Starting phenix.real_space_refine on Mon Nov 18 13:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/11_2024/8sp3_40673_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/11_2024/8sp3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/11_2024/8sp3_40673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/11_2024/8sp3_40673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/11_2024/8sp3_40673_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/11_2024/8sp3_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.25, per 1000 atoms: 0.45 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: 4.22 Conformation dependent library (CDL) restraints added in 1.9 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: 5.58 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: 5.91 Time building geometry restraints manager: 4.87 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: 21.140 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 36.170 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.890 ------------------------------------------------------------------------------- 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= 0.212 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 *********************** 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 : 1.742 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: 0.3115 time to fit residues: 167.7469 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 : 1.605 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 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= 0.166 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 *********************** 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 : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.6574 (mp) cc_final: 0.6267 (mp) REVERT: A 8 SER cc_start: 0.8112 (t) cc_final: 0.7687 (p) REVERT: A 209 ARG cc_start: 0.6988 (mtp85) cc_final: 0.6719 (mtp85) REVERT: A 210 TYR cc_start: 0.7140 (t80) cc_final: 0.6779 (t80) REVERT: A 213 TYR cc_start: 0.6482 (m-80) cc_final: 0.6071 (m-80) REVERT: A 246 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 255 PHE cc_start: 0.8428 (t80) cc_final: 0.8147 (t80) REVERT: A 263 ARG cc_start: 0.7355 (ttp80) cc_final: 0.6959 (ttp80) REVERT: A 279 ASP cc_start: 0.7918 (t70) cc_final: 0.7675 (t0) REVERT: A 399 GLU cc_start: 0.7614 (mp0) cc_final: 0.7250 (mp0) REVERT: B 115 TYR cc_start: 0.7432 (t80) cc_final: 0.7025 (t80) REVERT: B 132 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 254 TRP cc_start: 0.7502 (m100) cc_final: 0.7061 (m100) REVERT: B 321 TYR cc_start: 0.7809 (m-80) cc_final: 0.7311 (m-80) REVERT: B 417 SER cc_start: 0.8114 (t) cc_final: 0.7720 (m) REVERT: E 4 LYS cc_start: 0.6851 (mttm) cc_final: 0.6573 (mtpp) REVERT: E 15 ASN cc_start: 0.5306 (m-40) cc_final: 0.4744 (m-40) REVERT: E 59 LYS cc_start: 0.7741 (tppt) cc_final: 0.7415 (tppt) REVERT: E 93 PHE cc_start: 0.6552 (t80) cc_final: 0.6238 (t80) REVERT: E 128 LEU cc_start: 0.7195 (tp) cc_final: 0.6981 (tp) REVERT: E 286 GLU cc_start: 0.5143 (tp30) cc_final: 0.4924 (tp30) REVERT: E 290 LYS cc_start: 0.8210 (pttt) cc_final: 0.7846 (ptpp) REVERT: E 309 MET cc_start: 0.7479 (ttm) cc_final: 0.7277 (ttm) REVERT: E 364 GLN cc_start: 0.6483 (tt0) cc_final: 0.6147 (tm-30) REVERT: F 5 ILE cc_start: 0.7934 (pt) cc_final: 0.7700 (pt) REVERT: F 16 HIS cc_start: 0.6044 (m-70) cc_final: 0.5786 (m-70) REVERT: F 19 LYS cc_start: 0.7780 (mttp) cc_final: 0.7570 (mttt) REVERT: F 37 TYR cc_start: 0.7698 (m-80) cc_final: 0.7444 (m-80) REVERT: F 56 TYR cc_start: 0.5626 (t80) cc_final: 0.5146 (t80) REVERT: F 115 TYR cc_start: 0.7705 (t80) cc_final: 0.7375 (t80) REVERT: F 142 ILE cc_start: 0.7375 (mm) cc_final: 0.6890 (mt) REVERT: F 247 LYS cc_start: 0.7171 (mtpt) cc_final: 0.6914 (mtpp) REVERT: F 278 VAL cc_start: 0.8456 (t) cc_final: 0.8204 (p) REVERT: F 287 LYS cc_start: 0.7256 (mttm) cc_final: 0.6758 (mtmm) REVERT: F 311 THR cc_start: 0.8088 (t) cc_final: 0.7701 (p) REVERT: F 316 GLU cc_start: 0.6785 (tp30) cc_final: 0.6386 (tp30) REVERT: F 336 LYS cc_start: 0.8015 (mttp) cc_final: 0.7707 (mtmm) REVERT: F 342 SER cc_start: 