Starting phenix.real_space_refine on Mon Mar 11 00:59:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqv_15591/03_2024/8aqv_15591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqv_15591/03_2024/8aqv_15591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqv_15591/03_2024/8aqv_15591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqv_15591/03_2024/8aqv_15591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqv_15591/03_2024/8aqv_15591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqv_15591/03_2024/8aqv_15591.pdb" } resolution = 2.96 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= 0.026 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4117 2.51 5 N 1080 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6447 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4858 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1547 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.89, per 1000 atoms: 0.60 Number of scatterers: 6447 At special positions: 0 Unit cell: (88.2528, 87.2384, 119.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1213 8.00 N 1080 7.00 C 4117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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-ASN " NAG B1301 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 53.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.816A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.506A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.686A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.610A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 removed outlier: 3.606A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.590A pdb=" N TYR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 removed outlier: 3.895A pdb=" N GLU A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 220 through 233 removed outlier: 4.579A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.822A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.534A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.544A pdb=" N GLY A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 3.637A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.531A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 4.024A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 329' Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.620A pdb=" N ALA A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 402 through 413 removed outlier: 4.107A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.617A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.746A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.802A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.969A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.834A pdb=" N LYS A 541 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.504A pdb=" N LEU A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.824A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.532A pdb=" N TYR A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.693A pdb=" N ASP A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.917A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.754A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.701A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.715A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 removed outlier: 3.822A pdb=" N ALA A 209 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.960A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.241A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 252 hydrogen bonds defined for protein. 705 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: 1.63 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2067 1.34 - 1.46: 1512 1.46 - 1.58: 2992 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6629 Sorted by residual: bond pdb=" C ALA B 372 " pdb=" N PRO B 373 " ideal model delta sigma weight residual 1.333 1.374 -0.041 1.01e-02 9.80e+03 1.64e+01 bond pdb=" C GLU A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.331 1.347 -0.015 7.90e-03 1.60e+04 3.75e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C TYR A 279 " pdb=" N PRO A 280 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.85e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 ... (remaining 6624 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.71: 139 104.71 - 112.05: 2998 112.05 - 119.39: 2367 119.39 - 126.72: 3363 126.72 - 134.06: 138 Bond angle restraints: 9005 Sorted by residual: angle pdb=" C ASP A 338 " pdb=" CA ASP A 338 " pdb=" CB ASP A 338 " ideal model delta sigma weight residual 116.54 110.34 6.20 1.15e+00 7.56e-01 2.90e+01 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 113.71 108.69 5.02 9.50e-01 1.11e+00 2.80e+01 angle pdb=" N GLU A 483 " pdb=" CA GLU A 483 " pdb=" C GLU A 483 " ideal model delta sigma weight residual 114.75 109.32 5.43 1.26e+00 6.30e-01 1.85e+01 angle