Starting phenix.real_space_refine on Fri Mar 15 00:01:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plw_13504/03_2024/7plw_13504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plw_13504/03_2024/7plw_13504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plw_13504/03_2024/7plw_13504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plw_13504/03_2024/7plw_13504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plw_13504/03_2024/7plw_13504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plw_13504/03_2024/7plw_13504_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.001 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 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1722 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10139 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.39, per 1000 atoms: 0.63 Number of scatterers: 10139 At special positions: 0 Unit cell: (107.06, 134.62, 148.4, 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 63 16.00 P 2 15.00 Mg 1 11.99 O 1889 8.00 N 1722 7.00 C 6462 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: 4.27 Conformation dependent library (CDL) restraints added in 1.8 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2378 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 12 sheets defined 49.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.304A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.277A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.741A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.983A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.572A pdb=" N LYS A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.667A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLY A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.879A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.550A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.764A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.542A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.641A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.829A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 636 through 651 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.612A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 714 removed outlier: 6.384A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 753 through 791 removed outlier: 3.982A pdb=" N VAL A 756 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.999A pdb=" N GLN C 59 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.829A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 4.457A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.067A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 4.381A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 Proline residue: C 258 - end of helix removed outlier: 4.736A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.735A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.502A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 345 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.701A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.104A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 12 through 16 Processing sheet with id= C, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.657A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= E, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= F, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.652A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.448A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 8 through 11 removed outlier: 3.571A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.417A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 439 hydrogen bonds defined for protein. 1140 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: 3.19 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1694 1.32 - 1.44: 2731 1.44 - 1.56: 5825 1.56 - 1.69: 3 1.69 - 1.81: 102 Bond restraints: 10355 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.453 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.198 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.40e-02 5.10e+03 9.55e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.466 0.059 2.10e-02 2.27e+03 7.81e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.398 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 10350 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.78: 309 106.78 - 114.18: 5910 114.18 - 121.58: 5505 121.58 - 128.98: 2193 128.98 - 136.38: 68 Bond angle restraints: 13985 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.69 11.01 1.80e+00 3.09e-01 3.74e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 108.88 -5.88 1.10e+00 8.26e-01 2.86e+01 angle