0.8337 (m) cc_final: 0.8107 (t) outliers start: 20 outliers final: 10 residues processed: 311 average time/residue: 0.3279 time to fit residues: 148.6625 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 : 1.923 ------------------------------------------------------------------------------- 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 91 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 16838 Z= 0.488 Angle : 0.767 9.180 23128 Z= 0.406 Chirality : 0.049 0.181 2538 Planarity : 0.005 0.068 2632 Dihedral : 18.612 177.102 3014 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.08 % Allowed : 11.57 % Favored : 85.35 % 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: -0.94 (0.20), residues: 1764 helix: 0.77 (0.22), residues: 556 sheet: -0.20 (0.28), residues: 383 loop : -1.85 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 269 HIS 0.011 0.002 HIS E 358 PHE 0.031 0.003 PHE B 482 TYR 0.037 0.003 TYR B 321 ARG 0.007 0.001 ARG E 362 *********************** 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 361 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 312 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6404 (tpm170) cc_final: 0.5989 (tpm170) REVERT: A 209 ARG cc_start: 0.7154 (mtp85) cc_final: 0.6858 (mtp85) REVERT: A 213 TYR cc_start: 0.6675 (m-80) cc_final: 0.5938 (m-80) REVERT: A 263 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7231 (ttp80) REVERT: A 279 ASP cc_start: 0.8057 (t70) cc_final: 0.7749 (t0) REVERT: A 348 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7490 (mttt) REVERT: A 366 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7620 (ttpt) REVERT: A 399 GLU cc_start: 0.7772 (mp0) cc_final: 0.7304 (mp0) REVERT: A 411 LYS cc_start: 0.5658 (tttp) cc_final: 0.5156 (ttpp) REVERT: B 226 GLU cc_start: 0.7674 (mp0) cc_final: 0.7359 (mp0) REVERT: B 321 TYR cc_start: 0.8113 (m-80) cc_final: 0.7656 (m-80) REVERT: B 412 VAL cc_start: 0.8329 (t) cc_final: 0.8076 (p) REVERT: E 4 LYS cc_start: 0.6917 (mttm) cc_final: 0.6573 (mtpp) REVERT: E 15 ASN cc_start: 0.5598 (m-40) cc_final: 0.5030 (m-40) REVERT: E 59 LYS cc_start: 0.7980 (tppt) cc_final: 0.7547 (tppt) REVERT: E 93 PHE cc_start: 0.6660 (t80) cc_final: 0.5974 (t80) REVERT: F 40 LYS cc_start: 0.7589 (mmmt) cc_final: 0.7195 (mptt) REVERT: F 74 MET cc_start: 0.3596 (ptm) cc_final: 0.3258 (ptm) REVERT: F 85 LYS cc_start: 0.6918 (mttm) cc_final: 0.6566 (mttm) REVERT: F 115 TYR cc_start: 0.8069 (t80) cc_final: 0.7749 (t80) REVERT: F 142 ILE cc_start: 0.7501 (mm) cc_final: 0.7130 (mm) REVERT: F 247 LYS cc_start: 0.7368 (mtpt) cc_final: 0.7048 (mtpt) REVERT: F 278 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8289 (m) REVERT: F 287 LYS cc_start: 0.7553 (mttm) cc_final: 0.7311 (ttmt) REVERT: F 316 GLU cc_start: 0.7028 (tp30) cc_final: 0.6704 (tp30) REVERT: F 342 SER cc_start: 0.8443 (m) cc_final: 0.8119 (t) outliers start: 49 outliers final: 35 residues processed: 327 average time/residue: 0.3002 time to fit residues: 142.3287 Evaluate side-chains 328 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 180 SER 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 366 LYS 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 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 309 ASP 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 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain F residue 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 278 VAL 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 163 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 157 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16838 Z= 0.257 Angle : 0.617 7.800 23128 Z= 0.329 Chirality : 0.043 0.174 2538 Planarity : 0.004 0.059 2632 Dihedral : 18.367 179.264 3014 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.21 % Allowed : 14.84 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.20), residues: 1764 helix: 1.33 (0.23), residues: 544 sheet: -0.18 (0.28), residues: 369 loop : -1.81 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 319 HIS 0.006 0.001 HIS F 207 PHE 0.031 0.002 PHE B 93 TYR 0.019 0.001 TYR A 251 ARG 