Starting phenix.real_space_refine on Tue Feb 13 13:06:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/02_2024/8aqt_15589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/02_2024/8aqt_15589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/02_2024/8aqt_15589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/02_2024/8aqt_15589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/02_2024/8aqt_15589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/02_2024/8aqt_15589.pdb" } resolution = 4.4 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= -0.001 sd= 0.049 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 4033 2.51 5 N 1055 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6321 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4744 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 557} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1535 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 10, 'TRANS': 182} 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: 4.07, per 1000 atoms: 0.64 Number of scatterers: 6321 At special positions: 0 Unit cell: (86.086, 91.3836, 116.547, 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 1196 8.00 N 1055 7.00 C 4033 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 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=2.03 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: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 48.9% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 23 through 53 Processing helix chain 'A' and resid 56 through 80 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.623A pdb=" N GLN A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.350A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 4.222A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.509A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.847A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.827A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.592A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.030A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 239' Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.756A pdb=" N TYR A 243 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.503A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.330A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.733A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.368A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.070A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.076A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.995A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.682A pdb=" N LYS A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.645A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.258A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.777A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.968A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.721A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 removed outlier: 3.934A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.210A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.875A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.241A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.885A pdb=" N THR A 347 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 349 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.597A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 564 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: 1.55 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1476 1.33 - 1.45: 1554 1.45 - 1.58: 3405 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6494 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CA SER B 477 " pdb=" CB SER B 477 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.69e-02 3.50e+03 6.75e+00 bond pdb=" C PRO B 479 " pdb=" O PRO B 479 " ideal model delta sigma weight residual 1.235 1.208 0.027 1.30e-02 5.92e+03 4.40e+00 bond pdb=" CB PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" N THR B 478 " pdb=" CA THR B 478 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.41e-02 5.03e+03 2.44e+00 ... (remaining 6489 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 208 106.99 - 113.76: 3422 113.76 - 120.52: 2654 120.52 - 127.28: 2452 127.28 - 134.04: 83 Bond angle restraints: 8819 Sorted by residual: angle pdb=" C PRO B 479 " pdb=" CA PRO B 479 " pdb=" CB PRO B 479 " ideal model delta sigma weight residual 111.56 100.23 11.33 1.65e+00 3.67e-01 4.71e+01 angle pdb=" N PRO B 479 " pdb=" CA PRO B 479 " pdb=" C PRO B 479 " ideal model delta sigma weight residual 112.47 121.36 -8.89 2.06e+00 2.36e-01 1.86e+01 angle pdb=" N GLN A 287 " pdb=" CA GLN A 287 " pdb=" C GLN A 287 " ideal model delta sigma weight residual 114.31 109.56 4.75 1.29e+00 6.01e-01 1.35e+01 angle pdb=" N PRO A 389 " pdb=" CA PRO A 389 " pdb=" C PRO