Starting phenix.real_space_refine on Sun Mar 17 01:20:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/03_2024/8sp3_40673_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/03_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_40673/03_2024/8sp3_40673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/03_2024/8sp3_40673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/03_2024/8sp3_40673_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sp3_40673/03_2024/8sp3_40673_neut.pdb" } 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 Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "F TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.64, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 7.07 Conformation dependent library (CDL) restraints added in 2.3 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: 5.07 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: 5.37 Time building geometry restraints manager: 7.43 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: 99.85 - 106.68: 856 106.68 - 113.51: 9098 113.51 - 120.35: 6359 120.35 - 127.18: 6492 127.18 - 134.01: 323 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.050 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 46.300 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.310 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.542 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: 0.3030 time to fit residues: 163.2108 Evaluate side-chains 295 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.863 ------------------------------------------------------------------------------- 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: 0.9980 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 142 optimal weight: 0.4980 chunk 55 optimal weight: 0.2980 chunk 86 optimal weight: 0.0570 chunk 106 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16838 Z= 0.204 Angle : 0.565 12.384 23128 Z= 0.297 Chirality : 0.041 0.171 2538 Planarity : 0.004 0.047 2632 Dihedral : 18.155 177.897 3014 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.89 % Allowed : 7.80 % Favored : 90.31 % 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: -0.24 (0.20), residues: 1764 helix: 1.63 (0.23), residues: 559 sheet: 0.06 (0.29), residues: 373 loop : -1.57 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 86 HIS 0.005 0.001 HIS F 207 PHE 0.023 0.002 PHE B 30 TYR 0.016 0.001 TYR B 6 ARG 0.005 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 341 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 311 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8116 (t) cc_final: 0.7712 (p) REVERT: A 209 ARG cc_start: 0.7009 (mtp85) cc_final: 0.6739 (mtp85) REVERT: A 210 TYR cc_start: 0.7157 (t80) cc_final: 0.6877 (t80) REVERT: A 213 TYR cc_start: 0.6494 (m-80) cc_final: 0.6087 (m-80) REVERT: A 255 PHE cc_start: 0.8462 (t80) cc_final: 0.8245 (t80) REVERT: A 263 ARG cc_start: 0.7496 (ttp80) cc_final: 0.7097 (ttp80) REVERT: A 279 ASP cc_start: 0.7942 (t70) cc_final: 0.7700 (t0) REVERT: A 399 GLU cc_start: 0.7634 (mp0) cc_final: 0.7281 (mp0) REVERT: B 138 VAL cc_start: 0.8537 (t) cc_final: 0.8289 (m) REVERT: B 254 TRP cc_start: 0.7534 (m100) cc_final: 0.7174 (m100) REVERT: B 321 TYR cc_start: 0.7884 (m-80) cc_final: 0.7291 (m-80) REVERT: B 412 VAL cc_start: 0.8322 (t) cc_final: 0.8060 (p) REVERT: B 417 SER cc_start: 0.8100 (t) cc_final: 0.7677 (m) REVERT: E 4 LYS cc_start: 0.6844 (mttm) cc_final: 0.6479 (mtpp) REVERT: E 15 ASN cc_start: 0.5382 (m-40) cc_final: 0.4844 (m-40) REVERT: E 59 LYS cc_start: 0.7762 (tppt) cc_final: 0.7402 (tppt) REVERT: E 93 PHE cc_start: 0.6535 (t80) cc_final: 0.6186 (t80) REVERT: E 128 LEU cc_start: 0.7168 (tp) cc_final: 0.6949 (tp) REVERT: E 246 ILE cc_start: 0.7146 (pt) cc_final: 0.6879 (mt) REVERT: E 286 GLU cc_start: 0.5163 (tp30) cc_final: 0.4950 (tp30) REVERT: E 290 LYS cc_start: 0.8219 (pttt) cc_final: 