pdb=" N THR B 523 " pdb=" CA THR B 523 " pdb=" C THR B 523 " ideal model delta sigma weight residual 114.56 109.14 5.42 1.27e+00 6.20e-01 1.82e+01 angle pdb=" C PHE B 371 " pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 121.80 131.07 -9.27 2.44e+00 1.68e-01 1.44e+01 ... (remaining 9000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3633 17.79 - 35.58: 266 35.58 - 53.37: 38 53.37 - 71.16: 18 71.16 - 88.96: 5 Dihedral angle restraints: 3960 sinusoidal: 1639 harmonic: 2321 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -145.69 59.69 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CA GLN A 86 " pdb=" C GLN A 86 " pdb=" N GLU A 87 " pdb=" CA GLU A 87 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU A 87 " pdb=" C GLU A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 488 0.027 - 0.054: 276 0.054 - 0.080: 116 0.080 - 0.107: 44 0.107 - 0.134: 17 Chirality restraints: 941 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB THR A 55 " pdb=" CA THR A 55 " pdb=" OG1 THR A 55 " pdb=" CG2 THR A 55 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 938 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO B 337 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 88 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ILE A 88 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 88 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN A 89 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 235 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.019 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 190 2.71 - 3.26: 6126 3.26 - 3.81: 9501 3.81 - 4.35: 12542 4.35 - 4.90: 21501 Nonbonded interactions: 49860 Sorted by model distance: nonbonded pdb=" NH2 ARG A 245 " pdb=" O PHE A 603 " model vdw 2.164 2.520 nonbonded pdb=" NH2 ARG B 454 " pdb=" O SER B 469 " model vdw 2.213 2.520 nonbonded pdb=" O THR A 548 " pdb=" NE2 GLN A 552 " model vdw 2.229 2.520 nonbonded pdb=" OE2 GLU A 227 " pdb=" OH TYR A 454 " model vdw 2.281 2.440 nonbonded pdb=" NE ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.296 2.520 ... (remaining 49855 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 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: 5.970 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: 15.470 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 20.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6629 Z= 0.216 Angle : 0.710 9.272 9005 Z= 0.430 Chirality : 0.042 0.134 941 Planarity : 0.004 0.047 1168 Dihedral : 12.963 88.956 2449 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.84 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.30), residues: 785 helix: -0.39 (0.29), residues: 348 sheet: 0.24 (0.86), residues: 43 loop : -1.42 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.007 0.001 HIS A 401 PHE 0.016 0.001 PHE A 369 TYR 0.022 0.002 TYR B 501 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.8589 (mtt) cc_final: 0.8339 (mtp) REVERT: A 508 ASN cc_start: 0.8108 (m110) cc_final: 0.7827 (m-40) REVERT: B 357 ARG cc_start: 0.8523 (ttp80) cc_final: 0.7971 (ttt90) REVERT: B 405 ASN cc_start: 0.7716 (m-40) cc_final: 0.7467 (m110) REVERT: B 440 LYS cc_start: 0.8887 (mmtp) cc_final: 0.8509 (mtpm) REVERT: B 469 SER cc_start: 0.8236 (t) cc_final: 0.7994 (p) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 1.2421 time to fit residues: 164.2563 Evaluate side-chains 76 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 81 GLN A 102 GLN A 121 ASN A 188 ASN A 330 ASN A 368 ASN A 397 ASN A 522 GLN A 540 HIS B 388 ASN B 450 ASN B 487 ASN B 506 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6629 Z= 0.185 Angle : 0.554 10.330 9005 Z= 0.287 Chirality : 0.042 0.141 941 Planarity : 0.004 0.043 1168 Dihedral : 4.084 27.525 927 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.59 % Favored : 94.78 % Rotamer: Outliers : 2.19 % Allowed : 9.33 % Favored : 88.48 % 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: -0.82 (0.30), residues: 785 helix: 0.15 (0.29), residues: 357 sheet: 0.51 (0.86), residues: 43 loop : -1.32 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.018 0.001 PHE A 369 TYR 0.024 0.001 TYR A 255 ARG 0.007 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6161 (mt0) REVERT: A 298 MET cc_start: 0.8538 (mtt) cc_final: 0.8296 (mtp) REVERT: A 430 GLU cc_start: 0.8330 (tt0) cc_final: 0.8111 (mt-10) REVERT: A 439 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7413 (mp) REVERT: B 357 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7952 (ttt90) REVERT: B 378 LYS cc_start: 0.7413 (tptp) cc_final: 0.7174 (mmmt) REVERT: B 405 ASN cc_start: 0.7835 (m-40) cc_final: 0.7530 (m-40) REVERT: B 440 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8538 (mtpm) REVERT: B 458 LYS cc_start: 0.7675 (pttt) cc_final: 0.7413 (ptpp) outliers start: 15 outliers final: 5 residues processed: 97 average time/residue: 