Starting phenix.real_space_refine on Mon Mar 11 06:45:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epz_31251/03_2024/7epz_31251_updated.pdb" } resolution = 3.4 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= 0.004 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 S 27 5.16 5 Cl 1 4.86 5 C 4867 2.51 5 N 1192 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B GLU 482": "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: 7431 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3643 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 22, 'TRANS': 445} Chain: "B" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3541 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 23, 'TRANS': 429} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'J9O': 1, 'PX8': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.56, per 1000 atoms: 0.61 Number of scatterers: 7431 At special positions: 0 Unit cell: (83.699, 83.699, 127.179, 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) Cl 1 17.00 S 27 16.00 P 2 15.00 O 1342 8.00 N 1192 7.00 C 4867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 158 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.5 seconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 4 sheets defined 46.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.605A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 288 through 300 Processing helix chain 'A' and resid 325 through 341 removed outlier: 3.804A pdb=" N VAL A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.567A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.782A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 451 through 459 removed outlier: 3.659A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.592A pdb=" N ASP A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 61 through 72 Proline residue: B 66 - end of helix removed outlier: 3.525A pdb=" N ASN B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 104 removed outlier: 4.056A pdb=" N GLY B 87 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 122 through 148 removed outlier: 3.668A pdb=" N ARG B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix removed outlier: 3.784A pdb=" N VAL B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 162 through 181 removed outlier: 3.788A pdb=" N LEU B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 206 removed outlier: 3.763A pdb=" N ARG B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 3.848A pdb=" N TYR B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 245 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 265 through 289 removed outlier: 3.608A pdb=" N ALA B 275 " --> pdb=" O CYS B 271 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN B 285 " --> pdb=" O TYR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.693A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.698A pdb=" N ALA B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 366 through 381 Proline residue: B 374 - end of helix removed outlier: 3.657A pdb=" N ILE B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 412 removed outlier: 3.973A pdb=" N ASN B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA B 395 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 443 removed outlier: 3.966A pdb=" N ALA B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 removed outlier: 5.107A pdb=" N ILE B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLY B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 478 through 492 removed outlier: 3.704A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= B, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.159A pdb=" N LEU A 376 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL A 348 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A 378 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 400 " --> pdb=" O ALA A 379 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 432 through 434 Processing sheet with id= D, first strand: chain 'A' and resid 541 through 544 removed outlier: 3.674A pdb=" N HIS A 557 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 567 " --> pdb=" O LEU A 623 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 777 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: 1.96 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 2 1.14 - 1.31: 1147 1.31 - 1.48: 3131 1.48 - 1.64: 3280 1.64 - 1.81: 50 Bond restraints: 7610 Sorted by residual: bond pdb=" C11 J9O B 601 " pdb=" N06 J9O B 601 " ideal model delta sigma weight residual 1.449 0.974 0.475 2.00e-02 2.50e+03 