0.7787 (ptpp) REVERT: F 16 HIS cc_start: 0.6135 (m-70) cc_final: 0.5861 (m-70) REVERT: F 40 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7636 (mmmt) REVERT: F 56 TYR cc_start: 0.5520 (t80) cc_final: 0.5041 (t80) REVERT: F 115 TYR cc_start: 0.7757 (t80) cc_final: 0.7388 (t80) REVERT: F 247 LYS cc_start: 0.7159 (mtpt) cc_final: 0.6809 (mtpp) REVERT: F 278 VAL cc_start: 0.8487 (t) cc_final: 0.8206 (p) REVERT: F 287 LYS cc_start: 0.7324 (mttm) cc_final: 0.6824 (mtmm) REVERT: F 311 THR cc_start: 0.8103 (t) cc_final: 0.7761 (p) REVERT: F 336 LYS cc_start: 0.8018 (mttp) cc_final: 0.7715 (mtmm) outliers start: 30 outliers final: 17 residues processed: 320 average time/residue: 0.3071 time to fit residues: 141.1820 Evaluate side-chains 313 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 296 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 504 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 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: 0.6980 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 132 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 16838 Z= 0.362 Angle : 0.665 7.599 23128 Z= 0.353 Chirality : 0.045 0.171 2538 Planarity : 0.005 0.050 2632 Dihedral : 18.419 178.048 3014 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.08 % Allowed : 12.64 % Favored : 84.28 % 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: 1.22 (0.23), residues: 552 sheet: -0.04 (0.30), residues: 335 loop : -1.77 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 269 HIS 0.009 0.001 HIS E 358 PHE 0.024 0.003 PHE B 93 TYR 0.029 0.002 TYR B 321 ARG 0.005 0.001 ARG B 407 *********************** 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 360 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 311 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.8017 (p0) cc_final: 0.7815 (p0) REVERT: A 209 ARG cc_start: 0.7141 (mtp85) cc_final: 0.6829 (mtp85) REVERT: A 213 TYR cc_start: 0.6634 (m-80) cc_final: 0.6062 (m-80) REVERT: A 279 ASP cc_start: 0.8060 (t70) cc_final: 0.7772 (t0) REVERT: A 334 VAL cc_start: 0.7491 (t) cc_final: 0.7164 (m) REVERT: A 366 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7508 (ttpt) REVERT: A 399 GLU cc_start: 0.7740 (mp0) cc_final: 0.7276 (mp0) REVERT: A 400 LYS cc_start: 0.7665 (mttt) cc_final: 0.7362 (mttm) REVERT: A 408 VAL cc_start: 0.8207 (t) cc_final: 0.7717 (p) REVERT: B 138 VAL cc_start: 0.8561 (t) cc_final: 0.8294 (m) REVERT: B 226 GLU cc_start: 0.7640 (mp0) cc_final: 0.7428 (mp0) REVERT: B 229 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 254 TRP cc_start: 0.7649 (m100) cc_final: 0.7431 (m100) REVERT: B 321 TYR cc_start: 0.8073 (m-80) cc_final: 0.7743 (m-80) REVERT: B 412 VAL cc_start: 0.8280 (t) cc_final: 0.8029 (p) REVERT: E 4 LYS cc_start: 0.6893 (mttm) cc_final: 0.6560 (mtpp) REVERT: E 15 ASN cc_start: 0.5554 (m-40) cc_final: 0.5005 (m-40) REVERT: E 59 LYS cc_start: 0.7926 (tppt) cc_final: 0.7464 (tppt) REVERT: E 93 PHE cc_start: 0.6632 (t80) cc_final: 0.6026 (t80) REVERT: E 119 ASP cc_start: 0.7969 (t0) cc_final: 0.7626 (t0) REVERT: E 360 SER cc_start: 0.7516 (m) cc_final: 0.7136 (m) REVERT: F 16 HIS cc_start: 0.6364 (m-70) cc_final: 0.6061 (m-70) REVERT: F 54 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5888 (mpp80) REVERT: F 74 MET cc_start: 0.3195 (ptm) cc_final: 0.2953 (ptm) REVERT: F 115 TYR cc_start: 0.7977 (t80) cc_final: 0.7596 (t80) REVERT: F 142 ILE cc_start: 0.7464 (mm) cc_final: 0.7135 (mm) REVERT: F 287 LYS cc_start: 0.7497 (mttm) cc_final: 0.7238 (ttmt) REVERT: F 316 GLU cc_start: 0.6984 (tp30) cc_final: 0.6708 (tp30) REVERT: F 336 LYS cc_start: 0.8161 (mttp) cc_final: 0.7914 (mtmm) REVERT: F 409 ASN cc_start: 0.7815 (m-40) cc_final: 0.7576 (m-40) outliers start: 49 outliers final: 35 residues processed: 326 average time/residue: 0.2905 time to fit residues: 137.2422 Evaluate side-chains 338 