1.3115 time to fit residues: 134.0885 Evaluate side-chains 81 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 549 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.0030 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 536 ASN A 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6629 Z= 0.183 Angle : 0.535 10.391 9005 Z= 0.274 Chirality : 0.041 0.166 941 Planarity : 0.004 0.037 1168 Dihedral : 3.985 26.634 927 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.71 % Favored : 94.65 % Rotamer: Outliers : 2.33 % Allowed : 11.81 % Favored : 85.86 % 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: -0.65 (0.30), residues: 785 helix: 0.33 (0.29), residues: 361 sheet: 0.57 (0.86), residues: 43 loop : -1.29 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.019 0.001 TYR A 255 ARG 0.004 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6139 (mt0) REVERT: A 210 GLU cc_start: 0.8322 (tp30) cc_final: 0.7998 (pt0) REVERT: A 298 MET cc_start: 0.8553 (mtt) cc_final: 0.8317 (mtp) REVERT: A 430 GLU cc_start: 0.8319 (tt0) cc_final: 0.7882 (mt-10) REVERT: B 357 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8015 (ttt90) REVERT: B 405 ASN cc_start: 0.7843 (m-40) cc_final: 0.7531 (m110) REVERT: B 440 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8583 (mtpm) REVERT: B 458 LYS cc_start: 0.7684 (pttt) cc_final: 0.7378 (ptpp) REVERT: B 471 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7336 (mt-10) outliers start: 16 outliers final: 5 residues processed: 91 average time/residue: 1.3485 time to fit residues: 128.9401 Evaluate side-chains 78 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0020 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 chunk 42 optimal weight: 0.6980 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6629 Z= 0.132 Angle : 0.494 10.648 9005 Z= 0.252 Chirality : 0.040 0.168 941 Planarity : 0.004 0.037 1168 Dihedral : 3.715 25.949 927 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.59 % Favored : 94.78 % Rotamer: Outliers : 2.48 % Allowed : 12.24 % Favored : 85.28 % 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: -0.36 (0.31), residues: 785 helix: 0.69 (0.29), residues: 354 sheet: 0.43 (0.84), residues: 43 loop : -1.20 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.016 0.001 TYR A 255 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.713 Fit side-chains REVERT: A 34 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8855 (tm-30) REVERT: A 75 GLU cc_start: 0.7934 (tt0) cc_final: 0.7620 (tm-30) REVERT: A 89 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6099 (mt0) REVERT: A 219 ARG cc_start: 0.6425 (ptt-90) cc_final: 0.6086 (ptt180) REVERT: A 430 GLU cc_start: 0.8315 (tt0) cc_final: 0.7859 (mt-10) REVERT: B 357 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8007 (ttt90) REVERT: B 405 ASN cc_start: 0.7812 (m-40) cc_final: 0.7523 (m110) REVERT: B 440 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8553 (mtpm) REVERT: B 458 LYS cc_start: 0.7555 (pttt) cc_final: 0.7134 (ptpt) outliers start: 17 outliers final: 6 residues processed: 90 average time/residue: 1.0932 time to fit residues: 104.2589 Evaluate side-chains 82 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 31 optimal weight: 0.0070 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.0060 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 overall best weight: 0.6114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6629 Z= 0.161 Angle : 0.508 10.537 9005 Z= 0.257 Chirality : 0.040 0.139 941 Planarity : 0.004 0.034 1168 Dihedral : 3.693 25.715 927 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.59 % Favored : 94.78 % Rotamer: Outliers : 3.35 % Allowed : 12.68 % Favored : 83.97 % 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: -0.28 (0.31), residues: 785 helix: 0.70 (0.29), residues: 357 sheet: 0.47 (0.83), residues: 43 loop : -1.11 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.011 0.001 PHE A 369 TYR 0.016 0.001 TYR A 255 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.725 Fit side-chains REVERT: A 34 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8863 (tm-30) REVERT: A 75 GLU cc_start: 0.7975 (tt0) cc_final: 0.7651 (tm-30) REVERT: A 89 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6025 (mt0) REVERT: A 210 GLU cc_start: 0.8230 (tp30) cc_final: 0.7856 (pt0) REVERT: A 219 ARG cc_start: 0.6487 (ptt-90) cc_final: 0.6116 (ptt180) REVERT: A 430 GLU cc_start: 0.8318 (tt0) cc_final: 0.7940 (mt-10) REVERT: B 357 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8039 (ttt90) REVERT: B 405 ASN cc_start: 0.7810 (m-40) cc_final: 0.7440 (m-40) REVERT: B 440 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8583 (mtpm) REVERT: B 458 LYS cc_start: 0.7608 (pttt) cc_final: 0.7189 (ptpt) outliers start: 23 outliers final: 8 residues processed: 96 average time/residue: 1.0504 time to fit residues: 