5.64e+02 bond pdb=" C10 J9O B 601 " pdb=" N06 J9O B 601 " ideal model delta sigma weight residual 1.454 1.121 0.333 2.00e-02 2.50e+03 2.77e+02 bond pdb=" C12 J9O B 601 " pdb=" N06 J9O B 601 " ideal model delta sigma weight residual 1.448 1.148 0.300 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C10 J9O B 601 " pdb=" C15 J9O B 601 " ideal model delta sigma weight residual 1.518 1.724 -0.206 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C10 J9O B 601 " pdb=" C16 J9O B 601 " ideal model delta sigma weight residual 1.526 1.722 -0.196 2.00e-02 2.50e+03 9.57e+01 ... (remaining 7605 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.79: 251 106.79 - 114.66: 4530 114.66 - 122.52: 4629 122.52 - 130.39: 871 130.39 - 138.26: 46 Bond angle restraints: 10327 Sorted by residual: angle pdb=" C11 J9O B 601 " pdb=" N06 J9O B 601 " pdb=" C12 J9O B 601 " ideal model delta sigma weight residual 111.83 129.76 -17.93 3.00e+00 1.11e-01 3.57e+01 angle pdb=" N VAL B 171 " pdb=" CA VAL B 171 " pdb=" C VAL B 171 " ideal model delta sigma weight residual 111.81 106.69 5.12 8.60e-01 1.35e+00 3.55e+01 angle pdb=" N ILE B 168 " pdb=" CA ILE B 168 " pdb=" C ILE B 168 " ideal model delta sigma weight residual 111.90 107.09 4.81 8.10e-01 1.52e+00 3.53e+01 angle pdb=" C ALA A 208 " pdb=" N PRO A 209 " pdb=" CA PRO A 209 " ideal model delta sigma weight residual 119.76 114.11 5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" N VAL A 173 " pdb=" CA VAL A 173 " pdb=" C VAL A 173 " ideal model delta sigma weight residual 111.90 107.78 4.12 8.10e-01 1.52e+00 2.58e+01 ... (remaining 10322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.01: 4080 20.01 - 40.02: 414 40.02 - 60.02: 88 60.02 - 80.03: 10 80.03 - 100.04: 14 Dihedral angle restraints: 4606 sinusoidal: 1963 harmonic: 2643 Sorted by residual: dihedral pdb=" CA LYS B 473 " pdb=" C LYS B 473 " pdb=" N PRO B 474 " pdb=" CA PRO B 474 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA PRO B 474 " pdb=" C PRO B 474 " pdb=" N ARG B 475 " pdb=" CA ARG B 475 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA SER B 445 " pdb=" C SER B 445 " pdb=" N ASP B 446 " pdb=" CA ASP B 446 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 4603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1158 0.139 - 0.278: 39 0.278 - 0.417: 1 0.417 - 0.556: 1 0.556 - 0.695: 1 Chirality restraints: 1200 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C10 J9O B 601 " pdb=" C15 J9O B 601 " pdb=" C16 J9O B 601 " pdb=" N06 J9O B 601 " both_signs ideal model delta sigma weight residual False 2.30 1.81 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.19 -0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 1197 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 473 " -0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO B 474 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 474 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 474 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 461 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO B 462 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 462 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 462 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 366 " -0.025 2.00e-02 2.50e+03 2.49e-02 7.74e+00 pdb=" CG ASN A 366 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 366 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 366 " 0.014 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.019 2.00e-02 2.50e+03 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2183 2.81 - 3.33: 6585 3.33 - 3.86: 11900 3.86 - 4.38: 13546 4.38 - 4.90: 23302 Nonbonded interactions: 57516 Sorted by model distance: nonbonded pdb=" OD1 ASP A 493 " pdb=" OG SER A 496 " model vdw 2.288 2.440 nonbonded pdb=" O TYR A 251 " pdb=" OG SER A 254 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR B 241 " pdb=" OD1 ASP B 386 " model vdw 2.292 2.440 nonbonded pdb=" OG SER A 505 " pdb=" OD1 ASN A 507 " model vdw 2.292 2.440 nonbonded pdb=" OG SER B 75 " pdb=" O ALA B 224 " model vdw 2.294 2.440 ... (remaining 57511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 3.920 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.240 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.012 0.475 7610 Z= 0.825 Angle : 1.172 17.934 10327 Z= 0.628 Chirality : 0.065 0.695 1200 Planarity : 0.008 0.087 1266 Dihedral : 17.280 100.036 2905 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.81 % Favored : 89.75 % Rotamer: Outliers : 1.03 % Allowed : 11.55 % Favored : 87.42 % 