Starting phenix.real_space_refine on Mon Aug 5 08:18:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/08_2024/8z9a_39858_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/08_2024/8z9a_39858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/08_2024/8z9a_39858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/08_2024/8z9a_39858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/08_2024/8z9a_39858_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9a_39858/08_2024/8z9a_39858_neut.cif" } resolution = 3.0 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= 0.007 sd= 0.129 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 72 5.16 5 C 8695 2.51 5 N 1981 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 11": "OD1" <-> "OD2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "B ASP 6": "OD1" <-> "OD2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "D ASP 5": "OD1" <-> "OD2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ASP 290": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13021 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 395} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 395} Chain breaks: 1 Chain: "C" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3140 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 379} Chain breaks: 2 Chain: "D" Number of atoms: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2905 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 7, 'TRANS': 349} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'PC1': 1, 'SOU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.50, per 1000 atoms: 0.58 Number of scatterers: 13021 At special positions: 0 Unit cell: (115.56, 129.47, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 7 15.00 O 2266 8.00 N 1981 7.00 C 8695 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: 5.32 Conformation dependent library (CDL) restraints added in 2.3 seconds 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2994 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 80.7% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.593A pdb=" N ASP A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.657A pdb=" N GLY A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 65 removed outlier: 3.740A pdb=" N MET A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 95 removed outlier: 3.754A pdb=" N HIS A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.933A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 116 through 152 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 191 through 237 removed outlier: 3.525A pdb=" N GLU A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.700A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 336 Processing helix chain 'A' and resid 337 through 359 removed outlier: 3.787A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 405 removed outlier: 3.558A pdb=" N ILE A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N MET A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 441 through 463 removed outlier: 3.549A pdb=" N PHE A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.521A pdb=" N ASP B 11 " --> pdb=" O GLY B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 36 through 66 Processing helix chain 'B' and resid 69 through 95 removed outlier: 3.807A pdb=" N HIS B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 3.888A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 116 through 152 removed outlier: 3.656A pdb=" N SER B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 156 removed outlier: 4.256A pdb=" N GLY B 156 " --> pdb=" O THR B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 191 through 237 removed outlier: 3.522A pdb=" N TYR B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 245 removed outlier: 3.590A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 336 Processing helix chain 'B' and resid 337 through 359 removed outlier: 3.834A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 398 removed outlier: 3.961A pdb=" N PHE B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS B 388 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 441 through 463 removed outlier: 3.672A pdb=" N PHE B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 36 through 66 Processing helix chain 'C' and resid 69 through 95 removed outlier: 3.698A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 removed outlier: 3.906A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TRP C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 