final: 0.7360 (tppt) REVERT: F 16 HIS cc_start: 0.6219 (m-70) cc_final: 0.5890 (m-70) REVERT: F 44 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7451 (mp) REVERT: F 115 TYR cc_start: 0.8044 (t80) cc_final: 0.7726 (t80) REVERT: F 142 ILE cc_start: 0.7455 (mm) cc_final: 0.7099 (mm) REVERT: F 287 LYS cc_start: 0.7415 (mttm) cc_final: 0.7130 (mtmt) REVERT: F 311 THR cc_start: 0.8173 (t) cc_final: 0.7954 (p) REVERT: F 316 GLU cc_start: 0.6693 (tp30) cc_final: 0.6463 (tp30) REVERT: F 342 SER cc_start: 0.8433 (m) cc_final: 0.8148 (t) REVERT: F 356 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7121 (tm-30) REVERT: F 362 LYS cc_start: 0.7544 (mptt) cc_final: 0.7153 (mttt) REVERT: F 436 GLU cc_start: 0.5075 (mt-10) cc_final: 0.4242 (mt-10) outliers start: 50 outliers final: 37 residues processed: 308 average time/residue: 0.2891 time to fit residues: 131.2547 Evaluate side-chains 316 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 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 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 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 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 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 44 ILE 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 247 LYS 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 87 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 92 optimal weight: 0.0020 chunk 151 optimal weight: 0.0030 chunk 10 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.188373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.154904 restraints weight = 24350.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.159068 restraints weight = 14014.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161722 restraints weight = 9857.264| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16838 Z= 0.116 Angle : 0.556 10.222 23128 Z= 0.293 Chirality : 0.041 0.168 2538 Planarity : 0.004 0.042 2632 Dihedral : 18.141 178.816 3014 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.58 % Allowed : 18.49 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1764 helix: 1.60 (0.23), residues: 568 sheet: 0.02 (0.28), residues: 369 loop : -1.67 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 20 HIS 0.002 0.001 HIS F 207 PHE 0.030 0.001 PHE B 93 TYR 0.021 0.001 TYR E 251 ARG 0.005 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 614) hydrogen bonds : angle 4.34364 ( 1858) covalent geometry : bond 0.00259 (16838) covalent geometry : angle 0.55644 (23128) *********************** 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: 41 poor density : 283 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6436 (mp) cc_final: 0.6113 (mp) REVERT: A 8 SER cc_start: 0.8096 (t) cc_final: 0.7659 (p) REVERT: A 94 ILE cc_start: 0.8442 (mt) cc_final: 0.8197 (mm) REVERT: A 107 ASP cc_start: 0.5657 (m-30) cc_final: 0.5438 (m-30) REVERT: A 189 GLU cc_start: 0.6514 (tm-30) cc_final: 0.5506 (tp30) REVERT: A 209 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6756 (mtp180) REVERT: A 213 TYR cc_start: 0.6511 (m-80) cc_final: 0.6099 (m-80) REVERT: A 222 ASP cc_start: 0.5995 (m-30) cc_final: 0.5774 (m-30) REVERT: A 240 ARG cc_start: 0.6385 (mtt180) cc_final: 0.5912 (mtt-85) REVERT: A 279 ASP cc_start: 0.8069 (t70) cc_final: 0.7785 (t0) REVERT: A 399 GLU cc_start: 0.7703 (mp0) cc_final: 0.7197 (mp0) REVERT: A 400 LYS cc_start: 0.7338 (mttt) cc_final: 0.7133 (mttm) REVERT: B 74 MET cc_start: 0.5389 (mmm) cc_final: 0.5006 (tpp) REVERT: B 254 TRP cc_start: 0.7547 (m100) cc_final: 0.6967 (m100) REVERT: B 417 SER cc_start: 0.8000 (t) cc_final: 0.7697 (m) REVERT: E 4 LYS cc_start: 0.6891 (mttm) cc_final: 0.6522 (mtpp) REVERT: E 59 LYS cc_start: 0.7910 (tppt) cc_final: 0.7549 (tppt) REVERT: E 63 VAL cc_start: 0.7548 (t) cc_final: 0.7289 (p) REVERT: E 93 PHE cc_start: 0.6623 (t80) cc_final: 0.5835 (t80) REVERT: E 119 ASP cc_start: 0.8185 (t0) cc_final: 0.7796 (t70) REVERT: E 171 TYR cc_start: 0.6384 (m-80) cc_final: 0.6101 (m-80) REVERT: E 277 MET cc_start: 0.6661 (tpp) cc_final: 0.6404 (tpt) REVERT: E 411 LYS cc_start: 0.7582 (ttmt) cc_final: 0.7349 (tppt) REVERT: F 16 HIS cc_start: 0.6208 (m-70) cc_final: 0.5874 (m-70) REVERT: F 115 TYR cc_start: 0.7990 (t80) cc_final: 0.7649 (t80) REVERT: F 142 ILE cc_start: 0.7420 (mm) cc_final: 0.7077 (mm) REVERT: F 287 LYS cc_start: 0.7386 (mttm) cc_final: 0.7131 (mtmt) REVERT: F 316 GLU cc_start: 0.6623 (tp30) cc_final: 0.6389 (tp30) REVERT: F 342 SER cc_start: 0.8401 (m) cc_final: 0.8148 (t) REVERT: F 356 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7118 (tm-30) outliers start: 41 outliers final: 33 