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: -4.43 (0.21), residues: 917 helix: -2.79 (0.17), residues: 456 sheet: -1.61 (0.62), residues: 63 loop : -3.27 (0.24), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 397 HIS 0.005 0.002 HIS A 539 PHE 0.021 0.002 PHE A 627 TYR 0.014 0.002 TYR A 226 ARG 0.006 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.7207 (t60) REVERT: B 221 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: B 296 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 338 VAL cc_start: 0.8972 (t) cc_final: 0.8238 (t) REVERT: B 438 MET cc_start: 0.7882 (mmt) cc_final: 0.7535 (mmt) REVERT: B 470 TRP cc_start: 0.7151 (t-100) cc_final: 0.6576 (t-100) REVERT: B 472 LYS cc_start: 0.8881 (mmpt) cc_final: 0.8136 (tptm) REVERT: B 473 LYS cc_start: 0.4679 (tttm) cc_final: 0.4412 (mttt) REVERT: B 478 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7215 (ttp80) outliers start: 8 outliers final: 2 residues processed: 174 average time/residue: 0.2164 time to fit residues: 49.2974 Evaluate side-chains 134 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 319 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 266 HIS A 353 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7610 Z= 0.186 Angle : 0.709 9.150 10327 Z= 0.343 Chirality : 0.046 0.386 1200 Planarity : 0.005 0.065 1266 Dihedral : 12.909 83.112 1264 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.49 % Favored : 90.40 % Rotamer: Outliers : 2.82 % Allowed : 16.43 % Favored : 80.74 % 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: -2.92 (0.25), residues: 917 helix: -1.26 (0.23), residues: 448 sheet: -0.83 (0.67), residues: 59 loop : -2.90 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.005 0.001 HIS A 266 PHE 0.015 0.001 PHE A 337 TYR 0.010 0.001 TYR A 629 ARG 0.003 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8309 (p90) cc_final: 0.7186 (p90) REVERT: B 257 GLU cc_start: 0.7892 (tp30) cc_final: 0.7554 (tp30) REVERT: B 296 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7638 (mt-10) REVERT: B 410 LEU cc_start: 0.9164 (tp) cc_final: 0.8777 (tt) REVERT: B 425 LEU cc_start: 0.8382 (pt) cc_final: 0.8074 (mp) REVERT: B 472 LYS cc_start: 0.8784 (mmpt) cc_final: 0.8126 (tptt) outliers start: 22 outliers final: 14 residues processed: 156 average time/residue: 0.2049 time to fit residues: 42.1922 Evaluate side-chains 139 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 269 GLN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7610 Z= 0.184 Angle : 0.669 8.963 10327 Z= 0.322 Chirality : 0.045 0.343 1200 Planarity : 0.005 0.062 1266 Dihedral : 11.674 73.917 1259 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.49 % Favored : 90.40 % Rotamer: Outliers : 3.08 % Allowed : 17.84 % Favored : 79.08 % 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: -2.27 (0.26), residues: 917 helix: -0.62 (0.24), residues: 448 sheet: -0.77 (0.67), residues: 59 loop : -2.67 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 397 HIS 0.004 0.001 HIS B 110 PHE 0.009 0.001 PHE A 371 TYR 0.011 0.001 TYR A 629 ARG 0.008 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 266 HIS cc_start: 0.7988 (p-80) cc_final: 0.7623 (p-80) REVERT: A 313 TYR cc_start: 0.8529 (p90) cc_final: 0.7490 (p90) REVERT: B 296 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7895 (mt-10) REVERT: B 348 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7455 (pt0) REVERT: B 357 MET cc_start: 0.7830 (tpp) cc_final: 0.7302 (mmt) REVERT: B 410 LEU cc_start: 0.9145 (tp) cc_final: 0.8806 (tt) REVERT: B 425 LEU cc_start: 0.8404 (pt) cc_final: 0.8203 (mt) REVERT: B 472 LYS cc_start: 0.8724 (mmpt) cc_final: 0.8177 (mtmt) REVERT: B 473 LYS cc_start: 0.4870 (ttpt) cc_final: 0.4556 (mttt) outliers start: 24 outliers final: 16 residues processed: 157 average time/residue: 0.1741 time to fit residues: 37.8713 Evaluate side-chains 139 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.0060 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 269 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7610 Z= 0.193 Angle : 0.652 8.656 10327 Z= 0.315 Chirality : 0.045 0.312 1200 Planarity : 0.005 0.062 1266 Dihedral : 10.501 63.251 1257 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.16 % Favored : 90.73 % Rotamer: Outliers : 3.08 % Allowed : 19.90 % Favored : 77.02 % 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: -1.97 (0.26), residues: 917 helix: -0.28 (0.25), residues: 455 sheet: -0.74 (0.68), residues: 59 loop : -2.64 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 397 HIS 0.004 0.001 