149 removed outlier: 4.176A pdb=" N LYS C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 127 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 135 " --> pdb=" O MET C 131 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 237 removed outlier: 3.702A pdb=" N ILE C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 304 through 336 Processing helix chain 'C' and resid 336 through 358 removed outlier: 3.838A pdb=" N LEU C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 397 removed outlier: 3.903A pdb=" N ILE C 382 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 426 Processing helix chain 'C' and resid 441 through 463 Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.954A pdb=" N MET D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 46 Processing helix chain 'D' and resid 50 through 77 removed outlier: 3.566A pdb=" N PHE D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 124 Proline residue: D 119 - end of helix Processing helix chain 'D' and resid 149 through 200 removed outlier: 3.925A pdb=" N SER D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 164 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 256 removed outlier: 5.032A pdb=" N LYS D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 263 through 271 removed outlier: 3.952A pdb=" N ALA D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.746A pdb=" N ASN D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 removed outlier: 3.876A pdb=" N LYS D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 310 through 322 Processing helix chain 'D' and resid 337 through 360 removed outlier: 3.930A pdb=" N LEU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 433 through 434 removed outlier: 3.919A pdb=" N PHE A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 163 Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 330 960 hydrogen bonds defined for protein. 2862 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1889 1.31 - 1.44: 3948 1.44 - 1.57: 7391 1.57 - 1.69: 15 1.69 - 1.82: 116 Bond restraints: 13359 Sorted by residual: bond pdb=" CA SER D 271 " pdb=" CB SER D 271 " ideal model delta sigma weight residual 1.536 1.443 0.093 1.53e-02 4.27e+03 3.72e+01 bond pdb=" CA SER D 270 " pdb=" CB SER D 270 " ideal model delta sigma weight residual 1.531 1.438 0.093 1.72e-02 3.38e+03 2.90e+01 bond pdb=" C21 PC1 B 502 " pdb=" O21 PC1 B 502 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C21 PC1 C 501 " pdb=" O21 PC1 C 501 " ideal model delta sigma weight residual 1.331 1.405 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C21 PC1 A 502 " pdb=" O21 PC1 A 502 " ideal model delta sigma weight residual 1.331 1.405 -0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 13354 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.86: 175 105.86 - 112.91: 7527 112.91 - 119.96: 4444 119.96 - 127.01: 5793 127.01 - 134.06: 145 Bond angle restraints: 18084 Sorted by residual: angle pdb=" CA PRO D 119 " pdb=" N PRO D 119 " pdb=" CD PRO D 119 " ideal model delta sigma weight residual 112.00 103.08 8.92 1.40e+00 5.10e-01 4.06e+01 angle pdb=" N ILE D 124 " pdb=" CA ILE D 124 " pdb=" C ILE D 124 " ideal model delta sigma weight residual 112.29 106.85 5.44 9.40e-01 1.13e+00 3.35e+01 angle pdb=" N SER D 271 " pdb=" CA SER D 271 " pdb=" C SER D 271 " ideal model delta sigma weight residual 113.72 106.48 7.24 1.30e+00 5.92e-01 3.10e+01 angle pdb=" O12 PC1 C 501 " pdb=" P PC1 C 501 " pdb=" O14 PC1 C 501 " ideal model delta sigma weight residual 123.67 109.06 14.61 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O12 PC1 B 502 " pdb=" P PC1 B 502 " pdb=" O14 PC1 B 502 " ideal model delta sigma weight residual 123.67 109.29 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 18079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6812 17.71 - 35.42: 731 35.42 - 53.14: 212 53.14 - 70.85: 60 70.85 - 88.56: 11 Dihedral angle restraints: 7826 sinusoidal: 3199 harmonic: 4627 Sorted by residual: dihedral pdb=" CA ASP D 133 " pdb=" C ASP D 133 " pdb=" N PRO D 134 " pdb=" CA PRO D 134 " ideal model delta harmonic sigma weight residual -180.00 -134.40 -45.60 0 5.00e+00 4.00e-02 8.32e+01 dihedral pdb=" CA VAL D 307 " pdb=" C VAL D 307 " pdb=" N SER D 308 " pdb=" CA SER D 308 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA SER D 310 " pdb=" C SER D 310 " pdb=" N PHE D 311 " pdb=" CA PHE D 311 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 7823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1357 