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 300 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 212 ASN 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 127 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 346 ASP 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 119 SER Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 246 SER 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 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 85 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16838 Z= 0.247 Angle : 0.585 8.111 23128 Z= 0.310 Chirality : 0.042 0.190 2538 Planarity : 0.004 0.055 2632 Dihedral : 18.269 179.153 3014 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.14 % Allowed : 15.66 % Favored : 81.19 % 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: -0.52 (0.20), residues: 1764 helix: 1.53 (0.23), residues: 544 sheet: -0.01 (0.30), residues: 331 loop : -1.76 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 254 HIS 0.006 0.001 HIS F 207 PHE 0.028 0.002 PHE B 93 TYR 0.019 0.002 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 346 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 296 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ARG cc_start: 0.7066 (mtp85) cc_final: 0.6771 (mtp85) REVERT: A 213 TYR cc_start: 0.6551 (m-80) cc_final: 0.6045 (m-80) REVERT: A 279 ASP cc_start: 0.8075 (t70) cc_final: 0.7770 (t0) REVERT: A 366 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7551 (ttpt) REVERT: A 399 GLU cc_start: 0.7714 (mp0) cc_final: 0.7251 (mp0) REVERT: A 408 VAL cc_start: 0.8201 (t) cc_final: 0.7731 (p) REVERT: B 229 LEU cc_start: 0.8160 (mt) cc_final: 0.7954 (mp) REVERT: B 254 TRP cc_start: 0.7619 (m100) cc_final: 0.7335 (m100) REVERT: B 321 TYR cc_start: 0.8062 (m-80) cc_final: 0.7579 (m-80) REVERT: B 412 VAL cc_start: 0.8259 (t) cc_final: 0.7994 (p) REVERT: B 417 SER cc_start: 0.8044 (t) cc_final: 0.7696 (m) REVERT: E 4 LYS cc_start: 0.6874 (mttm) cc_final: 0.6534 (mtpp) REVERT: E 15 ASN cc_start: 0.5675 (m-40) cc_final: 0.5108 (m-40) REVERT: E 59 LYS cc_start: 0.7913 (tppt) cc_final: 0.7528 (tppt) REVERT: E 63 VAL cc_start: 0.7351 (t) cc_final: 0.7132 (p) REVERT: E 93 PHE cc_start: 0.6585 (t80) cc_final: 0.6156 (t80) REVERT: E 119 ASP cc_start: 0.8019 (t0) cc_final: 0.7659 (t0) REVERT: E 229 LYS cc_start: 0.4309 (tttt) cc_final: 0.4012 (tmtt) REVERT: F 16 HIS cc_start: 0.6314 (m-70) cc_final: 0.5986 (m-70) REVERT: F 40 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7524 (mptt) REVERT: F 54 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.5962 (mpp80) REVERT: F 74 MET cc_start: 0.3172 (ptm) cc_final: 0.2930 (ptm) REVERT: F 142 ILE cc_start: 0.7428 (mm) cc_final: 0.7074 (mm) REVERT: F 287 LYS cc_start: 0.7467 (mttm) cc_final: 0.7206 (ttmt) REVERT: F 311 THR cc_start: 0.8127 (t) cc_final: 0.7883 (p) REVERT: F 336 LYS cc_start: 0.7839 (mttp) cc_final: 0.7620 (mtmm) REVERT: F 409 ASN cc_start: 0.7703 (m-40) cc_final: 0.7479 (m-40) outliers start: 50 outliers final: 35 residues processed: 315 average time/residue: 0.2988 time to fit residues: 137.3461 Evaluate side-chains 328 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 291 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 352 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 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 437 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 121 optimal weight: 0.0770 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: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2962 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= 0.264 Angle : 0.596 8.718 23128 Z= 0.316 Chirality : 0.043 0.168 2538 Planarity : 0.004 0.061 2632 Dihedral : 18.300 177.545 3014 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.40 % Allowed : 15.85 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1764 helix: 1.36 (0.23), residues: 556 sheet: -0.04 (0.30), residues: 333 loop : -1.81 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 254 HIS 0.006 0.001 HIS F 207 PHE 0.028 0.002 PHE B 93 TYR 0.020 0.002 TYR A 171 ARG 0.004 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 365 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 295 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.6409 (tm-30) cc_final: 0.5584 (tm-30) REVERT: A 209 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6839 (mtp85) REVERT: A 213 TYR cc_start: 0.6553 (m-80) cc_final: 0.6247 (m-80) REVERT: A 245 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: A 263 ARG cc_start: 0.7741 (ttp80) cc_final: 0.6627 (ttp80) REVERT: A 269 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6544 (mt) REVERT: A 279 ASP cc_start: 0.8110 (t70) cc_final: 0.7834 (t0) REVERT: A 366 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7553 (ttpt) REVERT: A 400 LYS cc_start: 0.7379 (mttt) cc_final: 0.7119 (mttm) REVERT: A 408 VAL cc_start: 0.8154 (t) cc_final: 0.7694 (p) REVERT: A 411 LYS cc_start: 0.5494 (tttp) cc_final: 0.5106 (ttpp) REVERT: A 415 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8267 (m) REVERT: B 3 GLU cc_start: 0.6490 (mm-30) cc_final: 0.6163 (mm-30) REVERT: B 254 TRP cc_start: 0.7629 (m100) cc_final: 0.7385 (m100) REVERT: B 364 ARG cc_start: 0.7286 (mtt90) cc_final: 0.7061 (mtt90) REVERT: B 417 SER cc_start: 0.8006 (t) cc_final: 0.7668 (m) REVERT: E 4 LYS cc_start: 0.6889 (mttm) cc_final: 0.6535 (mtpp) REVERT: E 15 ASN cc_start: 0.5706 (m-40) cc_final: 0.5241 (m-40) REVERT: E 59 LYS cc_start: 0.7913 (tppt) cc_final: 0.7497 (tppt) REVERT: E 93 PHE cc_start: 0.6612 (t80) cc_final: 0.6165 (t80) REVERT: E 128 LEU cc_start: 0.7162 (tp) cc_final: 0.6841 (tp) REVERT: F 16 HIS cc_start: 0.6293 (m-70) cc_final: 0.5974 (m-70) REVERT: F 40 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7479 (mptt) REVERT: F 44 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7360 (mp) REVERT: F 54 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5478 (mpp80) REVERT: F 74 MET cc_start: 0.3342 (ptm) cc_final: 0.3114 (ptm) REVERT: F 142 ILE cc_start: 0.7447 (mm) cc_final: 0.7107 (mm) REVERT: F 287 LYS cc_start: 0.7467 (mttm) cc_final: 0.7231 (ttmt) REVERT: F 311 THR cc_start: 0.8180 (t) cc_final: 0.7921 (p) REVERT: F 316 GLU cc_start: 0.6826 (tp30) cc_final: 0.6594 (tp30) outliers start: 70 outliers final: 51 residues processed: 326 average time/residue: 0.2912 time to fit residues: 139.0537 Evaluate side-chains 346 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 289 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 172 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 352 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 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 122 MET Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 176 optimal weight: 0.2980 chunk 146 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3204 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= 0.247 Angle : 0.590 11.677 23128 Z= 0.311 Chirality : 0.042 0.169 2538 Planarity : 0.004 0.057 2632 Dihedral : 18.248 178.232 3014 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.90 % Allowed : 17.23 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.23), residues: 550 sheet: 0.03 (0.30), residues: 333 loop : -1.82 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 319 HIS 0.005 0.001 HIS F 207 PHE 0.028 0.002 PHE F 93 TYR 0.020 0.002 TYR A 251 ARG 0.006 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 354 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 292 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6294 (tpm170) cc_final: 0.6078 (tpm170) REVERT: A 189 GLU cc_start: 0.6509 (tm-30) cc_final: 0.5468 (tm-30) REVERT: A 209 ARG cc_start: 0.7150 (mtp85) cc_final: 0.6842 (mtp180) REVERT: A 213 TYR cc_start: 0.6558 (m-80) cc_final: 0.6267 (m-80) REVERT: A 244 GLU