HIS B 110 PHE 0.021 0.001 PHE B 239 TYR 0.012 0.001 TYR B 464 ARG 0.004 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7862 (p-80) REVERT: A 313 TYR cc_start: 0.8575 (p90) cc_final: 0.7739 (p90) REVERT: B 296 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7863 (tt0) REVERT: B 357 MET cc_start: 0.7868 (tpp) cc_final: 0.7284 (mmt) REVERT: B 410 LEU cc_start: 0.9134 (tp) cc_final: 0.8819 (tt) REVERT: B 472 LYS cc_start: 0.8746 (mmpt) cc_final: 0.8182 (mtmt) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 0.1779 time to fit residues: 36.3401 Evaluate side-chains 147 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 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 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7610 Z= 0.161 Angle : 0.651 8.908 10327 Z= 0.307 Chirality : 0.044 0.300 1200 Planarity : 0.004 0.063 1266 Dihedral : 9.743 55.149 1257 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.83 % Favored : 91.06 % Rotamer: Outliers : 2.44 % Allowed : 20.92 % Favored : 76.64 % 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: -1.64 (0.27), residues: 917 helix: 0.02 (0.25), residues: 449 sheet: -0.65 (0.69), residues: 59 loop : -2.48 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 397 HIS 0.008 0.001 HIS A 266 PHE 0.014 0.001 PHE B 239 TYR 0.014 0.001 TYR A 629 ARG 0.003 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8517 (p90) cc_final: 0.7635 (p90) REVERT: B 212 GLN cc_start: 0.7703 (tt0) cc_final: 0.7421 (tt0) REVERT: B 296 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7873 (tt0) REVERT: B 357 MET cc_start: 0.7811 (tpp) cc_final: 0.7249 (mmt) REVERT: B 410 LEU cc_start: 0.9082 (tp) cc_final: 0.8819 (tt) REVERT: B 472 LYS cc_start: 0.8636 (mmpt) cc_final: 0.8138 (mtmt) outliers start: 19 outliers final: 15 residues processed: 152 average time/residue: 0.1732 time to fit residues: 36.3494 Evaluate side-chains 142 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7610 Z= 0.230 Angle : 0.674 8.376 10327 Z= 0.319 Chirality : 0.045 0.293 1200 Planarity : 0.005 0.073 1266 Dihedral : 9.165 51.542 1257 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.27 % Favored : 90.62 % Rotamer: Outliers : 3.21 % Allowed : 20.15 % Favored : 76.64 % 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: -1.48 (0.27), residues: 917 helix: 0.17 (0.25), residues: 446 sheet: -0.92 (0.66), residues: 63 loop : -2.37 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.005 0.001 HIS B 110 PHE 0.015 0.001 PHE B 426 TYR 0.011 0.001 TYR A 629 ARG 0.003 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8549 (p90) cc_final: 0.7700 (p90) REVERT: B 212 GLN cc_start: 0.7630 (tt0) cc_final: 0.7394 (tt0) REVERT: B 296 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7850 (tt0) REVERT: B 357 MET cc_start: 0.7823 (tpp) cc_final: 0.7211 (mmt) REVERT: B 410 LEU cc_start: 0.9127 (tp) cc_final: 0.8865 (tt) REVERT: B 473 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5893 (ptmt) outliers start: 25 outliers final: 20 residues processed: 140 average time/residue: 0.1747 time to fit residues: 34.2353 Evaluate side-chains 146 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 484 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7610 Z= 0.172 Angle : 0.674 15.222 10327 Z= 0.314 Chirality : 0.044 0.293 1200 Planarity : 0.004 0.071 1266 Dihedral : 8.744 53.004 1257 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.51 % Favored : 91.38 % Rotamer: Outliers : 2.70 % Allowed : 21.44 % Favored : 75.87 % 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: -1.31 (0.28), residues: 917 helix: 0.28 (0.25), residues: 449 sheet: -0.55 (0.70), residues: 59 loop : -2.28 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 397 HIS 0.004 0.001 HIS B 110 PHE 0.012 0.001 PHE A 291 TYR 0.016 0.001 TYR A 629 ARG 0.003 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8520 (p90) cc_final: 0.7714 (p90) REVERT: B 212 GLN cc_start: 0.7578 (tt0) cc_final: 0.7356 (tt0) REVERT: B 296 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7847 (tt0) REVERT: B 357 MET cc_start: 0.7866 (tpp) cc_final: 0.7270 (mmt) REVERT: B 410 LEU cc_start: 0.9092 (tp) cc_final: 0.8841 (tt) REVERT: B 473 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5805 (ptmt) outliers start: 21 outliers final: 18 residues processed: 140 average time/residue: 0.1707 time to fit residues: 33.4024 Evaluate side-chains 143 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7610 Z= 0.176 Angle : 0.666 13.243 10327 Z= 0.312 Chirality : 0.044 0.299 1200 Planarity : 0.004 0.076 1266 