0.032 - 0.064: 505 0.064 - 0.096: 151 0.096 - 0.127: 42 0.127 - 0.159: 8 Chirality restraints: 2063 Sorted by residual: chirality pdb=" C2 PC1 B 502 " pdb=" C1 PC1 B 502 " pdb=" C3 PC1 B 502 " pdb=" O21 PC1 B 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB ILE C 237 " pdb=" CA ILE C 237 " pdb=" CG1 ILE C 237 " pdb=" CG2 ILE C 237 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" C2 PC1 A 502 " pdb=" C1 PC1 A 502 " pdb=" C3 PC1 A 502 " pdb=" O21 PC1 A 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2060 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SOU D 402 " 0.051 2.00e-02 2.50e+03 1.38e-01 2.39e+02 pdb=" C11 SOU D 402 " 0.015 2.00e-02 2.50e+03 pdb=" C12 SOU D 402 " -0.124 2.00e-02 2.50e+03 pdb=" C8 SOU D 402 " -0.165 2.00e-02 2.50e+03 pdb=" C9 SOU D 402 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 SOU D 402 " -0.106 2.00e-02 2.50e+03 8.76e-02 9.59e+01 pdb=" C4 SOU D 402 " 0.137 2.00e-02 2.50e+03 pdb=" C5 SOU D 402 " 0.032 2.00e-02 2.50e+03 pdb=" C6 SOU D 402 " 0.019 2.00e-02 2.50e+03 pdb=" C7 SOU D 402 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 118 " -0.085 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO D 119 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.066 5.00e-02 4.00e+02 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 340 2.71 - 3.26: 13266 3.26 - 3.81: 21982 3.81 - 4.35: 26751 4.35 - 4.90: 46142 Nonbonded interactions: 108481 Sorted by model distance: nonbonded pdb=" O VAL D 116 " pdb=" OH TYR D 157 " model vdw 2.163 3.040 nonbonded pdb=" OE2 GLU A 320 " pdb=" OH TYR C 409 " model vdw 2.180 3.040 nonbonded pdb=" O PHE D 10 " pdb=" OG1 THR D 14 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR B 409 " pdb=" OE2 GLU C 320 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR C 92 " pdb=" OG SER C 338 " model vdw 2.215 3.040 ... (remaining 108476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 156 or resid 175 through 463 or resid 501)) selection = (chain 'B' and (resid 5 through 156 or resid 175 through 463 or resid 501)) selection = chain 'C' } 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 individual isotropic 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.060 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.005 0.093 13359 Z= 0.341 Angle : 0.835 14.611 18084 Z= 0.361 Chirality : 0.039 0.159 2063 Planarity : 0.006 0.138 2140 Dihedral : 16.754 88.562 4832 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.56 % Allowed : 17.41 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 2.18 (0.22), residues: 1541 helix: 2.10 (0.15), residues: 1209 sheet: 1.55 (1.04), residues: 24 loop : -1.28 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.004 0.001 HIS A 388 PHE 0.020 0.001 PHE B 385 TYR 0.021 0.001 TYR C 44 ARG 0.007 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: D 5 ASP cc_start: 0.7007 (t0) cc_final: 0.6762 (t0) outliers start: 22 outliers final: 19 residues processed: 188 average time/residue: 1.0155 time to fit residues: 212.2207 Evaluate side-chains 175 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 322 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN C 72 GLN C 214 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13359 Z= 0.235 Angle : 0.475 7.549 18084 Z= 0.251 Chirality : 0.038 0.160 2063 Planarity : 0.004 0.076 2140 Dihedral : 11.767 77.802 2040 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.33 % Allowed : 14.65 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 2.70 (0.22), residues: 1541 helix: 2.47 (0.15), residues: 1217 sheet: 1.69 (1.07), residues: 24 loop : -1.22 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 408 HIS 0.004 0.001 HIS C 343 PHE 0.022 0.001 PHE B 385 TYR 0.018 0.001 TYR C 53 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 1.400 Fit side-chains REVERT: A 312 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7777 (ttt-90) REVERT: B 42 LYS cc_start: 0.7648 (mtpt) cc_final: 0.7063 (mmtt) REVERT: B 178 ARG cc_start: 0.8513 (ttm170) cc_final: 0.8237 (ttm170) REVERT: C 135 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6981 (tp) REVERT: C 136 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6624 (pp) REVERT: D 5 ASP cc_start: 0.6954 (t0) cc_final: 0.6643 (t0) REVERT: D 309 LYS cc_start: 0.8887 (tmtt) cc_final: 0.8409 (tptt) outliers start: 47 outliers final: 19 residues processed: 203 average time/residue: 1.0649 time to fit residues: 239.1386 Evaluate side-chains 173 