Starting phenix.real_space_refine on Fri Mar 15 00:37:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm0_13508/03_2024/7pm0_13508_updated.pdb" } resolution = 3.6 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: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6482 2.51 5 N 1723 2.21 5 O 1897 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 ARG 12": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A TYR 387": "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 GLU 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ASP 521": "OD1" <-> "OD2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 372": "NH1" <-> "NH2" 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: 10169 Number of models: 1 Model: "" Number of chains: 3 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: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6130 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 27, 'TRANS': 723} Chain breaks: 3 Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2980 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="PHE C 375 "'] Classifications: {'peptide': 371, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351, None: 4} Not linked: pdbres="PHE C 375 " pdbres="ADP C 401 " Not linked: pdbres="ADP C 401 " pdbres="PO4 C 402 " Not linked: pdbres="PO4 C 402 " pdbres=" MG C 403 " Not linked: pdbres=" MG C 403 " pdbres="9UE C 404 " 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 Time building chain proxies: 5.86, per 1000 atoms: 0.58 Number of scatterers: 10169 At special positions: 0 Unit cell: (104.5, 132, 152.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1897 8.00 N 1723 7.00 C 6482 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: 4.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 13 sheets defined 49.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.204A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.541A 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: 4.279A 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 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 121 through 128 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 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 184 Processing helix chain 'A' and resid 192 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 260 through 270 removed outlier: 4.843A pdb=" N ALA A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 5.291A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.778A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.675A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.529A 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: 4.229A 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 removed outlier: 3.857A pdb=" N MET A 478 " --> pdb=" O GLN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.589A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 removed outlier: 4.027A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.663A pdb=" N LYS A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 removed outlier: 5.905A pdb=" N LEU A 565 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 566 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.829A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.066A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 653 removed outlier: 3.616A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.584A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.666A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 removed outlier: 3.800A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.448A 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 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 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: 3.859A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.643A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.648A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.544A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.475A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 374 removed outlier: 3.570A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Proline residue: C 367 - end of helix removed outlier: 5.138A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.177A 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 removed outlier: 3.653A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.060A pdb=" N ARG A 660 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN A 111 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 662 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.512A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 377 through 381 Processing sheet with id= F, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= G, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.589A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 340 through 344 removed outlier: 3.707A pdb=" N ARG A 343 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 8 through 12 removed outlier: 3.550A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.524A pdb=" N THR C 66 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.697A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.349A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 437 hydrogen bonds defined for protein. 