Dihedral : 8.266 55.385 1257 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.94 % Favored : 90.95 % Rotamer: Outliers : 2.82 % Allowed : 21.69 % Favored : 75.48 % 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: -1.18 (0.28), residues: 917 helix: 0.43 (0.25), residues: 449 sheet: -0.47 (0.70), residues: 59 loop : -2.27 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 397 HIS 0.004 0.001 HIS B 110 PHE 0.015 0.001 PHE B 426 TYR 0.015 0.001 TYR A 629 ARG 0.003 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8510 (p90) cc_final: 0.7678 (p90) REVERT: A 534 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 296 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7831 (tt0) REVERT: B 357 MET cc_start: 0.7823 (tpp) cc_final: 0.7211 (mmt) REVERT: B 410 LEU cc_start: 0.9090 (tp) cc_final: 0.8853 (tt) outliers start: 22 outliers final: 19 residues processed: 144 average time/residue: 0.1742 time to fit residues: 35.4091 Evaluate side-chains 146 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 86 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7610 Z= 0.164 Angle : 0.665 13.393 10327 Z= 0.312 Chirality : 0.044 0.308 1200 Planarity : 0.004 0.082 1266 Dihedral : 7.891 55.626 1257 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.51 % Favored : 91.38 % Rotamer: Outliers : 2.18 % Allowed : 22.59 % Favored : 75.22 % 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: -0.99 (0.28), residues: 917 helix: 0.56 (0.25), residues: 449 sheet: -0.31 (0.70), residues: 59 loop : -2.16 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 470 HIS 0.005 0.001 HIS B 110 PHE 0.014 0.001 PHE B 426 TYR 0.014 0.001 TYR A 629 ARG 0.007 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8475 (p90) cc_final: 0.7706 (p90) REVERT: A 534 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 296 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7827 (tt0) REVERT: B 357 MET cc_start: 0.7867 (tpp) cc_final: 0.7283 (mmt) outliers start: 17 outliers final: 16 residues processed: 143 average time/residue: 0.1710 time to fit residues: 34.1803 Evaluate side-chains 145 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 0.0770 chunk 7 optimal weight: 0.0060 chunk 55 optimal weight: 0.0980 chunk 44 optimal weight: 0.3980 chunk 57 optimal weight: 0.0870 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.0730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7610 Z= 0.153 Angle : 0.656 13.450 10327 Z= 0.304 Chirality : 0.043 0.321 1200 Planarity : 0.004 0.078 1266 Dihedral : 7.301 54.603 1257 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.27 % Favored : 90.62 % Rotamer: Outliers : 1.80 % Allowed : 22.98 % Favored : 75.22 % 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 (0.28), residues: 917 helix: 0.76 (0.26), residues: 449 sheet: -0.07 (0.72), residues: 59 loop : -2.09 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 470 HIS 0.003 0.001 HIS B 110 PHE 0.013 0.001 PHE B 391 TYR 0.016 0.001 TYR B 412 ARG 0.006 0.000 ARG B 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8386 (p90) cc_final: 0.7823 (p90) REVERT: B 221 PHE cc_start: 0.7457 (m-80) cc_final: 0.7176 (m-80) REVERT: B 274 MET cc_start: 0.8733 (tpp) cc_final: 0.8422 (mmm) REVERT: B 357 MET cc_start: 0.7815 (tpp) cc_final: 0.7277 (mmt) REVERT: B 444 TYR cc_start: 0.7376 (t80) cc_final: 0.7175 (t80) outliers start: 14 outliers final: 11 residues processed: 158 average time/residue: 0.1827 time to fit residues: 41.1502 Evaluate side-chains 141 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 473 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 63 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106969 restraints weight = 13304.024| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.19 r_work: 0.3181 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7610 Z= 0.189 Angle : 0.670 13.021 10327 Z= 0.313 Chirality : 0.044 0.323 1200 Planarity : 0.004 0.083 1266 Dihedral : 7.210 53.141 1257 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.94 % Favored : 90.95 % Rotamer: Outliers : 1.80 % Allowed : 23.88 % Favored : 74.33 % 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: -0.69 (0.28), residues: 917 helix: 0.82 (0.26), residues: 445 sheet: -0.16 (0.70), residues: 59 loop : -2.00 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 470 HIS 0.006 0.001 HIS B 110 PHE 0.014 0.001 PHE B 426 TYR 0.023 0.001 TYR B 464 ARG 0.010 0.000 ARG B 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.46 seconds wall clock time: 34 minutes 36.74 seconds (2076.74 seconds total)