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13359 Z= 0.170 Angle : 0.439 7.733 18084 Z= 0.232 Chirality : 0.037 0.160 2063 Planarity : 0.003 0.067 2140 Dihedral : 11.141 77.704 2021 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.04 % Allowed : 15.71 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 3.02 (0.22), residues: 1541 helix: 2.72 (0.14), residues: 1216 sheet: 1.67 (1.04), residues: 24 loop : -1.19 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS A 233 PHE 0.018 0.001 PHE A 385 TYR 0.020 0.001 TYR C 53 ARG 0.007 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 172 time to evaluate : 1.461 Fit side-chains REVERT: A 312 ARG cc_start: 0.8087 (ttt180) cc_final: 0.7685 (mtp180) REVERT: B 42 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7039 (mmtt) REVERT: B 178 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8120 (ttm170) REVERT: C 135 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7003 (tp) REVERT: C 136 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6785 (pp) REVERT: D 5 ASP cc_start: 0.6907 (t0) cc_final: 0.6594 (t0) outliers start: 43 outliers final: 16 residues processed: 197 average time/residue: 1.0324 time to fit residues: 225.6928 Evaluate side-chains 168 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 400 MET Chi-restraints excluded: chain C residue 462 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS D 214 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13359 Z= 0.285 Angle : 0.494 8.421 18084 Z= 0.257 Chirality : 0.039 0.157 2063 Planarity : 0.003 0.062 2140 Dihedral : 11.251 88.747 2019 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.96 % Allowed : 15.85 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 2.92 (0.22), residues: 1541 helix: 2.63 (0.14), residues: 1213 sheet: 1.69 (1.02), residues: 24 loop : -1.11 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 408 HIS 0.006 0.001 HIS A 233 PHE 0.025 0.001 PHE B 385 TYR 0.021 0.001 TYR C 53 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 170 time to evaluate : 1.411 Fit side-chains REVERT: A 312 ARG cc_start: 0.8120 (ttt180) cc_final: 0.7662 (mtp180) REVERT: A 384 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8202 (tpp) REVERT: B 42 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7108 (mmtt) REVERT: B 178 ARG cc_start: 0.8432 (ttm170) cc_final: 0.8061 (ttm170) REVERT: C 21 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7558 (mt) REVERT: C 136 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.6895 (pp) REVERT: C 216 MET cc_start: 0.8328 (mmp) cc_final: 0.8027 (mmt) REVERT: D 5 ASP cc_start: 0.6890 (t0) cc_final: 0.6557 (t0) outliers start: 56 outliers final: 24 residues processed: 207 average time/residue: 1.0259 time to fit residues: 235.6313 Evaluate side-chains 186 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS C 424 GLN D 214 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13359 Z= 0.205 Angle : 0.465 9.261 18084 Z= 0.242 Chirality : 0.037 0.153 2063 Planarity : 0.003 0.058 2140 Dihedral : 11.036 88.070 2019 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.04 % Allowed : 17.76 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 3.07 (0.22), residues: 1541 helix: 2.74 (0.14), residues: 1213 sheet: 1.75 (1.00), residues: 24 loop : -1.09 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.011 0.001 HIS B 407 PHE 0.019 0.001 PHE A 385 TYR 0.018 0.001 TYR C 53 ARG 0.008 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 1.426 Fit side-chains REVERT: A 312 ARG cc_start: 0.8107 (ttt180) cc_final: 0.7651 (mtp180) REVERT: A 384 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8246 (tpp) REVERT: B 42 LYS cc_start: 0.7661 (mtpt) cc_final: 0.7109 (mmtt) REVERT: B 178 ARG cc_start: 0.8432 (ttm170) cc_final: 0.8046 (ttm170) REVERT: B 462 LEU cc_start: 0.7474 (tt) cc_final: 0.7042 (mp) REVERT: C 21 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7520 (mt) REVERT: C 136 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6962 (pp) REVERT: D 5 ASP cc_start: 0.6961 (t0) cc_final: 0.6677 (t0) REVERT: D 86 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7973 (tp-100) outliers start: 43 outliers final: 22 residues processed: 199 average time/residue: 1.0456 time to fit residues: 230.4652 Evaluate side-chains 181 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13359 Z= 0.176 Angle : 0.450 9.882 18084 Z= 0.234 Chirality : 0.037 0.148 2063 Planarity : 0.003 0.057 2140 Dihedral : 10.807 87.532 2019 