0.005 0.000 ARG B 407 *********************** 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: 51 poor density : 292 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6250 (tpm170) cc_final: 0.5877 (tpm170) REVERT: A 183 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 209 ARG cc_start: 0.7121 (mtp85) cc_final: 0.6817 (mtp85) REVERT: A 213 TYR cc_start: 0.6596 (m-80) cc_final: 0.6260 (m-80) REVERT: A 279 ASP cc_start: 0.8063 (t70) cc_final: 0.7544 (t0) REVERT: A 366 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7582 (ttpt) REVERT: A 386 ASP cc_start: 0.7291 (t70) cc_final: 0.6804 (t0) REVERT: A 399 GLU cc_start: 0.7746 (mp0) cc_final: 0.7253 (mp0) REVERT: A 408 VAL cc_start: 0.8277 (t) cc_final: 0.7769 (p) REVERT: A 415 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8311 (m) REVERT: B 412 VAL cc_start: 0.8284 (t) cc_final: 0.8015 (p) REVERT: B 417 SER cc_start: 0.8074 (t) cc_final: 0.7675 (m) REVERT: E 4 LYS cc_start: 0.6926 (mttm) cc_final: 0.6501 (mtpp) REVERT: E 15 ASN cc_start: 0.5363 (m-40) cc_final: 0.4802 (m-40) REVERT: E 59 LYS cc_start: 0.7925 (tppt) cc_final: 0.7563 (tppt) REVERT: E 93 PHE cc_start: 0.6614 (t80) cc_final: 0.6234 (t80) REVERT: E 210 TYR cc_start: 0.7310 (t80) cc_final: 0.6994 (t80) REVERT: E 364 GLN cc_start: 0.6650 (tt0) cc_final: 0.6235 (tm-30) REVERT: F 16 HIS cc_start: 0.6282 (m-70) cc_final: 0.5987 (m-70) REVERT: F 40 LYS cc_start: 0.7587 (mmmt) cc_final: 0.7239 (mptt) REVERT: F 54 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5933 (mpp80) REVERT: F 74 MET cc_start: 0.3548 (ptm) cc_final: 0.3330 (ptm) REVERT: F 115 TYR cc_start: 0.8045 (t80) cc_final: 0.7734 (t80) REVERT: F 142 ILE cc_start: 0.7456 (mm) cc_final: 0.7085 (mm) REVERT: F 247 LYS cc_start: 0.7448 (mtpt) cc_final: 0.7151 (mtpp) REVERT: F 287 LYS cc_start: 0.7488 (mttm) cc_final: 0.7246 (ttmt) REVERT: F 311 THR cc_start: 0.8212 (t) cc_final: 0.7952 (p) REVERT: F 316 GLU cc_start: 0.6810 (tp30) cc_final: 0.6573 (tp30) REVERT: F 342 SER cc_start: 0.8410 (m) cc_final: 0.8114 (t) outliers start: 51 outliers final: 35 residues processed: 314 average time/residue: 0.3143 time to fit residues: 142.6511 Evaluate side-chains 325 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER 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 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 381 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 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 146 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 116 ASN A 160 HIS A 357 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16838 Z= 0.316 Angle : 0.653 11.686 23128 Z= 0.346 Chirality : 0.044 0.167 2538 Planarity : 0.004 0.043 2632 Dihedral : 18.432 176.747 3014 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.77 % Allowed : 16.98 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.79 (0.20), residues: 1764 helix: 1.24 (0.23), residues: 536 sheet: -0.23 (0.28), residues: 371 loop : -1.88 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 254 HIS 0.006 0.001 HIS F 207 PHE 0.039 0.002 PHE F 93 TYR 0.021 0.002 TYR A 171 ARG 0.003 0.000 ARG B 407 *********************** 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 350 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6237 (tpm170) cc_final: 0.5841 (tpm170) REVERT: A 189 GLU cc_start: 0.6592 (tm-30) cc_final: 0.5342 (tm-30) REVERT: A 209 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6810 (mtp85) REVERT: A 213 TYR cc_start: 0.6591 (m-80) cc_final: 0.6269 (m-80) REVERT: A 279 ASP cc_start: 0.8079 (t70) cc_final: 0.7743 (t0) REVERT: A 366 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7576 (ttpt) REVERT: A 399 GLU cc_start: 0.7750 (mp0) cc_final: 0.7258 (mp0) REVERT: A 400 LYS cc_start: 0.7564 (mttt) cc_final: 0.6843 (mttm) REVERT: A 411 LYS cc_start: 0.5716 (tttp) cc_final: 0.5262 (ttpp) REVERT: A 415 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8294 (m) REVERT: B 3 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6208 (mm-30) REVERT: B 9 GLU cc_start: 0.7752 (mp0) cc_final: 0.7503 (mp0) REVERT: B 364 ARG cc_start: 0.7302 (mtt90) cc_final: 0.7098 (mtt90) REVERT: B 417 SER cc_start: 0.8069 (t) cc_final: 0.7675 (m) REVERT: E 4 LYS cc_start: 0.6927 (mttm) cc_final: 0.6504 (mtpp) REVERT: E 15 ASN cc_start: 0.5838 (m-40) cc_final: 0.5346 (m-40) REVERT: E 93 PHE cc_start: 0.6640 (t80) cc_final: 0.6267 (t80) REVERT: E 210 TYR cc_start: 0.7313 (t80) cc_final: 0.6998 (t80) REVERT: E 411 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7451 (tppt) REVERT: F 16 HIS cc_start: 0.6311 (m-70) cc_final: 0.5989 (m-70) REVERT: F 40 LYS cc_start: 0.7652 (mmmt) cc_final: 0.7309 (mptt) REVERT: F 44 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7485 (mp) REVERT: F 54 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5487 (mpp80) REVERT: F 74 MET cc_start: 0.3691 (ptm) cc_final: 0.3478 (ptm) REVERT: F 142 ILE cc_start: 0.7488 (mm) cc_final: 0.7115 (mm) REVERT: F 287 LYS cc_start: 0.7507 (mttm) cc_final: 0.7284 (mtmt) REVERT: F 311 THR cc_start: 0.8232 (t) cc_final: 0.7955 (p) REVERT: F 316 GLU cc_start: 0.6805 (tp30) cc_final: 0.6551 (tp30) REVERT: F 342 SER cc_start: 0.8451 (m) cc_final: 0.8127 (t) outliers start: 60 outliers final: 40 residues processed: 316 average time/residue: 0.2938 time to fit residues: 135.9008 Evaluate side-chains 328 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 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 339 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 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 Chi-restraints excluded: chain F residue 465 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 176 optimal weight: 0.1980 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3287 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= 0.236 Angle : 0.602 10.060 23128 Z= 0.320 Chirality : 0.043 0.183 2538 Planarity : 0.004 0.058 2632 Dihedral : 18.343 178.130 3014 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.27 % Allowed : 17.67 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.66 (0.20), residues: 1764 helix: 1.36 (0.23), residues: 548 sheet: -0.17 (0.28), residues: 370 loop : -1.84 (0.20), residues: 846 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 0.036 0.002 PHE F 93 TYR 0.020 0.001 TYR A 251 ARG 0.005 0.000 ARG F 213 *********************** 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 338 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8409 (mt) cc_final: 0.8164 (mm) REVERT: A 126 ARG cc_start: 0.6224 (tpm170) cc_final: 0.5759 (tpm170) REVERT: A 189 GLU cc_start: 0.6610 (tm-30) cc_final: 0.5301 (tm-30) REVERT: A 209 ARG cc_start: 0.7079 (mtp85) cc_final: 0.6795 (mtp180) REVERT: A 213 TYR cc_start: 0.6544 (m-80) cc_final: 0.6287 (m-80) REVERT: A 279 ASP cc_start: 0.8084 (t70) cc_final: 0.7760 (t0) REVERT: A 346 ASP cc_start: 0.6925 (p0) cc_final: 0.6718 (p0) REVERT: A 366 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7539 (ttpt) REVERT: A 399 GLU cc_start: 0.7721 (mp0) cc_final: 0.7218 (mp0) REVERT: A 411 LYS cc_start: 0.5602 (tttp) cc_final: 0.5277 (ttpp) REVERT: A 415 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8288 (m) REVERT: B 9 GLU cc_start: 0.7732 (mp0) cc_final: 0.7345 (mt-10) REVERT: B 334 GLU cc_start: 0.7548 (mp0) cc_final: 0.7291 (mp0) REVERT: B 417 SER cc_start: 0.8056 (t) cc_final: 0.7696 (m) REVERT: E 4 LYS cc_start: 0.6932 (mttm) cc_final: 0.6619 (mtpp) REVERT: E 15 ASN cc_start: 0.5775 (m-40) cc_final: 0.5319 (m-40) REVERT: E 59 LYS cc_start: 0.7923 (tppt) cc_final: 0.7576 (tppt) REVERT: E 63 VAL cc_start: 0.7531 (t) cc_final: 0.7287 (p) REVERT: E 75 LEU cc_start: 0.6048 (mt) cc_final: 0.5764 (mt) REVERT: E 93 PHE cc_start: 0.6624 (t80) cc_final: 0.5927 (t80) REVERT: E 210 TYR cc_start: 0.7241 (t80) cc_final: 0.6867 (t80) REVERT: E 269 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6488 (mt) REVERT: E 364 GLN cc_start: 0.6638 (tt0) cc_final: 0.6364 (tm-30) REVERT: E 411 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7402 (tppt) REVERT: F 16 HIS cc_start: 0.6295 (m-70) cc_final: 0.5982 (m-70) REVERT: F 40 LYS cc_start: 0.7645 (mmmt) cc_final: 0.7351 (mptt) REVERT: F 44 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7438 (mp) REVERT: F 142 ILE cc_start: 0.7461 (mm) cc_final: 0.7103 (mm) REVERT: F 247 LYS cc_start: 0.7343 (mtpt) cc_final: 0.6971 (mtpp) REVERT: F 311 THR cc_start: 0.8219 (t) cc_final: 0.7947 (p) REVERT: F 316 GLU cc_start: 0.6754 (tp30) cc_final: 0.6493 (tp30) REVERT: F 342 SER cc_start: 0.8433 (m) cc_final: 0.8127 (t) REVERT: F 362 LYS cc_start: 0.7713 (mppt) cc_final: 0.7493 (mptt) REVERT: F 409 ASN cc_start: 0.7871 (m-40) cc_final: 0.7600 (m-40) REVERT: F 436 GLU cc_start: 0.5012 (mt-10) cc_final: 0.4376 (mt-10) outliers start: 52 outliers final: 40 residues processed: 306 average time/residue: 0.3042 time to fit residues: 136.9679 Evaluate side-chains 322 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 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 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 269 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN F 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16838 Z= 0.231 Angle : 0.598 9.548 23128 Z= 0.317 Chirality : 0.042 0.168 2538 Planarity : 0.004 0.043 2632 Dihedral : 18.324 177.601 3014 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.46 % Allowed : 17.80 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.20), residues: 1764 helix: 1.43 (0.23), residues: 549 sheet: -0.11 (0.29), residues: 365 loop : -1.84 (0.20), residues: 850 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 0.037 0.002 PHE F 93 TYR 0.017 0.001 TYR A 251 ARG 0.006 0.000 ARG B 364 *********************** 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 346 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6162 (tpm170) cc_final: 0.5798 (tpm170) REVERT: A 174 ASN cc_start: 0.7987 (p0) cc_final: 0.7602 (p0) REVERT: A 183 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 189 GLU cc_start: 0.6694 (tm-30) cc_final: 0.5688 (tm-30) REVERT: A 213 TYR cc_start: 0.6556 (m-80) cc_final: 0.6285 (m-80) REVERT: A 245 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: A 279 ASP cc_start: 0.8078 (t70) cc_final: 0.7766 (t0) REVERT: A 346 ASP cc_start: 0.7022 (p0) cc_final: 0.6813 (p0) REVERT: A 366 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7485 (ttpt) REVERT: A 400 LYS cc_start: 0.7508 (mttt) cc_final: 0.7228 (mttm) REVERT: A 411 LYS cc_start: 0.5666 (tttp) cc_final: 0.5116 (ttpp) REVERT: A 415 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8291 (m) REVERT: B 9 GLU cc_start: 0.7782 (mp0) cc_final: 0.7189 (mt-10) REVERT: B 254 TRP cc_start: 0.7600 (m100) cc_final: 0.7018 (m100) REVERT: B 417 SER cc_start: 0.8016 (t) cc_final: 0.7678 (m) REVERT: E 4 LYS cc_start: 0.6939 (mttm) cc_final: 0.6613 (mtpp) REVERT: E 15 ASN cc_start: 0.5811 (m-40) cc_final: 0.5337 (m-40) REVERT: E 59 LYS cc_start: 0.7918 (tppt) cc_final: 0.7592 (tppt) REVERT: E 93 PHE cc_start: 0.6617 (t80) cc_final: 0.5942 (t80) REVERT: E 119 ASP cc_start: 0.8134 (t0) cc_final: 0.7756 (t0) REVERT: E 210 TYR cc_start: 0.7196 (t80) cc_final: 0.6776 (t80) REVERT: E 269 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6548 (mt) REVERT: E 309 MET cc_start: 0.7352 (ttm) cc_final: 0.6942 (ttm) REVERT: E 364 GLN cc_start: 0.6579 (tt0) cc_final: 0.6266 (tm-30) REVERT: E 411 LYS cc_start: 0.7626 (ttmt) cc_final: 0.7352 (tppt) REVERT: F 16 HIS cc_start: 0.6288 (m-70) cc_final: 0.5987 (m-70) REVERT: F 40 LYS cc_start: 0.7603 (mmmt) cc_final: 0.7329 (mptt) REVERT: F 44 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7460 (mp) REVERT: F 142 ILE cc_start: 0.7469 (mm) cc_final: 0.7112 (mm) REVERT: F 247 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6953 (mtpp) REVERT: F 311 THR cc_start: 0.8215 (t) cc_final: 0.7982 (p) REVERT: F 316 GLU cc_start: 0.6735 (tp30) cc_final: 0.6501 (tp30) REVERT: F 342 SER cc_start: 0.8426 (m) cc_final: 0.8150 (t) REVERT: F 436 GLU cc_start: 0.5078 (mt-10) cc_final: 0.4223 (mt-10) outliers start: 55 outliers final: 43 residues processed: 311 average time/residue: 0.2956 time to fit residues: 135.8181 Evaluate side-chains 336 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 291 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 84 CYS 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 