1209 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: 2.57 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2916 1.33 - 1.47: 2821 1.47 - 1.60: 4544 1.60 - 1.73: 3 1.73 - 1.87: 102 Bond restraints: 10386 Sorted by residual: bond pdb=" C4 9UE C 404 " pdb=" C5 9UE C 404 " ideal model delta sigma weight residual 0.880 1.498 -0.618 2.00e-02 2.50e+03 9.53e+02 bond pdb=" C11 9UE C 404 " pdb=" C12 9UE C 404 " ideal model delta sigma weight residual 2.064 1.523 0.541 2.00e-02 2.50e+03 7.32e+02 bond pdb=" C9 9UE C 404 " pdb=" N1 9UE C 404 " ideal model delta sigma weight residual 1.863 1.363 0.500 2.00e-02 2.50e+03 6.26e+02 bond pdb=" O 9UE C 404 " pdb=" C4 9UE C 404 " ideal model delta sigma weight residual 0.887 1.333 -0.446 2.00e-02 2.50e+03 4.98e+02 bond pdb=" C7 9UE C 404 " pdb=" C8 9UE C 404 " ideal model delta sigma weight residual 1.139 1.528 -0.389 2.00e-02 2.50e+03 3.79e+02 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 96.97 - 105.08: 214 105.08 - 113.19: 5610 113.19 - 121.30: 5744 121.30 - 129.42: 2394 129.42 - 137.53: 66 Bond angle restraints: 14028 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " ideal model delta sigma weight residual 73.46 131.29 -57.83 3.00e+00 1.11e-01 3.72e+02 angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C22 9UE C 404 " ideal model delta sigma weight residual 176.54 123.36 53.18 3.00e+00 1.11e-01 3.14e+02 angle pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 78.92 130.68 -51.76 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C13 9UE C 404 " pdb=" C14 9UE C 404 " pdb=" C16 9UE C 404 " ideal model delta sigma weight residual 67.70 114.36 -46.66 3.00e+00 1.11e-01 2.42e+02 angle pdb=" N3 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 73.72 117.86 -44.14 3.00e+00 1.11e-01 2.16e+02 ... (remaining 14023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 6098 32.13 - 64.25: 112 64.25 - 96.38: 35 96.38 - 128.50: 7 128.50 - 160.63: 4 Dihedral angle restraints: 6256 sinusoidal: 2572 harmonic: 3684 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 62.63 -122.63 1 2.00e+01 2.50e-03 3.69e+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 300.00 178.49 121.51 1 2.00e+01 2.50e-03 3.65e+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 58.88 -118.88 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 6253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1508 0.139 - 0.278: 17 0.278 - 0.417: 1 0.417 - 0.556: 1 0.556 - 0.695: 1 Chirality restraints: 1528 Sorted by residual: chirality pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C29 9UE C 404 " pdb=" C5 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -1.95 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C12 9UE C 404 " pdb=" C11 9UE C 404 " pdb=" C13 9UE C 404 " pdb=" C17 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.99 2.45 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1525 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.137 9.50e-02 1.11e+02 7.89e-02 3.27e+01 pdb=" NE ARG A 248 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " 0.371 9.50e-02 1.11e+02 1.70e-01 3.26e+01 pdb=" NE ARG A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 254 " -0.341 9.50e-02 1.11e+02 1.57e-01 3.07e+01 pdb=" NE ARG C 254 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG C 254 " 0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG C 254 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG C 254 " -0.036 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 60 2.58 - 3.16: 8855 3.16 - 3.74: 15119 3.74 - 4.32: 21395 4.32 - 4.90: 35260 Nonbonded interactions: 80689 Sorted by model distance: nonbonded pdb=" O3 PO4 C 402 " pdb="MG MG C 403 " model vdw 2.002 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 403 " model vdw 2.008 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.089 2.440 nonbonded pdb=" O GLU B 118 " pdb=" NH2 ARG A 779 " model vdw 2.207 2.520 nonbonded pdb=" NH2 ARG B 37 " pdb=" O PRO B 43 " model vdw 2.211 2.520 ... (remaining 80684 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: 1.340 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: 6.910 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 30.410 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.014 0.618 10386 Z= 0.891 Angle : 1.419 57.827 14028 Z= 0.620 Chirality : 0.057 0.695 1528 Planarity : 0.010 0.170 1797 Dihedral : 16.298 160.630 3882 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -1.27 (0.20), residues: 1242 helix: -1.40 (0.17), residues: 592 sheet: 0.10 (0.37), residues: 157 loop : -0.13 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 374 HIS 0.014 0.002 HIS A 418 PHE 0.036 0.002 PHE A 707 TYR 0.036 0.007 TYR A 113 ARG 0.096 0.011 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 PHE cc_start: 0.8549 (m-80) cc_final: 0.8292 (m-10) REVERT: A 359 ILE cc_start: 0.9448 (mt) cc_final: 0.9241 (mm) REVERT: C 195 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 227 MET cc_start: 0.8685 (tpp) cc_final: 0.8480 (tpt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2667 time to fit residues: 63.7779 Evaluate side-chains 101 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 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 125 ASN A 200 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 726 GLN C 41 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10386 Z= 0.236 Angle : 0.896 47.968 14028 Z= 0.396 Chirality : 0.046 0.326 1528 Planarity : 0.004 0.049 1797 Dihedral : 13.020 176.406 1400 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.83 % Allowed : 7.01 % Favored : 92.16 % 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: 