A 389 " ideal model delta sigma weight residual 112.47 119.46 -6.99 2.06e+00 2.36e-01 1.15e+01 angle pdb=" C ILE A 468 " pdb=" CA ILE A 468 " pdb=" CB ILE A 468 " ideal model delta sigma weight residual 109.33 112.46 -3.13 9.80e-01 1.04e+00 1.02e+01 ... (remaining 8814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 3664 24.45 - 48.90: 187 48.90 - 73.36: 28 73.36 - 97.81: 3 97.81 - 122.26: 3 Dihedral angle restraints: 3885 sinusoidal: 1600 harmonic: 2285 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 93.00 156.68 -63.68 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -139.48 53.48 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.79 53.21 1 1.00e+01 1.00e-02 3.85e+01 ... (remaining 3882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 730 0.050 - 0.101: 170 0.101 - 0.151: 26 0.151 - 0.201: 2 0.201 - 0.252: 1 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA PRO A 389 " pdb=" N PRO A 389 " pdb=" C PRO A 389 " pdb=" CB PRO A 389 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA CYS B 480 " pdb=" N CYS B 480 " pdb=" C CYS B 480 " pdb=" CB CYS B 480 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 6.01e-01 ... (remaining 926 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.40e+01 pdb=" N PRO A 389 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 475 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ALA B 475 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA B 475 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 476 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 469 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " 0.030 5.00e-02 4.00e+02 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 207 2.71 - 3.26: 6506 3.26 - 3.81: 9278 3.81 - 4.35: 11190 4.35 - 4.90: 17785 Nonbonded interactions: 44966 Sorted by model distance: nonbonded pdb=" O LEU A 370 " pdb=" ND1 HIS A 374 " model vdw 2.165 2.520 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.225 2.440 nonbonded pdb=" OE2 GLU A 227 " pdb=" OH TYR A 454 " model vdw 2.226 2.440 nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.239 2.440 nonbonded pdb=" NZ LYS A 247 " pdb=" O LEU A 281 " model vdw 2.240 2.520 ... (remaining 44961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.240 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.720 Find NCS groups from input model: 0.170 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 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 0.086 6494 Z= 0.215 Angle : 0.695 11.326 8819 Z= 0.394 Chirality : 0.044 0.252 929 Planarity : 0.006 0.122 1142 Dihedral : 14.457 122.259 2401 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.43 % Favored : 93.79 % Rotamer: Outliers : 0.45 % Allowed : 0.15 % Favored : 99.41 % Cbeta Deviations : 0.14 % 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: -1.80 (0.29), residues: 773 helix: -0.56 (0.30), residues: 297 sheet: 2.44 (1.08), residues: 22 loop : -1.91 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 48 HIS 0.006 0.001 HIS A 374 PHE 0.016 0.001 PHE A 390 TYR 0.009 0.001 TYR A 215 ARG 0.005 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8580 (mt0) cc_final: 0.8254 (mt0) REVERT: A 74 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 461 TRP cc_start: 0.7929 (m-10) cc_final: 0.7554 (m-10) REVERT: A 539 LEU cc_start: 0.7599 (mt) cc_final: 0.7331 (tp) REVERT: B 386 LYS cc_start: 0.9115 (pttm) cc_final: 0.8733 (tttm) REVERT: B 421 TYR cc_start: 0.8677 (m-80) cc_final: 0.8354 (m-80) REVERT: B 466 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7391 (mmm160) outliers start: 3 outliers final: 3 residues processed: 173 average time/residue: 0.1969 time to fit residues: 43.4947 Evaluate side-chains 96 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 188 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 508 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 422 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6494 Z= 0.263 Angle : 0.708 10.250 8819 Z= 0.362 Chirality : 0.048 0.333 929 Planarity : 0.006 0.123 1142 Dihedral : 9.253 113.311 913 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.47 % Favored : 93.27 % Rotamer: Outliers : 0.59 % Allowed : 5.64 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.90 (0.29), residues: 773 helix: -0.62 (0.30), residues: 296 sheet: 1.45 (1.06), residues: 25 loop : -1.94 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 473 HIS 0.007 0.001 HIS A 374 PHE 0.032 0.002 PHE A 314 TYR 0.012 0.002 TYR B 508 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8179 (pp20) cc_final: 0.7906 (mp0) REVERT: A 74 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 190 MET cc_start: 0.7988 (tpp) cc_final: 0.7776 (tpt) REVERT: A 539 LEU cc_start: 0.7583 (mt) cc_final: 0.7002 (tp) REVERT: B 386 LYS cc_start: 0.9060 (pttm) cc_final: 0.8546 (tttm) REVERT: B 421 TYR cc_start: 0.8678 (m-80) cc_final: 