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 126 ILE 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 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 108 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16838 Z= 0.242 Angle : 0.619 10.640 23128 Z= 0.326 Chirality : 0.043 0.167 2538 Planarity : 0.004 0.043 2632 Dihedral : 18.333 177.495 3014 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.27 % Allowed : 19.18 % Favored : 77.55 % 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: -0.66 (0.20), residues: 1764 helix: 1.33 (0.23), residues: 553 sheet: -0.15 (0.28), residues: 370 loop : -1.85 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 319 HIS 0.005 0.001 HIS F 207 PHE 0.034 0.002 PHE F 93 TYR 0.021 0.001 TYR A 251 ARG 0.005 0.000 ARG B 364 *********************** 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 340 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8389 (mt) cc_final: 0.8113 (mm) REVERT: A 126 ARG cc_start: 0.6169 (tpm170) cc_final: 0.5782 (tpm170) REVERT: A 174 ASN cc_start: 0.8010 (p0) cc_final: 0.7659 (p0) REVERT: A 189 GLU cc_start: 0.6812 (tm-30) cc_final: 0.5342 (tm-30) REVERT: A 213 TYR cc_start: 0.6565 (m-80) cc_final: 0.6318 (m-80) REVERT: A 279 ASP cc_start: 0.8044 (t70) cc_final: 0.7756 (t0) REVERT: A 366 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7480 (ttpt) REVERT: A 400 LYS cc_start: 0.7519 (mttt) cc_final: 0.7101 (mttm) REVERT: A 411 LYS cc_start: 0.5715 (tttp) cc_final: 0.5369 (ttpp) REVERT: A 415 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8277 (m) REVERT: B 9 GLU cc_start: 0.7801 (mp0) cc_final: 0.7501 (mp0) REVERT: B 254 TRP cc_start: 0.7635 (m100) cc_final: 0.5666 (m100) REVERT: B 417 SER cc_start: 0.8005 (t) cc_final: 0.7654 (m) REVERT: E 4 LYS cc_start: 0.6936 (mttm) cc_final: 0.6610 (mtpp) REVERT: E 15 ASN cc_start: 0.5847 (m-40) cc_final: 0.5369 (m-40) REVERT: E 59 LYS cc_start: 0.7947 (tppt) cc_final: 0.7595 (tppt) REVERT: E 63 VAL cc_start: 0.7630 (t) cc_final: 0.7355 (p) REVERT: E 93 PHE cc_start: 0.6628 (t80) cc_final: 0.5921 (t80) REVERT: E 119 ASP cc_start: 0.8143 (t0) cc_final: 0.7767 (t0) REVERT: E 210 TYR cc_start: 0.7190 (t80) cc_final: 0.6767 (t80) REVERT: E 233 TYR cc_start: 0.6862 (t80) cc_final: 0.6639 (t80) REVERT: E 269 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6566 (mt) REVERT: E 364 GLN cc_start: 0.6646 (tt0) cc_final: 0.6416 (tm-30) REVERT: E 411 LYS cc_start: 0.7614 (ttmt) cc_final: 0.7401 (tppt) REVERT: F 14 PHE cc_start: 0.7493 (m-80) cc_final: 0.7066 (m-80) REVERT: F 16 HIS cc_start: 0.6333 (m-70) cc_final: 0.6025 (m-70) REVERT: F 40 LYS cc_start: 0.7614 (mmmt) cc_final: 0.7337 (mptt) REVERT: F 44 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7453 (mp) REVERT: F 142 ILE cc_start: 0.7480 (mm) cc_final: 0.7121 (mm) REVERT: F 247 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6953 (mtpp) REVERT: F 311 THR cc_start: 0.8215 (t) cc_final: 0.8003 (p) REVERT: F 316 GLU cc_start: 0.6747 (tp30) cc_final: 0.6492 (tp30) REVERT: F 342 SER cc_start: 0.8433 (m) cc_final: 0.8148 (t) outliers start: 52 outliers final: 44 residues processed: 308 average time/residue: 0.3000 time to fit residues: 136.3174 Evaluate side-chains 334 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 303 ASP Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 84 CYS 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 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 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 269 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 375 THR 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 126 ILE 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 330 LEU Chi-restraints excluded: chain F residue 356 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 0.0870 chunk 154 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16838 Z= 0.231 Angle : 0.615 9.715 23128 Z= 0.324 Chirality : 0.043 0.168 2538 Planarity : 0.004 0.042 2632 Dihedral : 18.333 177.695 3014 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.33 % Allowed : 19.50 % Favored : 77.17 % 