0.80 (0.23), residues: 1242 helix: 0.50 (0.20), residues: 611 sheet: 0.78 (0.39), residues: 163 loop : 0.77 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 374 HIS 0.009 0.001 HIS A 418 PHE 0.021 0.002 PHE A 707 TYR 0.013 0.002 TYR A 147 ARG 0.009 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 PHE cc_start: 0.8544 (m-80) cc_final: 0.8310 (m-10) REVERT: B 105 MET cc_start: 0.9077 (mmp) cc_final: 0.8779 (tpp) REVERT: B 110 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8773 (tpt170) REVERT: B 120 MET cc_start: 0.6423 (mtp) cc_final: 0.5669 (mtt) REVERT: A 364 MET cc_start: 0.8690 (mmm) cc_final: 0.8440 (mmm) REVERT: A 416 VAL cc_start: 0.9253 (t) cc_final: 0.9048 (p) REVERT: C 192 ILE cc_start: 0.9203 (tt) cc_final: 0.8906 (tt) REVERT: C 195 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7639 (mt-10) REVERT: C 236 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7295 (tp) outliers start: 9 outliers final: 4 residues processed: 125 average time/residue: 0.2217 time to fit residues: 40.5681 Evaluate side-chains 100 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 410 ASN A 455 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10386 Z= 0.218 Angle : 0.847 47.096 14028 Z= 0.361 Chirality : 0.043 0.203 1528 Planarity : 0.004 0.056 1797 Dihedral : 12.535 170.293 1400 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.48 % Allowed : 8.58 % Favored : 89.94 % 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: 1.38 (0.24), residues: 1242 helix: 1.09 (0.21), residues: 606 sheet: 0.92 (0.40), residues: 163 loop : 0.93 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 79 HIS 0.007 0.001 HIS A 418 PHE 0.024 0.002 PHE B 12 TYR 0.011 0.001 TYR A 456 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8844 (tpt170) REVERT: A 135 MET cc_start: 0.8013 (mmm) cc_final: 0.7811 (mmt) REVERT: A 441 PHE cc_start: 0.7987 (m-80) cc_final: 0.7687 (t80) REVERT: A 507 ASP cc_start: 0.8132 (m-30) cc_final: 0.7747 (m-30) REVERT: C 236 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7086 (tp) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 0.2143 time to fit residues: 35.5410 Evaluate side-chains 97 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.0570 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10386 Z= 0.183 Angle : 0.812 47.210 14028 Z= 0.343 Chirality : 0.042 0.207 1528 Planarity : 0.004 0.056 1797 Dihedral : 12.055 159.339 1400 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.92 % Allowed : 10.79 % Favored : 88.28 % 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: 1.54 (0.24), residues: 1242 helix: 1.34 (0.21), residues: 599 sheet: 0.83 (0.40), residues: 168 loop : 0.92 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 414 HIS 0.006 0.001 HIS A 418 PHE 0.011 0.001 PHE A 553 TYR 0.010 0.001 TYR A 456 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.188 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 105 MET cc_start: 0.9123 (mmp) cc_final: 0.8812 (tpp) REVERT: B 110 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8834 (tpt170) REVERT: A 86 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9082 (mt) REVERT: A 507 ASP cc_start: 0.8094 (m-30) cc_final: 0.7719 (m-30) REVERT: C 236 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7704 (mm) outliers start: 10 outliers final: 5 residues processed: 105 average time/residue: 0.2093 time to fit residues: 32.4948 Evaluate side-chains 96 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10386 Z= 0.213 Angle : 0.816 47.224 14028 Z= 0.343 Chirality : 0.042 0.225 1528 Planarity : 0.004 0.055 1797 Dihedral : 11.724 151.361 1400 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.20 % Allowed : 11.53 % Favored : 87.27 % 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: 1.56 (0.24), residues: 1242 helix: 1.45 (0.21), residues: 604 sheet: 0.90 (0.41), residues: 164 loop : 0.74 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 414 HIS 0.007 0.001 HIS A 418 PHE 0.051 0.001 PHE B 12 TYR 0.011 0.001 TYR A 456 ARG 0.004 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.138 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 105 MET cc_start: 0.9120 (mmp) cc_final: 0.8770 (tpp) REVERT: B 110 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8717 (tpt170) REVERT: A 86 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9100 (mt) REVERT: A 507 ASP cc_start: 0.8123 (m-30) cc_final: 0.7733 (m-30) REVERT: C 72 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: C 195 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7433 (mt-10) outliers start: 13 outliers final: 5 residues processed: 101 average time/residue: 0.2119 time to fit residues: 31.8004 Evaluate side-chains 94 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 0.0570 chunk 63 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10386 Z= 0.199 Angle : 0.806 47.257 14028 Z= 0.338 Chirality : 0.042 0.243 1528 Planarity : 0.004 0.056 1797 Dihedral : 11.464 157.932 1400 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.66 % Allowed : 11.53 % Favored : 86.81 % 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: 1.59 (0.24), residues: 1242 helix: 1.54 (0.22), residues: 605 sheet: 0.74 (0.43), residues: 146 loop : 0.73 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.006 0.001 HIS A 418 PHE 0.022 0.001 PHE B 12 TYR 0.011 0.001 TYR A 658 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.087 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: B 