cc_start: 0.7777 (tp30) cc_final: 0.7480 (tp30) REVERT: A 279 ASP cc_start: 0.8089 (t70) cc_final: 0.7812 (t0) REVERT: A 366 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7471 (ttpt) REVERT: A 408 VAL cc_start: 0.8162 (t) cc_final: 0.7689 (p) REVERT: A 411 LYS cc_start: 0.5621 (tttp) cc_final: 0.5299 (ttpp) REVERT: B 254 TRP cc_start: 0.7659 (m100) cc_final: 0.7424 (m100) REVERT: B 364 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7094 (mtt90) REVERT: B 417 SER cc_start: 0.8007 (t) cc_final: 0.7634 (m) REVERT: E 4 LYS cc_start: 0.6866 (mttm) cc_final: 0.6504 (mtpp) REVERT: E 59 LYS cc_start: 0.7888 (tppt) cc_final: 0.7495 (tppt) REVERT: E 63 VAL cc_start: 0.7543 (t) cc_final: 0.7286 (p) REVERT: E 93 PHE cc_start: 0.6589 (t80) cc_final: 0.6186 (t80) REVERT: E 411 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7460 (tppt) REVERT: F 16 HIS cc_start: 0.6312 (m-70) cc_final: 0.5986 (m-70) REVERT: F 40 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7496 (mptt) REVERT: F 44 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7361 (mp) REVERT: F 74 MET cc_start: 0.3362 (ptm) cc_final: 0.3149 (ptm) REVERT: F 142 ILE cc_start: 0.7432 (mm) cc_final: 0.7089 (mm) REVERT: F 287 LYS cc_start: 0.7443 (mttm) cc_final: 0.7239 (mtmt) REVERT: F 311 THR cc_start: 0.8168 (t) cc_final: 0.7942 (p) REVERT: F 316 GLU cc_start: 0.6834 (tp30) cc_final: 0.6591 (tp30) outliers start: 62 outliers final: 55 residues processed: 317 average time/residue: 0.3006 time to fit residues: 141.4416 Evaluate side-chains 347 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 352 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 463 THR 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 191 ASN Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 392 TYR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 107 ASN F 296 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16838 Z= 0.260 Angle : 0.599 11.212 23128 Z= 0.316 Chirality : 0.042 0.210 2538 Planarity : 0.004 0.046 2632 Dihedral : 18.265 177.389 3014 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.96 % Allowed : 17.80 % Favored : 78.24 % 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: 1.40 (0.23), residues: 550 sheet: -0.02 (0.30), residues: 335 loop : -1.82 (0.20), residues: 879 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 0.028 0.002 PHE B 93 TYR 0.021 0.002 TYR A 251 ARG 0.006 0.000 ARG F 213 *********************** 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 353 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 290 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.6607 (tm-30) cc_final: 0.5423 (tm-30) REVERT: A 213 TYR cc_start: 0.6589 (m-80) cc_final: 0.6241 (m-80) REVERT: A 244 GLU cc_start: 0.7791 (tp30) cc_final: 0.7448 (tp30) REVERT: A 279 ASP cc_start: 0.8089 (t70) cc_final: 0.7798 (t0) REVERT: A 366 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7495 (ttpt) REVERT: A 408 VAL cc_start: 0.8137 (t) cc_final: 0.7684 (p) REVERT: A 411 LYS cc_start: 0.5701 (tttp) cc_final: 0.5156 (ttpp) REVERT: B 3 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6143 (mm-30) REVERT: B 9 GLU cc_start: 0.7649 (mp0) cc_final: 0.7258 (mp0) REVERT: B 364 ARG cc_start: 0.7306 (mtt90) cc_final: 0.7077 (mtt90) REVERT: B 417 SER cc_start: 0.8008 (t) cc_final: 0.7646 (m) REVERT: E 4 LYS cc_start: 0.6855 (mttm) cc_final: 0.6490 (mtpp) REVERT: E 59 LYS cc_start: 0.7876 (tppt) cc_final: 0.7513 (tppt) REVERT: E 63 VAL cc_start: 0.7632 (t) cc_final: 0.7349 (p) REVERT: E 93 PHE cc_start: 0.6620 (t80) cc_final: 0.6176 (t80) REVERT: E 269 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6562 (mt) REVERT: E 411 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7461 (tppt) REVERT: F 16 HIS cc_start: 0.6308 (m-70) cc_final: 0.5997 (m-70) REVERT: F 40 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7565 (mptt) REVERT: F 44 