pdb=" C TYR A 113 " pdb=" N GLU A 114 " pdb=" CA GLU A 114 " ideal model delta sigma weight residual 121.63 131.46 -9.83 1.92e+00 2.71e-01 2.62e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.20 4.20 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA EEP H 2 " pdb=" CB EEP H 2 " pdb=" CG EEP H 2 " ideal model delta sigma weight residual 115.99 103.73 12.26 3.00e+00 1.11e-01 1.67e+01 ... (remaining 13980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 6081 30.36 - 60.71: 127 60.71 - 91.07: 38 91.07 - 121.43: 0 121.43 - 151.78: 3 Dihedral angle restraints: 6249 sinusoidal: 2560 harmonic: 3689 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.78 -151.78 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 83.00 -143.00 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 175.06 124.95 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 6246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1078 0.048 - 0.096: 345 0.096 - 0.144: 93 0.144 - 0.192: 9 0.192 - 0.239: 3 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CA GLU A 512 " pdb=" N GLU A 512 " pdb=" C GLU A 512 " pdb=" CB GLU A 512 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA PHE C 255 " pdb=" N PHE C 255 " pdb=" C PHE C 255 " pdb=" CB PHE C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1525 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 196 " 0.133 9.50e-02 1.11e+02 7.65e-02 3.08e+01 pdb=" NE ARG C 196 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG C 196 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG C 196 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG C 196 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.004 2.00e-02 2.50e+03 3.78e-02 2.86e+01 pdb=" CG TYR C 306 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.113 9.50e-02 1.11e+02 6.59e-02 2.37e+01 pdb=" NE ARG A 677 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.023 2.00e-02 2.50e+03 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 2 2.04 - 2.75: 1288 2.75 - 3.47: 14461 3.47 - 4.18: 23557 4.18 - 4.90: 41905 Nonbonded interactions: 81213 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.323 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" OG SER A 78 " pdb=" O ALA A 753 " model vdw 2.168 2.440 nonbonded pdb=" N TRP H 1 " pdb=" O ALA H 7 " model vdw 2.196 2.520 nonbonded pdb=" OD1 ASP C 11 " pdb=" OG1 THR C 106 " model vdw 2.204 2.440 ... (remaining 81208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.110 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 31.810 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 0.119 10355 Z= 0.331 Angle : 0.843 12.259 13985 Z= 0.499 Chirality : 0.050 0.239 1528 Planarity : 0.008 0.116 1790 Dihedral : 15.157 151.783 3871 Min Nonbonded Distance : 1.323 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.69 (0.20), residues: 1236 helix: -1.74 (0.17), residues: 598 sheet: 0.50 (0.39), residues: 144 loop : -0.54 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 356 HIS 0.011 0.002 HIS A 418 PHE 0.037 0.003 PHE A 564 TYR 0.075 0.006 TYR A 113 ARG 0.093 0.011 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8263 (m-40) cc_final: 0.7988 (m-40) REVERT: B 50 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8839 (pttm) REVERT: B 110 ARG cc_start: 0.9072 (mtt-85) cc_final: 0.8447 (tpp80) REVERT: A 478 MET cc_start: 0.8209 (mmt) cc_final: 0.7822 (mmt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2817 time to fit residues: 57.6816 Evaluate side-chains 79 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 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 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 354 HIS A 463 GLN A 497 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN C 128 ASN C 162 ASN C 280 ASN C 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10355 Z= 0.189 Angle : 0.619 8.557 13985 Z= 0.330 Chirality : 0.042 0.191 1528 Planarity : 0.005 0.057 1790 Dihedral : 9.584 153.089 1397 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.02 % Allowed : 4.53 % Favored : 94.45 % 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: 0.47 (0.23), residues: 1236 helix: 0.45 (0.20), residues: 599 sheet: 0.79 (0.39), residues: 154 loop : 0.19 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.026 0.002 PHE B 12 TYR 0.029 0.001 TYR A 113 ARG 0.005 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8830 (mtp) cc_final: 0.8503 (mmm) REVERT: B 45 ASN cc_start: 0.8291 (m-40) cc_final: 0.8030 (m-40) REVERT: B 110 ARG cc_start: 0.9059 (mtt-85) cc_final: 0.8518 (tpp80) outliers start: 11 outliers final: 5 residues processed: 110 average time/residue: 0.2338 time to fit residues: 37.2825 Evaluate side-chains 75 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 