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: -0.64 (0.20), residues: 1764 helix: 1.37 (0.23), residues: 553 sheet: -0.18 (0.28), residues: 372 loop : -1.83 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 370 HIS 0.005 0.001 HIS F 207 PHE 0.034 0.002 PHE B 93 TYR 0.021 0.001 TYR A 251 ARG 0.005 0.000 ARG B 364 *********************** 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 339 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 286 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8408 (mt) cc_final: 0.8153 (mm) REVERT: A 126 ARG cc_start: 0.6157 (tpm170) cc_final: 0.5759 (tpm170) REVERT: A 174 ASN cc_start: 0.8007 (p0) cc_final: 0.7665 (p0) REVERT: A 189 GLU cc_start: 0.6795 (tm-30) cc_final: 0.5327 (tm-30) REVERT: A 213 TYR cc_start: 0.6553 (m-80) cc_final: 0.6305 (m-80) REVERT: A 279 ASP cc_start: 0.8054 (t70) cc_final: 0.7767 (t0) REVERT: A 348 LYS cc_start: 0.7794 (mttt) cc_final: 0.7569 (mttt) REVERT: A 366 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7484 (ttpt) REVERT: A 400 LYS cc_start: 0.7477 (mttt) cc_final: 0.7086 (mttm) REVERT: A 411 LYS cc_start: 0.5722 (tttp) cc_final: 0.5385 (ttpp) REVERT: A 415 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8211 (m) REVERT: B 9 GLU cc_start: 0.7811 (mp0) cc_final: 0.7504 (mp0) REVERT: B 254 TRP cc_start: 0.7622 (m100) cc_final: 0.5643 (m100) REVERT: B 417 SER cc_start: 0.7994 (t) cc_final: 0.7645 (m) REVERT: E 4 LYS cc_start: 0.6926 (mttm) cc_final: 0.6584 (mtpp) REVERT: E 15 ASN cc_start: 0.5893 (m-40) cc_final: 0.5445 (m-40) REVERT: E 59 LYS cc_start: 0.7950 (tppt) cc_final: 0.7608 (tppt) REVERT: E 63 VAL cc_start: 0.7656 (t) cc_final: 0.7367 (p) REVERT: E 93 PHE cc_start: 0.6617 (t80) cc_final: 0.5919 (t80) REVERT: E 119 ASP cc_start: 0.8122 (t0) cc_final: 0.7748 (t0) REVERT: E 210 TYR cc_start: 0.7186 (t80) cc_final: 0.6772 (t80) REVERT: E 233 TYR cc_start: 0.6810 (t80) cc_final: 0.6563 (t80) REVERT: E 269 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6555 (mt) REVERT: E 364 GLN cc_start: 0.6699 (tt0) cc_final: 0.6456 (tm-30) REVERT: E 411 LYS cc_start: 0.7616 (ttmt) cc_final: 0.7393 (tppt) REVERT: F 16 HIS cc_start: 0.6359 (m-70) cc_final: 0.6058 (m-70) REVERT: F 40 LYS cc_start: 0.7624 (mmmt) cc_final: 0.7343 (mptt) REVERT: F 44 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7450 (mp) REVERT: F 142 ILE cc_start: 0.7473 (mm) cc_final: 0.7138 (mm) REVERT: F 247 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6940 (mtpp) REVERT: F 311 THR cc_start: 0.8239 (t) cc_final: 0.8007 (p) REVERT: F 316 GLU cc_start: 0.6738 (tp30) cc_final: 0.6495 (tp30) REVERT: F 342 SER cc_start: 0.8436 (m) cc_final: 0.8129 (t) outliers start: 53 outliers final: 46 residues processed: 307 average time/residue: 0.2938 time to fit residues: 132.5223 Evaluate side-chains 333 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 197 ARG 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 366 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 84 CYS 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 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 496 ILE 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 269 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 375 THR 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 126 ILE 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 330 LEU Chi-restraints excluded: chain F residue 356 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.6980 chunk 172 optimal weight: 0.0980 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16838 Z= 0.254 Angle : 0.635 12.501 23128 Z= 0.333 Chirality : 0.043 0.167 2538 Planarity : 0.004 0.042 2632 Dihedral : 18.354 177.260 3014 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.27 % Allowed : 19.87 % Favored : 76.86 % 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: -0.67 (0.20), residues: 1764 helix: 1.34 (0.23), residues: 553 sheet: -0.21 (0.28), residues: 370 loop : -1.85 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 319 HIS 0.005 0.001 HIS F 207 PHE 0.032 0.002 PHE B 93 TYR 0.020 0.001 TYR B 280 ARG 0.005 0.000 ARG B 364 ********************** 