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7403 (mp) REVERT: F 74 MET cc_start: 0.3437 (ptm) cc_final: 0.3223 (ptm) REVERT: F 142 ILE cc_start: 0.7450 (mm) cc_final: 0.7117 (mm) REVERT: F 311 THR cc_start: 0.8161 (t) cc_final: 0.7957 (p) REVERT: F 316 GLU cc_start: 0.6854 (tp30) cc_final: 0.6611 (tp30) outliers start: 63 outliers final: 55 residues processed: 320 average time/residue: 0.2809 time to fit residues: 131.9911 Evaluate side-chains 344 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 286 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 352 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 191 ASN 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 336 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 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: 0.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 111 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 chunk 16 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 360 HIS ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16838 Z= 0.202 Angle : 0.568 9.843 23128 Z= 0.299 Chirality : 0.041 0.169 2538 Planarity : 0.004 0.049 2632 Dihedral : 18.227 178.543 3014 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.03 % Allowed : 18.11 % Favored : 77.86 % 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: -0.49 (0.20), residues: 1764 helix: 1.52 (0.23), residues: 550 sheet: -0.08 (0.28), residues: 375 loop : -1.78 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 319 HIS 0.004 0.001 HIS F 207 PHE 0.034 0.002 PHE F 93 TYR 0.022 0.001 TYR A 251 ARG 0.004 0.000 ARG F 213 *********************** 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 348 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 284 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.6616 (tm-30) cc_final: 0.5183 (tm-30) REVERT: A 209 ARG cc_start: 0.7038 (mtp85) cc_final: 0.6382 (mtp85) REVERT: A 213 TYR cc_start: 0.6568 (m-80) cc_final: 0.6284 (m-80) REVERT: A 244 GLU cc_start: 0.7765 (tp30) cc_final: 0.7543 (tp30) REVERT: A 279 ASP cc_start: 0.8103 (t70) cc_final: 0.7798 (t0) REVERT: A 366 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7488 (ttpt) REVERT: A 411 LYS cc_start: 0.5666 (tttp) cc_final: 0.5097 (ttpp) REVERT: B 9 GLU cc_start: 0.7597 (mp0) cc_final: 0.6944 (mt-10) REVERT: B 226 GLU cc_start: 0.7771 (mp0) cc_final: 0.7472 (mp0) REVERT: B 254 TRP cc_start: 0.7660 (m100) cc_final: 0.7379 (m100) REVERT: B 364 ARG cc_start: 0.7302 (mtt90) cc_final: 0.7088 (mtt90) REVERT: B 417 SER cc_start: 0.7982 (t) cc_final: 0.7652 (m) REVERT: E 4 LYS cc_start: 0.6821 (mttm) cc_final: 0.6455 (mtpp) REVERT: E 59 LYS cc_start: 0.7881 (tppt) cc_final: 0.7541 (tppt) REVERT: E 63 VAL cc_start: 0.7622 (t) cc_final: 0.7373 (p) REVERT: E 93 PHE cc_start: 0.6569 (t80) cc_final: 0.6164 (t80) REVERT: E 119 ASP cc_start: 0.8167 (t0) cc_final: 0.7794 (t0) REVERT: E 269 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6543 (mt) REVERT: E 411 LYS cc_start: 0.7677 (ttmt) cc_final: 0.7385 (tppt) REVERT: F 16 HIS cc_start: 0.6308 (m-70) cc_final: 0.5987 (m-70) REVERT: F 40 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7528 (mptt) REVERT: F 44 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7367 (mp) REVERT: F 74 MET cc_start: 0.3371 (ptm) cc_final: 0.3161 (ptm) REVERT: F 142 ILE cc_start: 0.7428 (mm) cc_final: 0.7120 (mm) REVERT: F 311 THR cc_start: 0.8165 (t) cc_final: 0.7957 (p) REVERT: F 316 GLU cc_start: 0.6795 (tp30) cc_final: 0.6564 (tp30) outliers start: 64 outliers final: 51 residues processed: 313 average time/residue: 0.2845 time to fit residues: 130.5396 Evaluate side-chains 336 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 282 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 SER 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 212 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 352 