162 ASN C 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10355 Z= 0.223 Angle : 0.590 7.266 13985 Z= 0.308 Chirality : 0.042 0.182 1528 Planarity : 0.005 0.056 1790 Dihedral : 9.012 153.299 1397 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.02 % Allowed : 6.28 % Favored : 92.70 % 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: 0.76 (0.23), residues: 1236 helix: 0.83 (0.21), residues: 604 sheet: 0.65 (0.38), residues: 160 loop : 0.23 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 484 HIS 0.010 0.001 HIS B 147 PHE 0.023 0.002 PHE C 255 TYR 0.019 0.001 TYR A 490 ARG 0.003 0.000 ARG A 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.387 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: symmetry clash REVERT: B 45 ASN cc_start: 0.8101 (m-40) cc_final: 0.7891 (m-40) REVERT: B 73 MET cc_start: 0.7762 (tmm) cc_final: 0.7442 (tmm) REVERT: A 364 MET cc_start: 0.8223 (mmp) cc_final: 0.7989 (mmt) REVERT: A 478 MET cc_start: 0.8212 (mmm) cc_final: 0.7467 (mmp) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.2255 time to fit residues: 28.5565 Evaluate side-chains 72 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A 430 HIS ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10355 Z= 0.188 Angle : 0.544 8.983 13985 Z= 0.282 Chirality : 0.040 0.177 1528 Planarity : 0.004 0.046 1790 Dihedral : 8.626 152.772 1397 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.11 % Allowed : 7.76 % Favored : 91.13 % 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: 1.05 (0.24), residues: 1236 helix: 1.18 (0.21), residues: 597 sheet: 0.55 (0.38), residues: 168 loop : 0.31 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 484 HIS 0.007 0.001 HIS C 275 PHE 0.021 0.001 PHE C 255 TYR 0.011 0.001 TYR A 490 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASN cc_start: 0.8014 (m110) cc_final: 0.7795 (m-40) REVERT: B 73 MET cc_start: 0.7561 (tmm) cc_final: 0.7151 (tmm) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.2220 time to fit residues: 26.6354 Evaluate side-chains 72 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 310 GLN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A 418 HIS ** A 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10355 Z= 0.218 Angle : 0.551 10.071 13985 Z= 0.285 Chirality : 0.040 0.177 1528 Planarity : 0.004 0.049 1790 Dihedral : 8.460 149.593 1397 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.20 % Allowed : 8.69 % Favored : 90.11 % 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: 1.08 (0.24), residues: 1236 helix: 1.27 (0.22), residues: 598 sheet: 0.50 (0.37), residues: 168 loop : 0.24 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.007 0.001 HIS C 275 PHE 0.020 0.001 PHE A 470 TYR 0.012 0.001 TYR A 490 ARG 0.002 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.7202 (tmm) cc_final: 0.6898 (tmm) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 0.2176 time to fit residues: 24.9633 Evaluate side-chains 74 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10355 Z= 0.167 Angle : 0.522 11.027 13985 Z= 0.270 Chirality : 0.040 0.174 1528 Planarity : 0.004 0.051 1790 Dihedral : 8.135 145.975 1397 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 9.43 % Favored : 89.46 % 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: 1.21 (0.24), residues: 1236 helix: 1.37 (0.22), residues: 601 sheet: 0.59 (0.38), residues: 168 loop : 0.29 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 414 HIS 0.025 0.001 HIS A 418 PHE 0.021 0.001 PHE A 470 TYR 0.009 0.001 TYR A 490 ARG 0.003 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6963 (tmm) cc_final: 0.6564 (tmm) REVERT: B 110 ARG cc_start: 0.9064 (mmt180) cc_final: 0.8657 (mmt90) REVERT: A 418 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.7894 (t-90) REVERT: C 292 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6325 (p0) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.2084 time to fit residues: 24.5835 Evaluate side-chains 75 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 292 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS A 429 GLN ** A 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10355 Z= 0.153 Angle : 0.536 11.601 13985 Z= 0.273 Chirality : 0.039 0.172 1528 Planarity : 0.004 0.051 1790 Dihedral : 7.861 138.576 1397 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.39 % Allowed : 9.89 % Favored : 88.72 % 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: 1.25 (0.24), residues: 1236 helix: 1.38 (0.22), residues: 605 sheet: 0.64 (0.38), residues: 166 loop : 0.33 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 484 HIS 0.007 0.001 HIS B 111 PHE 0.015 0.001 PHE A 470 TYR 0.008 0.001 TYR A 490 ARG 0.002 