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 340 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8384 (mt) cc_final: 0.8102 (mm) REVERT: A 107 ASP cc_start: 0.5743 (m-30) cc_final: 0.5524 (m-30) REVERT: A 174 ASN cc_start: 0.8034 (p0) cc_final: 0.7685 (p0) REVERT: A 183 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 189 GLU cc_start: 0.6820 (tm-30) cc_final: 0.5540 (tp30) REVERT: A 213 TYR cc_start: 0.6620 (m-80) cc_final: 0.6127 (m-80) REVERT: A 279 ASP cc_start: 0.8065 (t70) cc_final: 0.7781 (t0) REVERT: A 348 LYS cc_start: 0.7796 (mttt) cc_final: 0.7593 (mttt) REVERT: A 366 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7485 (ttpt) REVERT: A 400 LYS cc_start: 0.7515 (mttt) cc_final: 0.7119 (mttm) REVERT: A 411 LYS cc_start: 0.5777 (tttp) cc_final: 0.5434 (ttpp) REVERT: A 415 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8209 (m) REVERT: B 254 TRP cc_start: 0.7640 (m100) cc_final: 0.7328 (m100) REVERT: B 417 SER cc_start: 0.7976 (t) cc_final: 0.7629 (m) REVERT: E 4 LYS cc_start: 0.6924 (mttm) cc_final: 0.6581 (mtpp) REVERT: E 15 ASN cc_start: 0.5915 (m-40) cc_final: 0.5478 (m-40) REVERT: E 59 LYS cc_start: 0.7934 (tppt) cc_final: 0.7600 (tppt) REVERT: E 63 VAL cc_start: 0.7722 (t) cc_final: 0.7427 (p) REVERT: E 93 PHE cc_start: 0.6623 (t80) cc_final: 0.5935 (t80) REVERT: E 119 ASP cc_start: 0.8164 (t0) cc_final: 0.7790 (t0) REVERT: E 233 TYR cc_start: 0.6805 (t80) cc_final: 0.6563 (t80) REVERT: E 269 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6592 (mt) REVERT: E 411 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7401 (tppt) REVERT: F 14 PHE cc_start: 0.7481 (m-80) cc_final: 0.7207 (m-80) REVERT: F 40 LYS cc_start: 0.7639 (mmmt) cc_final: 0.7359 (mptt) REVERT: F 44 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7454 (mp) REVERT: F 142 ILE cc_start: 0.7483 (mm) cc_final: 0.7152 (mm) REVERT: F 247 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6957 (mtpp) REVERT: F 311 THR cc_start: 0.8232 (t) cc_final: 0.8012 (p) REVERT: F 316 GLU cc_start: 0.6767 (tp30) cc_final: 0.6518 (tp30) REVERT: F 342 SER cc_start: 0.8431 (m) cc_final: 0.8130 (t) outliers start: 52 outliers final: 45 residues processed: 309 average time/residue: 0.2948 time to fit residues: 134.8698 Evaluate side-chains 337 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 287 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 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 366 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 84 CYS 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 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 496 ILE 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 269 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 375 THR 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 126 ILE 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 330 LEU Chi-restraints excluded: chain F residue 356 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.3980 chunk 153 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 0.0030 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.188972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156007 restraints weight = 24333.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160049 restraints weight = 14296.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.162651 restraints weight = 10172.193| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16838 Z= 0.212 Angle : 0.610 12.248 23128 Z= 0.319 Chirality : 0.042 0.167 2538 Planarity : 0.004 0.042 2632 Dihedral : 18.279 177.769 3014 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.40 % Allowed : 19.75 % Favored : 76.86 % 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: -0.61 (0.20), residues: 1764 helix: 1.47 (0.23), residues: 554 sheet: -0.24 (0.28), residues: 373 loop : -1.84 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 370 HIS 0.004 0.001 HIS F 207 PHE 0.031 0.002 PHE F 93 TYR 0.023 0.001 TYR A 221 ARG 0.005 0.000 ARG B 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3578.42 seconds wall clock time: 66 minutes 58.27 seconds (4018.27 seconds total)