residues processed: 302 average time/residue: 0.2763 time to fit residues: 123.5238 Evaluate side-chains 309 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 394 GLU Chi-restraints excluded: chain B residue 227 SER 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 164 VAL 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 408 VAL Chi-restraints excluded: chain F residue 19 LYS 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 247 LYS 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 375 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 29 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 135 optimal weight: 0.0000 chunk 25 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 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 = 0.4314 r_free = 0.4314 target = 0.189180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156322 restraints weight = 24266.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.160297 restraints weight = 14211.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162891 restraints weight = 10126.110| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16838 Z= 0.175 Angle : 0.612 9.825 23128 Z= 0.323 Chirality : 0.043 0.187 2538 Planarity : 0.004 0.041 2632 Dihedral : 18.211 177.068 3014 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.45 % Allowed : 18.74 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1764 helix: 1.45 (0.23), residues: 566 sheet: 0.02 (0.28), residues: 371 loop : -1.73 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 370 HIS 0.007 0.001 HIS B 217 PHE 0.028 0.002 PHE B 93 TYR 0.020 0.002 TYR E 251 ARG 0.004 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 614) hydrogen bonds : angle 4.59486 ( 1858) covalent geometry : bond 0.00398 (16838) covalent geometry : angle 0.61238 (23128) *********************** 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 326 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6511 (mp) cc_final: 0.6195 (mp) REVERT: A 94 ILE cc_start: 0.8453 (mt) cc_final: 0.8163 (mm) REVERT: A 174 ASN cc_start: 0.7985 (p0) cc_final: 0.7666 (p0) REVERT: A 189 GLU cc_start: 0.6623 (tm-30) cc_final: 0.5425 (tp30) REVERT: A 213 TYR cc_start: 0.6596 (m-80) cc_final: 0.6069 (m-80) REVERT: A 222 ASP cc_start: 0.6004 (m-30) cc_final: 0.5759 (m-30) REVERT: A 240 ARG cc_start: 0.6431 (mtt180) cc_final: 0.5964 (mtt180) REVERT: A 279 ASP cc_start: 0.8072 (t70) cc_final: 0.7789 (t0) REVERT: A 399 GLU cc_start: 0.7676 (mp0) cc_final: 0.7215 (mp0) REVERT: A 400 LYS cc_start: 0.7425 (mttt) cc_final: 0.7113 (mttm) REVERT: A 411 LYS cc_start: 0.5684 (tttp) cc_final: 0.5364 (ttpp) REVERT: B 9 GLU cc_start: 0.7730 (mp0) cc_final: 0.7386 (mt-10) REVERT: B 74 MET cc_start: 0.5509 (mmm) cc_final: 0.4637 (tpt) REVERT: B 213 ARG cc_start: 0.8330 (mtm180) cc_final: 0.8053 (mtp180) REVERT: B 254 TRP cc_start: 0.7594 (m100) cc_final: 0.7190 (m100) REVERT: B 417 SER cc_start: 0.7980 (t) cc_final: 0.7603 (m) REVERT: E 4 LYS cc_start: 0.6927 (mttm) cc_final: 0.6562 (mtpp) REVERT: E 59 LYS cc_start: 0.7944 (tppt) cc_final: 0.7606 (tppt) REVERT: E 63 VAL cc_start: 0.7630 (t) cc_final: 0.7359 (p) REVERT: E 93 PHE cc_start: 0.6649 (t80) cc_final: 0.5885 (t80) REVERT: E 119 ASP cc_start: 0.8208 (t0) cc_final: 0.7850 (t70) REVERT: E 411 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7432 (tppt) REVERT: F 16 HIS cc_start: 0.6290 (m-70) cc_final: 0.5973 (m-70) REVERT: F 115 TYR cc_start: 0.8034 (t80) cc_final: 0.7697 (t80) REVERT: F 142 ILE cc_start: 0.7470 (mm) cc_final: 0.7111 (mm) REVERT: F 247 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6981 (mtpp) REVERT: F 287 LYS cc_start: 0.7433 (mttm) cc_final: 0.7187 (mtmt) REVERT: F 316 GLU cc_start: 0.6752 (tp30) cc_final: 0.6500 (tp30) REVERT: F 356 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7239 (tm-30) REVERT: F 436 GLU cc_start: 0.5152 (mt-10) cc_final: 0.4131 (mt-10) outliers start: 39 outliers final: 36 residues processed: 300 average time/residue: 0.2833 time to fit residues: 125.0695 Evaluate side-chains 317 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 B residue 322 ASN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 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 5 ILE 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 247 LYS Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 83 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.189157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.155760 restraints weight = 24394.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.159856 restraints weight = 14323.