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 463 THR 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 191 ASN Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 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: 0.9980 chunk 168 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 154 optimal weight: 0.3980 chunk 162 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 HIS ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16838 Z= 0.215 Angle : 0.580 10.039 23128 Z= 0.305 Chirality : 0.042 0.168 2538 Planarity : 0.004 0.046 2632 Dihedral : 18.251 178.142 3014 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.77 % Allowed : 18.87 % Favored : 77.36 % 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: -0.48 (0.20), residues: 1764 helix: 1.49 (0.23), residues: 555 sheet: 0.07 (0.30), residues: 333 loop : -1.75 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 219 HIS 0.006 0.001 HIS B 217 PHE 0.032 0.002 PHE F 93 TYR 0.023 0.001 TYR A 251 ARG 0.004 0.000 ARG F 213 *********************** 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 344 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 284 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8383 (mt) cc_final: 0.8094 (mm) REVERT: A 183 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 189 GLU cc_start: 0.6651 (tm-30) cc_final: 0.5515 (tm-30) REVERT: A 213 TYR cc_start: 0.6575 (m-80) cc_final: 0.6268 (m-80) REVERT: A 245 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: A 279 ASP cc_start: 0.8071 (t70) cc_final: 0.7778 (t0) REVERT: A 303 ASP cc_start: 0.5650 (m-30) cc_final: 0.5169 (m-30) REVERT: A 366 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7488 (ttpt) REVERT: A 411 LYS cc_start: 0.5658 (tttp) cc_final: 0.5402 (ttpp) REVERT: B 9 GLU cc_start: 0.7609 (mp0) cc_final: 0.7262 (mt-10) REVERT: B 254 TRP cc_start: 0.7632 (m100) cc_final: 0.7371 (m100) REVERT: B 364 ARG cc_start: 0.7319 (mtt90) cc_final: 0.7102 (mtt90) REVERT: B 417 SER cc_start: 0.7957 (t) cc_final: 0.7629 (m) REVERT: E 4 LYS cc_start: 0.6820 (mttm) cc_final: 0.6459 (mtpp) REVERT: E 59 LYS cc_start: 0.7884 (tppt) cc_final: 0.7570 (tppt) REVERT: E 63 VAL cc_start: 0.7669 (t) cc_final: 0.7399 (p) REVERT: E 93 PHE cc_start: 0.6570 (t80) cc_final: 0.6160 (t80) REVERT: E 119 ASP cc_start: 0.8152 (t0) cc_final: 0.7779 (t0) REVERT: E 269 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6550 (mt) REVERT: E 411 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7378 (tppt) REVERT: F 14 PHE cc_start: 0.7492 (m-80) cc_final: 0.7178 (m-80) REVERT: F 16 HIS cc_start: 0.6314 (m-70) cc_final: 0.6025 (m-70) REVERT: F 40 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7564 (mptt) REVERT: F 44 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7367 (mp) REVERT: F 74 MET cc_start: 0.3387 (ptm) cc_final: 0.3177 (ptm) REVERT: F 142 ILE cc_start: 0.7440 (mm) cc_final: 0.7139 (mm) REVERT: F 311 THR cc_start: 0.8177 (t) cc_final: 0.7977 (p) REVERT: F 316 GLU cc_start: 0.6802 (tp30) cc_final: 0.6565 (tp30) outliers start: 60 outliers final: 48 residues processed: 313 average time/residue: 0.2933 time to fit residues: 135.0296 Evaluate side-chains 332 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 280 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 SER 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 291 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 352 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS 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 463 THR 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 191 ASN Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 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: 4.9990 chunk 172 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16838 Z= 0.249 Angle : 0.605 10.271 23128 Z= 0.318 Chirality : 0.042 0.175 2538 Planarity : 0.004 0.046 2632 Dihedral : 18.314 177.764 3014 