106.7531 Evaluate side-chains 83 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 401 HIS A 540 HIS A 607 ASN B 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6629 Z= 0.174 Angle : 0.526 10.543 9005 Z= 0.267 Chirality : 0.041 0.166 941 Planarity : 0.004 0.031 1168 Dihedral : 3.759 25.601 927 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.46 % Favored : 94.90 % Rotamer: Outliers : 3.06 % Allowed : 12.97 % Favored : 83.97 % 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: -0.20 (0.31), residues: 785 helix: 0.76 (0.29), residues: 357 sheet: 0.54 (0.83), residues: 43 loop : -1.06 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.016 0.001 TYR A 255 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.755 Fit side-chains REVERT: A 34 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8871 (tm-30) REVERT: A 75 GLU cc_start: 0.7983 (tt0) cc_final: 0.7665 (tm-30) REVERT: A 89 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6121 (mt0) REVERT: A 210 GLU cc_start: 0.8166 (tp30) cc_final: 0.7834 (pt0) REVERT: A 219 ARG cc_start: 0.6525 (ptt-90) cc_final: 0.6156 (ptt180) REVERT: A 246 ARG cc_start: 0.7433 (ttp80) cc_final: 0.6735 (ttp80) REVERT: A 430 GLU cc_start: 0.8312 (tt0) cc_final: 0.8011 (mt-10) REVERT: B 357 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8039 (ttt90) REVERT: B 405 ASN cc_start: 0.7856 (m-40) cc_final: 0.7481 (m-40) REVERT: B 440 LYS cc_start: 0.8897 (mmtp) cc_final: 0.8607 (mtpm) REVERT: B 458 LYS cc_start: 0.7574 (pttt) cc_final: 0.7160 (ptpt) REVERT: B 471 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7260 (mt-10) outliers start: 21 outliers final: 9 residues processed: 91 average time/residue: 1.1831 time to fit residues: 113.8722 Evaluate side-chains 85 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6629 Z= 0.212 Angle : 0.561 10.497 9005 Z= 0.283 Chirality : 0.042 0.192 941 Planarity : 0.004 0.029 1168 Dihedral : 3.959 25.539 927 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.84 % Favored : 94.52 % Rotamer: Outliers : 2.62 % Allowed : 13.12 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.31), residues: 785 helix: 0.74 (0.29), residues: 358 sheet: 0.60 (0.85), residues: 43 loop : -1.03 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.007 0.002 HIS A 241 PHE 0.011 0.001 PHE A 369 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.729 Fit side-chains REVERT: A 75 GLU cc_start: 0.8001 (tt0) cc_final: 0.7677 (tm-30) REVERT: A 89 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6035 (mt0) REVERT: A 210 GLU cc_start: 0.8151 (tp30) cc_final: 0.7841 (pt0) REVERT: A 219 ARG cc_start: 0.6708 (ptt-90) cc_final: 0.6346 (ptt180) REVERT: A 430 GLU cc_start: 0.8366 (tt0) cc_final: 0.8138 (mt-10) REVERT: B 357 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8155 (ttp80) REVERT: B 405 ASN cc_start: 0.7965 (m-40) cc_final: 0.7605 (m-40) REVERT: B 440 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8591 (mtpm) REVERT: B 458 LYS cc_start: 0.7666 (pttt) cc_final: 0.7369 (ptpp) REVERT: B 471 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7337 (mt-10) outliers start: 18 outliers final: 9 residues processed: 87 average time/residue: 1.2724 time to fit residues: 116.5764 Evaluate side-chains 80 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 0.0070 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 0.0770 chunk 72 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 241 HIS A 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6629 Z= 0.130 Angle : 0.504 10.799 9005 Z= 0.254 Chirality : 0.040 0.165 941 Planarity : 0.003 0.029 1168 Dihedral : 3.708 25.053 927 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.59 % Favored : 94.90 % Rotamer: Outliers : 2.04 % Allowed : 14.14 % Favored : 83.82 % 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: 0.01 (0.31), residues: 785 helix: 0.89 (0.29), residues: 359 sheet: 0.59 (0.85), residues: 43 loop : -0.91 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.008 0.001 HIS A 241 PHE 0.009 0.001 PHE A 369 TYR 0.015 0.001 TYR A 255 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.715 Fit side-chains REVERT: A 75 GLU cc_start: 0.7945 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 89 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6149 (mt0) REVERT: A 210 GLU cc_start: 0.8153 (tp30) cc_final: 0.7842 (pt0) REVERT: A 219 ARG cc_start: 0.6554 (ptt-90) cc_final: 0.6188 (ptt180) REVERT: A 255 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.4708 (t80) REVERT: A 430 GLU cc_start: 0.8302 (tt0) cc_final: 0.8017 (mt-10) REVERT: B 346 ARG cc_start: 0.7802 (mmt180) cc_final: 0.7247 (ptm160) REVERT: B 357 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8008 (ttt90) REVERT: B 405 ASN cc_start: 0.7920 (m-40) cc_final: 0.7560 (m-40) REVERT: B 440 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8545 (mtpm) REVERT: B 458 