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.04 % Allowed : 18.05 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.19 (0.22), residues: 1541 helix: 2.85 (0.14), residues: 1213 sheet: 1.87 (1.00), residues: 24 loop : -1.12 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.003 0.001 HIS A 233 PHE 0.017 0.001 PHE A 385 TYR 0.020 0.001 TYR B 92 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 1.434 Fit side-chains REVERT: A 312 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7635 (mtp180) REVERT: A 395 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: B 42 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7143 (mmtt) REVERT: B 178 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8227 (ttm170) REVERT: B 199 PHE cc_start: 0.8554 (t80) cc_final: 0.8253 (t80) REVERT: B 461 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: B 462 LEU cc_start: 0.7413 (tt) cc_final: 0.7049 (mp) REVERT: C 21 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7493 (mt) REVERT: C 136 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7002 (pp) REVERT: D 5 ASP cc_start: 0.6942 (t0) cc_final: 0.6670 (t0) REVERT: D 86 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7906 (tp-100) outliers start: 43 outliers final: 22 residues processed: 198 average time/residue: 1.1016 time to fit residues: 241.0086 Evaluate side-chains 183 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13359 Z= 0.254 Angle : 0.493 10.900 18084 Z= 0.254 Chirality : 0.038 0.148 2063 Planarity : 0.003 0.056 2140 Dihedral : 10.994 89.854 2019 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.18 % Allowed : 18.40 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.04 (0.22), residues: 1541 helix: 2.72 (0.14), residues: 1214 sheet: 1.83 (1.00), residues: 24 loop : -1.12 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 13 HIS 0.004 0.001 HIS A 212 PHE 0.023 0.001 PHE B 385 TYR 0.019 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 167 time to evaluate : 1.530 Fit side-chains REVERT: A 98 LYS cc_start: 0.8080 (mptm) cc_final: 0.7499 (mmtt) REVERT: A 229 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 312 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7663 (mtp180) REVERT: A 395 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: B 42 LYS cc_start: 0.7663 (mtpt) cc_final: 0.7114 (mmtt) REVERT: B 178 ARG cc_start: 0.8418 (ttm170) cc_final: 0.8157 (ttm170) REVERT: B 462 LEU cc_start: 0.7475 (tt) cc_final: 0.7125 (mp) REVERT: C 21 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 63 MET cc_start: 0.8101 (ttp) cc_final: 0.7854 (ttp) REVERT: C 136 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7066 (pp) REVERT: D 5 ASP cc_start: 0.6916 (t0) cc_final: 0.6651 (t0) outliers start: 45 outliers final: 25 residues processed: 197 average time/residue: 1.0927 time to fit residues: 237.5499 Evaluate side-chains 188 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS B 407 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13359 Z= 0.154 Angle : 0.455 11.288 18084 Z= 0.234 Chirality : 0.036 0.143 2063 Planarity : 0.003 0.054 2140 Dihedral : 10.722 88.354 2019 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.19 % Allowed : 19.32 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.31 (0.22), residues: 1541 helix: 2.93 (0.14), residues: 1212 sheet: 1.89 (0.99), residues: 24 loop : -1.07 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 408 HIS 0.008 0.001 HIS B 407 PHE 0.015 0.001 PHE A 385 TYR 0.022 0.001 TYR B 92 ARG 0.007 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.413 Fit side-chains REVERT: A 98 LYS cc_start: 0.8013 (mptm) cc_final: 0.7436 (mmtt) REVERT: A 312 ARG cc_start: 0.8064 (ttt180) cc_final: 0.7608 (mtp180) REVERT: A 395 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: A 436 LYS cc_start: 0.8420 (mttp) cc_final: 0.8044 (mtmp) REVERT: B 42 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7143 (mmtt) REVERT: B 178 ARG cc_start: 0.8417 (ttm170) cc_final: 0.8214 (ttm170) REVERT: B 199 PHE cc_start: 0.8547 (t80) cc_final: 0.8258 (t80) REVERT: B 461 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6274 (tp40) REVERT: B 462 LEU cc_start: 0.7418 (tt) cc_final: 0.7122 (mp) REVERT: C 21 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7585 (mt) REVERT: C 63 MET cc_start: 0.8086 (ttp) cc_final: 0.7838 (ttp) REVERT: C 129 SER cc_start: 0.7749 (t) cc_final: 0.7389 (m) REVERT: C 136 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7091 (pp) REVERT: D 5 ASP cc_start: 0.6938 (t0) cc_final: 0.6657 (t0) outliers start: 31 outliers final: 16 residues processed: 191 average time/residue: 1.0200 time to fit residues: 216.3406 Evaluate side-chains 177 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 0.4980 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS B 407 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13359 Z= 0.166 Angle : 0.471 12.634 18084 Z= 0.239 Chirality : 0.037 0.141 2063 Planarity : 0.003 0.054 2140 Dihedral : 10.509 88.654 2019 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.19 % Allowed : 19.89 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.33 (0.22), residues: 1541 helix: 2.93 (0.14), residues: 1215 sheet: 1.88 (0.99), residues: 24 loop : -1.02 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.003 0.001 HIS B 407 PHE 0.016 0.001 PHE B 385 TYR 0.025 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.428 Fit side-chains REVERT: A 229 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: A 312 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7645 (mtp180) REVERT: A 395 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: A 436 LYS cc_start: 0.8434 (mttp) cc_final: 0.8042 (mtmp) REVERT: B 42 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7146 (mmtt) REVERT: B 178 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8220 (ttm170) REVERT: B 199 PHE cc_start: 0.8567 (t80) cc_final: 0.8249 (t80) REVERT: B 461 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6295 (tp40) REVERT: B 462 LEU cc_start: 0.7413 (tt) cc_final: 0.7140 (mp) REVERT: C 63 MET cc_start: 0.8083 (ttp) cc_final: 0.7833 (ttp) REVERT: C 87 MET cc_start: 0.8173 (mmp) cc_final: 0.7139 (mmt) REVERT: C 129 SER cc_start: 0.7707 (t) cc_final: 0.7326 (m) REVERT: C 136 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7050 (pp) REVERT: C 244 LEU cc_start: 0.8640 (tt) cc_final: 0.8377 (pp) REVERT: D 5 ASP cc_start: 0.6925 (t0) cc_final: 0.6656 (t0) outliers start: 31 outliers final: 19 residues processed: 187 average time/residue: 1.0317 time to fit residues: 213.9936 Evaluate side-chains 184 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13359 Z= 0.203 Angle : 0.491 13.051 18084 Z= 0.249 Chirality : 0.037 0.156 2063 Planarity : 0.003 0.055 2140 Dihedral : 10.417 89.655 2019 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.05 % Allowed : 19.89 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.24 (0.22), residues: 1541 helix: 2.86 (0.14), residues: 1213 sheet: 1.90 (0.99), residues: 24 loop : -1.02 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 408 HIS 0.003 0.001 HIS B 233 PHE 0.020 0.001 PHE B 385 TYR 0.027 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.483 Fit side-chains REVERT: A 229 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: A 312 ARG cc_start: 0.8125 (ttt180) cc_final: 0.7645 (mtp180) REVERT: A 395 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: A 436 LYS cc_start: 0.8431 (mttp) cc_final: 0.8047 (mtmp) REVERT: B 461 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6388 (tp40) REVERT: B 462 LEU cc_start: 0.7477 (tt) cc_final: 0.7197 (mp) REVERT: C 87 MET cc_start: 0.8184 (mmp) cc_final: 0.7204 (mmt) REVERT: C 129 SER cc_start: 0.7747 (t) cc_final: 0.7347 (m) REVERT: C 136 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7059 (pp) REVERT: D 5 ASP cc_start: 0.6931 (t0) cc_final: 0.6650 (t0) outliers start: 29 outliers final: 19 residues processed: 186 average time/residue: 1.0789 time to fit residues: 222.6392 Evaluate side-chains 184 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 0.0370 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 307 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105653 restraints weight = 15122.899| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.11 r_work: 0.2920 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13359 Z= 0.198 Angle : 0.488 13.065 18084 Z= 0.248 Chirality : 0.037 0.150 2063 Planarity : 0.003 0.054 2140 Dihedral : 10.316 89.711 2019 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.05 % Allowed : 20.10 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.27 (0.22), residues: 1541 helix: 2.87 (0.14), residues: 1212 sheet: 1.97 (0.98), residues: 24 loop : -0.93 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.005 0.001 HIS B 407 PHE 0.018 0.001 PHE B 385 TYR 0.028 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.56 seconds wall clock time: 76 minutes 48.44 seconds (4608.44 seconds total)