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.162473 restraints weight = 10184.214| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.3709 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= 0.157 Angle : 0.606 8.971 23128 Z= 0.319 Chirality : 0.042 0.168 2538 Planarity : 0.004 0.042 2632 Dihedral : 18.210 177.719 3014 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.33 % Allowed : 19.62 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1764 helix: 1.48 (0.23), residues: 564 sheet: -0.05 (0.28), residues: 373 loop : -1.72 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 20 HIS 0.005 0.001 HIS F 207 PHE 0.032 0.002 PHE B 93 TYR 0.022 0.001 TYR E 251 ARG 0.004 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 614) hydrogen bonds : angle 4.52621 ( 1858) covalent geometry : bond 0.00355 (16838) covalent geometry : angle 0.60603 (23128) ********************** 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 323 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6516 (mp) cc_final: 0.6202 (mp) REVERT: A 94 ILE cc_start: 0.8461 (mt) cc_final: 0.8173 (mm) REVERT: A 174 ASN cc_start: 0.7965 (p0) cc_final: 0.7640 (p0) REVERT: A 189 GLU cc_start: 0.6683 (tm-30) cc_final: 0.5402 (tp30) REVERT: A 213 TYR cc_start: 0.6589 (m-80) cc_final: 0.6114 (m-80) REVERT: A 222 ASP cc_start: 0.5969 (m-30) cc_final: 0.5743 (m-30) REVERT: A 240 ARG cc_start: 0.6375 (mtt180) cc_final: 0.5868 (mtt-85) REVERT: A 279 ASP cc_start: 0.8103 (t70) cc_final: 0.7806 (t0) REVERT: A 399 GLU cc_start: 0.7655 (mp0) cc_final: 0.7171 (mp0) REVERT: A 411 LYS cc_start: 0.5714 (tttp) cc_final: 0.5404 (ttpp) REVERT: B 254 TRP cc_start: 0.7597 (m100) cc_final: 0.7182 (m100) REVERT: B 417 SER cc_start: 0.8002 (t) cc_final: 0.7644 (m) REVERT: E 4 LYS cc_start: 0.6906 (mttm) cc_final: 0.6535 (mtpp) REVERT: E 59 LYS cc_start: 0.7965 (tppt) cc_final: 0.7664 (tppt) REVERT: E 63 VAL cc_start: 0.7644 (t) cc_final: 0.7377 (p) REVERT: E 93 PHE cc_start: 0.6640 (t80) cc_final: 0.6154 (t80) REVERT: E 119 ASP cc_start: 0.8222 (t0) cc_final: 0.7849 (t70) REVERT: E 233 TYR cc_start: 0.6784 (t80) cc_final: 0.6555 (t80) REVERT: E 411 LYS cc_start: 0.7662 (ttmt) cc_final: 0.7432 (tppt) REVERT: F 14 PHE cc_start: 0.7434 (m-80) cc_final: 0.7041 (m-80) REVERT: F 16 HIS cc_start: 0.6298 (m-70) cc_final: 0.5986 (m-70) REVERT: F 115 TYR cc_start: 0.8021 (t80) cc_final: 0.7689 (t80) REVERT: F 142 ILE cc_start: 0.7483 (mm) cc_final: 0.7135 (mm) REVERT: F 243 ARG cc_start: 0.6835 (mtm180) cc_final: 0.6256 (mtm180) REVERT: F 247 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6999 (mtmm) REVERT: F 287 LYS cc_start: 0.7386 (mttm) cc_final: 0.7152 (mtmt) REVERT: F 316 GLU cc_start: 0.6747 (tp30) cc_final: 0.6478 (tp30) REVERT: F 342 SER cc_start: 0.8425 (m) cc_final: 0.8154 (t) REVERT: F 356 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7248 (tm-30) outliers start: 37 outliers final: 34 residues processed: 300 average time/residue: 0.2980 time to fit residues: 131.5258 Evaluate side-chains 319 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 SER 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 322 ASN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 178 ILE 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 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 247 LYS Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 4 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 40 optimal weight: 0.0050 chunk 91 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 151 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.189074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.155595 restraints weight = 24254.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.159715 restraints weight = 14281.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.162317 restraints weight = 10174.519| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16838 Z= 0.153 Angle : 0.601 8.900 23128 Z= 0.317 Chirality : 0.042 0.168 2538 Planarity : 0.004 0.041 2632 Dihedral : 18.216 177.348 3014 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.26 % Allowed : 19.62 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1764 helix: 1.54 (0.23), residues: 564 sheet: -0.05 (0.28), residues: 373 loop : -1.75 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 20 HIS 0.005 0.001 HIS F 207 PHE 0.033 0.002 PHE B 93 TYR 0.022 0.001 TYR E 251 ARG 0.004 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 614) hydrogen bonds : angle 4.51624 ( 1858) covalent geometry : bond 0.00348 (16838) covalent geometry : angle 0.60102 (23128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6467.90 seconds wall clock time: 114 minutes 21.83 seconds (6861.83 seconds total)