LYS cc_start: 0.7450 (pttt) cc_final: 0.7178 (ptpp) REVERT: B 471 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7271 (mt-10) outliers start: 14 outliers final: 8 residues processed: 87 average time/residue: 1.1473 time to fit residues: 105.4406 Evaluate side-chains 83 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6629 Z= 0.158 Angle : 0.520 10.638 9005 Z= 0.262 Chirality : 0.040 0.167 941 Planarity : 0.003 0.029 1168 Dihedral : 3.702 24.609 927 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.71 % Favored : 94.78 % Rotamer: Outliers : 2.33 % Allowed : 14.14 % Favored : 83.53 % 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: 0.09 (0.31), residues: 785 helix: 1.04 (0.29), residues: 353 sheet: 0.62 (0.85), residues: 43 loop : -0.93 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.008 0.001 HIS A 241 PHE 0.009 0.001 PHE A 369 TYR 0.016 0.001 TYR A 255 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.726 Fit side-chains REVERT: A 75 GLU cc_start: 0.7966 (tt0) cc_final: 0.7645 (tm-30) REVERT: A 89 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6094 (mt0) REVERT: A 210 GLU cc_start: 0.8132 (tp30) cc_final: 0.7842 (pt0) REVERT: A 219 ARG cc_start: 0.6623 (ptt-90) cc_final: 0.6227 (ptt180) REVERT: A 255 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.4531 (t80) REVERT: A 430 GLU cc_start: 0.8312 (tt0) cc_final: 0.8031 (mt-10) REVERT: B 346 ARG cc_start: 0.7827 (mmt180) cc_final: 0.7259 (ptm160) REVERT: B 357 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8041 (ttt90) REVERT: B 405 ASN cc_start: 0.7946 (m-40) cc_final: 0.7594 (m-40) REVERT: B 440 LYS cc_start: 0.8885 (mmtp) cc_final: 0.8596 (mtpm) REVERT: B 458 LYS cc_start: 0.7485 (pttt) cc_final: 0.7213 (ptpp) REVERT: B 471 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7316 (mt-10) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 1.1689 time to fit residues: 107.3149 Evaluate side-chains 84 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 6 optimal weight: 0.0010 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 overall best weight: 0.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.002 0.030 6629 Z= 0.116 Angle : 0.495 10.823 9005 Z= 0.246 Chirality : 0.039 0.157 941 Planarity : 0.003 0.029 1168 Dihedral : 3.520 24.672 927 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.08 % Favored : 95.41 % Rotamer: Outliers : 1.75 % Allowed : 14.87 % Favored : 83.38 % 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: 0.21 (0.31), residues: 785 helix: 1.15 (0.29), residues: 352 sheet: 0.68 (0.85), residues: 43 loop : -0.86 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.010 0.001 HIS A 241 PHE 0.007 0.001 PHE A 369 TYR 0.016 0.001 TYR A 255 ARG 0.001 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.762 Fit side-chains REVERT: A 75 GLU cc_start: 0.7916 (tt0) cc_final: 0.7593 (tm-30) REVERT: A 89 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6090 (mt0) REVERT: A 210 GLU cc_start: 0.8219 (tp30) cc_final: 0.7893 (pt0) REVERT: A 219 ARG cc_start: 0.6487 (ptt-90) cc_final: 0.6102 (ptt180) REVERT: A 255 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.4654 (t80) REVERT: A 430 GLU cc_start: 0.8246 (tt0) cc_final: 0.7975 (mt-10) REVERT: A 607 ASN cc_start: 0.5306 (t0) cc_final: 0.4637 (t0) REVERT: B 346 ARG cc_start: 0.7825 (mmt180) cc_final: 0.7226 (ptm160) REVERT: B 357 ARG cc_start: 0.8377 (ttp80) cc_final: 0.7977 (ttt90) REVERT: B 405 ASN cc_start: 0.7912 (m-40) cc_final: 0.7548 (m-40) REVERT: B 440 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8538 (mtpm) REVERT: B 458 LYS cc_start: 0.7406 (pttt) cc_final: 0.7129 (ptpp) REVERT: B 471 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7203 (mt-10) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 1.2205 time to fit residues: 108.3993 Evaluate side-chains 82 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.0060 chunk 25 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.179017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136348 restraints weight = 7487.040| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.53 r_work: 0.3293 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6629 Z= 0.134 Angle : 0.499 10.681 9005 Z= 0.249 Chirality : 0.039 0.143 941 Planarity : 0.003 0.029 1168 Dihedral : 3.506 24.214 927 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.46 % Favored : 95.03 % Rotamer: Outliers : 1.90 % Allowed : 14.87 % Favored : 83.24 % 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: 0.27 (0.31), residues: 785 helix: 1.20 (0.29), residues: 352 sheet: 0.71 (0.85), residues: 43 loop : -0.83 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.010 0.001 HIS A 241 PHE 0.009 0.001 PHE A 369 TYR 0.016 0.001 TYR A 255 ARG 0.002 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.98 seconds wall clock time: 51 minutes 37.91 seconds (3097.91 seconds total)