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9071 (mmt180) cc_final: 0.8692 (tpp-160) REVERT: C 292 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6427 (p0) outliers start: 15 outliers final: 9 residues processed: 83 average time/residue: 0.2381 time to fit residues: 28.5403 Evaluate side-chains 75 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 292 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10355 Z= 0.222 Angle : 0.574 10.826 13985 Z= 0.291 Chirality : 0.041 0.195 1528 Planarity : 0.004 0.050 1790 Dihedral : 7.748 129.039 1397 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.02 % Allowed : 10.54 % Favored : 88.45 % 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: 1.17 (0.24), residues: 1236 helix: 1.34 (0.22), residues: 606 sheet: 0.56 (0.38), residues: 166 loop : 0.27 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 484 HIS 0.012 0.001 HIS A 418 PHE 0.018 0.001 PHE C 255 TYR 0.009 0.001 TYR A 490 ARG 0.001 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9052 (mmt180) cc_final: 0.8655 (tpp-160) REVERT: B 120 MET cc_start: 0.6418 (pmm) cc_final: 0.5879 (pmm) REVERT: A 478 MET cc_start: 0.8216 (mmp) cc_final: 0.7985 (mmp) REVERT: C 292 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6451 (p0) outliers start: 11 outliers final: 10 residues processed: 74 average time/residue: 0.2312 time to fit residues: 25.3222 Evaluate side-chains 75 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 292 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10355 Z= 0.174 Angle : 0.548 10.477 13985 Z= 0.277 Chirality : 0.040 0.200 1528 Planarity : 0.004 0.050 1790 Dihedral : 7.415 121.998 1397 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.11 % Allowed : 10.44 % Favored : 88.45 % 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: 1.19 (0.24), residues: 1236 helix: 1.37 (0.22), residues: 602 sheet: 0.54 (0.38), residues: 166 loop : 0.28 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 781 HIS 0.008 0.001 HIS B 111 PHE 0.016 0.001 PHE C 255 TYR 0.016 0.001 TYR A 490 ARG 0.002 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9038 (mmt180) cc_final: 0.8469 (mmm-85) REVERT: B 120 MET cc_start: 0.6367 (pmm) cc_final: 0.5662 (pmm) REVERT: A 478 MET cc_start: 0.8178 (mmp) cc_final: 0.7964 (mmp) REVERT: C 292 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6448 (p0) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.2321 time to fit residues: 26.7050 Evaluate side-chains 75 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 292 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 638 HIS ** A 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10355 Z= 0.199 Angle : 0.568 10.331 13985 Z= 0.291 Chirality : 0.040 0.204 1528 Planarity : 0.004 0.050 1790 Dihedral : 7.227 114.421 1397 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.02 % Allowed : 10.72 % Favored : 88.26 % 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: 1.12 (0.24), residues: 1236 helix: 1.30 (0.22), residues: 605 sheet: 0.52 (0.38), residues: 166 loop : 0.24 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.010 0.001 HIS B 111 PHE 0.017 0.001 PHE C 255 TYR 0.009 0.001 TYR A 259 ARG 0.001 0.000 ARG A 763 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9065 (mmt180) cc_final: 0.8532 (mmm-85) REVERT: B 120 MET cc_start: 0.6426 (pmm) cc_final: 0.5696 (pmm) REVERT: A 478 MET cc_start: 0.8229 (mmp) cc_final: 0.8005 (mmp) REVERT: C 292 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6447 (p0) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.2295 time to fit residues: 25.0592 Evaluate side-chains 76 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 292 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.062724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.045035 restraints weight = 43121.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046746 restraints weight = 20528.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047892 restraints weight = 12622.344| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10355 Z= 0.197 Angle : 0.579 11.684 13985 Z= 0.295 Chirality : 0.041 0.264 1528 Planarity : 0.004 0.050 1790 Dihedral : 7.124 112.319 1397 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.92 % Allowed : 10.63 % Favored : 88.45 % 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: 1.10 (0.24), residues: 1236 helix: 1.28 (0.22), residues: 603 sheet: 0.56 (0.38), residues: 166 loop : 0.22 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 79 HIS 0.011 0.001 HIS B 111 PHE 0.016 0.001 PHE C 255 TYR 0.018 0.001 TYR A 490 ARG 0.001 0.000 ARG A 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.70 seconds wall clock time: 37 minutes 42.53 seconds (2262.53 seconds total)