110 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8698 (tpt170) REVERT: A 211 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8765 (t) REVERT: A 507 ASP cc_start: 0.8132 (m-30) cc_final: 0.7846 (m-30) outliers start: 18 outliers final: 9 residues processed: 107 average time/residue: 0.2061 time to fit residues: 32.6846 Evaluate side-chains 103 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 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 638 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10386 Z= 0.231 Angle : 0.830 47.231 14028 Z= 0.348 Chirality : 0.042 0.255 1528 Planarity : 0.004 0.053 1797 Dihedral : 11.362 161.683 1400 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.11 % Allowed : 12.45 % Favored : 86.44 % 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: 1.46 (0.24), residues: 1242 helix: 1.45 (0.22), residues: 606 sheet: 0.71 (0.43), residues: 146 loop : 0.62 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.017 0.001 PHE B 12 TYR 0.011 0.001 TYR A 456 ARG 0.002 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9148 (mmp) cc_final: 0.8759 (tpp) REVERT: B 110 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8693 (tpt170) REVERT: A 507 ASP cc_start: 0.8142 (m-30) cc_final: 0.7866 (m-30) outliers start: 12 outliers final: 7 residues processed: 99 average time/residue: 0.2069 time to fit residues: 30.8222 Evaluate side-chains 95 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 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 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10386 Z= 0.261 Angle : 0.842 47.250 14028 Z= 0.357 Chirality : 0.043 0.262 1528 Planarity : 0.004 0.054 1797 Dihedral : 11.299 164.771 1400 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.11 % Allowed : 13.01 % Favored : 85.89 % 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: 1.41 (0.24), residues: 1242 helix: 1.41 (0.22), residues: 605 sheet: 0.66 (0.43), residues: 146 loop : 0.59 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.013 0.001 PHE C 255 TYR 0.012 0.001 TYR A 658 ARG 0.003 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9161 (mmp) cc_final: 0.8764 (tpp) REVERT: A 305 MET cc_start: 0.8102 (tpp) cc_final: 0.7530 (mtt) REVERT: A 507 ASP cc_start: 0.8146 (m-30) cc_final: 0.7866 (m-30) REVERT: C 49 GLN cc_start: 0.8449 (pp30) cc_final: 0.8220 (pp30) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.2003 time to fit residues: 29.6373 Evaluate side-chains 95 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10386 Z= 0.201 Angle : 0.839 47.280 14028 Z= 0.354 Chirality : 0.042 0.265 1528 Planarity : 0.004 0.053 1797 Dihedral : 11.156 167.288 1400 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.01 % Allowed : 13.19 % Favored : 85.79 % 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: 1.47 (0.24), residues: 1242 helix: 1.46 (0.22), residues: 604 sheet: 0.81 (0.44), residues: 144 loop : 0.58 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.009 0.001 PHE C 255 TYR 0.011 0.001 TYR A 259 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9132 (mmp) cc_final: 0.8843 (tpp) REVERT: A 191 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8118 (t0) REVERT: A 305 MET cc_start: 0.8017 (tpp) cc_final: 0.7816 (mtt) REVERT: A 507 ASP cc_start: 0.8123 (m-30) cc_final: 0.7856 (m-30) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.2055 time to fit residues: 29.7729 Evaluate side-chains 95 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 82 optimal weight: 0.0010 chunk 124 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 60 optimal weight: 0.0470 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10386 Z= 0.162 Angle : 0.841 47.330 14028 Z= 0.352 Chirality : 0.042 0.281 1528 Planarity : 0.004 0.053 1797 Dihedral : 10.989 168.848 1400 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.92 % Allowed : 13.38 % Favored : 85.70 % 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: 1.49 (0.24), residues: 1242 helix: 1.54 (0.22), residues: 600 sheet: 0.74 (0.44), residues: 150 loop : 0.54 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.020 0.001 PHE B 16 TYR 0.013 0.001 TYR C 279 ARG 0.003 0.000 ARG A 784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9141 (mmp) cc_final: 0.8816 (tpp) REVERT: A 191 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8116 (t0) outliers start: 10 outliers final: 8 residues processed: 98 average time/residue: 0.2013 time to fit residues: 29.7428 Evaluate side-chains 98 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058938 restraints weight = 30262.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061139 restraints weight = 14881.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.062617 restraints weight = 9344.228| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10386 Z= 0.179 Angle : 0.850 47.355 14028 Z= 0.357 Chirality : 0.043 0.275 1528 Planarity : 0.004 0.053 1797 Dihedral : 10.952 170.619 1400 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.01 % Allowed : 13.19 % Favored : 85.79 % 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: 1.50 (0.24), residues: 1242 helix: 1.53 (0.22), residues: 600 sheet: 0.85 (0.44), residues: 146 loop : 0.54 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.019 0.001 PHE B 16 TYR 0.010 0.001 TYR A 658 ARG 0.003 0.000 ARG A 789 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.39 seconds wall clock time: 38 minutes 20.35 seconds (2300.35 seconds total)