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.46 % Allowed : 19.43 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1764 helix: 1.40 (0.23), residues: 555 sheet: 0.01 (0.30), residues: 335 loop : -1.73 (0.20), residues: 874 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 0.022 0.001 TYR A 251 ARG 0.005 0.000 ARG B 213 ********************** 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 334 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 279 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8430 (mt) cc_final: 0.8137 (mm) REVERT: A 183 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 189 GLU cc_start: 0.6722 (tm-30) cc_final: 0.5708 (tp30) REVERT: A 213 TYR cc_start: 0.6592 (m-80) cc_final: 0.6028 (m-80) REVERT: A 279 ASP cc_start: 0.8093 (t70) cc_final: 0.7796 (t0) REVERT: A 366 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7496 (ttpt) REVERT: A 411 LYS cc_start: 0.5762 (tttp) cc_final: 0.5436 (ttpp) REVERT: B 9 GLU cc_start: 0.7680 (mp0) cc_final: 0.7078 (mt-10) REVERT: B 254 TRP cc_start: 0.7660 (m100) cc_final: 0.7386 (m100) REVERT: B 364 ARG cc_start: 0.7328 (mtt90) cc_final: 0.7091 (mtt90) REVERT: B 417 SER cc_start: 0.7961 (t) cc_final: 0.7625 (m) REVERT: E 4 LYS cc_start: 0.6832 (mttm) cc_final: 0.6449 (mtpp) REVERT: E 59 LYS cc_start: 0.7882 (tppt) cc_final: 0.7574 (tppt) REVERT: E 63 VAL cc_start: 0.7694 (t) cc_final: 0.7410 (p) REVERT: E 93 PHE cc_start: 0.6592 (t80) cc_final: 0.6203 (t80) REVERT: E 269 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6537 (mt) REVERT: E 411 LYS cc_start: 0.7600 (ttmt) cc_final: 0.7375 (tppt) REVERT: F 14 PHE cc_start: 0.7492 (m-80) cc_final: 0.7270 (m-80) REVERT: F 16 HIS cc_start: 0.6329 (m-70) cc_final: 0.6036 (m-70) REVERT: F 40 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7534 (mptt) REVERT: F 44 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7391 (mp) REVERT: F 74 MET cc_start: 0.3487 (ptm) cc_final: 0.3280 (ptm) REVERT: F 142 ILE cc_start: 0.7474 (mm) cc_final: 0.7173 (mm) REVERT: F 243 ARG cc_start: 0.6816 (mtm180) cc_final: 0.6300 (mtm180) REVERT: F 311 THR cc_start: 0.8173 (t) cc_final: 0.7965 (p) outliers start: 55 outliers final: 49 residues processed: 303 average time/residue: 0.3144 time to fit residues: 141.1053 Evaluate side-chains 332 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 280 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 352 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 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 298 CYS 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 463 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 307 ASN Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 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: 0.8980 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 0.0000 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.187625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154805 restraints weight = 24538.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158806 restraints weight = 14355.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.161340 restraints weight = 10204.519| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16838 Z= 0.250 Angle : 0.607 10.167 23128 Z= 0.320 Chirality : 0.042 0.172 2538 Planarity : 0.004 0.045 2632 Dihedral : 18.315 177.691 3014 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.40 % Allowed : 19.62 % Favored : 76.98 % 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: -0.54 (0.20), residues: 1764 helix: 1.42 (0.23), residues: 554 sheet: -0.02 (0.30), residues: 335 loop : -1.75 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 370 HIS 0.005 0.001 HIS F 207 PHE 0.033 0.002 PHE F 93 TYR 0.022 0.001 TYR A 251 ARG 0.004 0.000 ARG F 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3676.93 seconds wall clock time: 68 minutes 19.33 seconds (4099.33 seconds total)