0.8244 (m-80) REVERT: B 440 ASN cc_start: 0.8574 (t0) cc_final: 0.8335 (t0) REVERT: B 518 LEU cc_start: 0.8532 (tp) cc_final: 0.8308 (tp) outliers start: 4 outliers final: 3 residues processed: 125 average time/residue: 0.1960 time to fit residues: 31.7995 Evaluate side-chains 89 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6494 Z= 0.195 Angle : 0.632 9.219 8819 Z= 0.317 Chirality : 0.046 0.336 929 Planarity : 0.005 0.121 1142 Dihedral : 8.813 110.596 913 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.92 % Favored : 94.70 % Rotamer: Outliers : 0.30 % Allowed : 3.71 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.73 (0.29), residues: 773 helix: -0.39 (0.30), residues: 292 sheet: 1.31 (1.04), residues: 25 loop : -1.88 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 461 HIS 0.003 0.001 HIS A 374 PHE 0.017 0.002 PHE A 314 TYR 0.014 0.001 TYR A 215 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8079 (m-30) cc_final: 0.7704 (m-30) REVERT: A 60 GLN cc_start: 0.8812 (mt0) cc_final: 0.8521 (mt0) REVERT: A 74 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 383 MET cc_start: 0.7905 (ptp) cc_final: 0.7231 (tpt) REVERT: A 539 LEU cc_start: 0.7615 (mt) cc_final: 0.7148 (tp) REVERT: B 390 LEU cc_start: 0.9116 (mt) cc_final: 0.8569 (tp) REVERT: B 421 TYR cc_start: 0.8663 (m-80) cc_final: 0.8247 (m-80) REVERT: B 440 ASN cc_start: 0.8616 (t0) cc_final: 0.8374 (t0) REVERT: B 518 LEU cc_start: 0.8507 (tp) cc_final: 0.8278 (tp) outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 0.1898 time to fit residues: 29.0291 Evaluate side-chains 87 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.0270 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 6494 Z= 0.189 Angle : 0.613 9.321 8819 Z= 0.301 Chirality : 0.046 0.330 929 Planarity : 0.005 0.119 1142 Dihedral : 8.567 109.229 913 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.95 % Favored : 93.79 % Rotamer: Outliers : 0.30 % Allowed : 4.15 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.51 (0.30), residues: 773 helix: -0.11 (0.31), residues: 293 sheet: 1.20 (1.02), residues: 25 loop : -1.82 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 461 HIS 0.003 0.001 HIS A 374 PHE 0.024 0.001 PHE A 452 TYR 0.010 0.001 TYR A 215 ARG 0.003 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8304 (m-30) cc_final: 0.7967 (m-30) REVERT: A 60 GLN cc_start: 0.8721 (mt0) cc_final: 0.8440 (mt0) REVERT: A 74 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7890 (tm-30) REVERT: A 539 LEU cc_start: 0.7766 (mt) cc_final: 0.7067 (tp) REVERT: B 390 LEU cc_start: 0.9046 (mt) cc_final: 0.8405 (tp) REVERT: B 421 TYR cc_start: 0.8650 (m-80) cc_final: 0.8227 (m-80) REVERT: B 440 ASN cc_start: 0.8628 (t0) cc_final: 0.8390 (t0) REVERT: B 518 LEU cc_start: 0.8527 (tp) cc_final: 0.8299 (tp) outliers start: 2 outliers final: 2 residues processed: 105 average time/residue: 0.1977 time to fit residues: 27.4461 Evaluate side-chains 86 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 0.0470 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.0040 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.0770 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 6494 Z= 0.177 Angle : 0.623 9.300 8819 Z= 0.302 Chirality : 0.046 0.338 929 Planarity : 0.005 0.116 1142 Dihedral : 8.261 107.217 913 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.92 % Favored : 94.83 % Rotamer: Outliers : 0.15 % Allowed : 1.93 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.36 (0.30), residues: 773 helix: -0.00 (0.31), residues: 299 sheet: 1.03 (0.97), residues: 29 loop : -1.74 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 461 HIS 0.002 0.001 HIS A 505 PHE 0.023 0.001 PHE A 452 TYR 0.009 0.001 TYR A 510 ARG 0.004 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8290 (m-30) cc_final: 0.7979 (m-30) REVERT: A 379 ILE cc_start: 0.8593 (tp) cc_final: 0.8161 (tp) REVERT: A 383 MET cc_start: 0.8075 (ptp) cc_final: 0.7284 (tpt) REVERT: A 539 LEU cc_start: 0.7439 (mt) cc_final: 0.7109 (tp) REVERT: B 390 LEU cc_start: 0.9013 (mt) cc_final: 0.8374 (tp) REVERT: B 421 TYR cc_start: 0.8598 (m-80) cc_final: 0.8155 (m-80) REVERT: B 440 ASN cc_start: 0.8629 (t0) cc_final: 0.8387 (t0) REVERT: B 518 LEU cc_start: 0.8540 (tp) cc_final: 0.8313 (tp) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.2030 time to fit residues: 28.0940 Evaluate side-chains 83 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.0670 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6494 Z= 0.190 Angle : 0.619 9.289 8819 Z= 0.304 Chirality : 0.046 0.313 929 Planarity : 0.005 0.115 1142 Dihedral : 8.342 108.260 913 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.21 % Favored : 93.53 % Rotamer: Outliers : 0.15 % Allowed : 1.63 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.30), residues: 773 helix: 0.03 (0.32), residues: 303 sheet: 1.15 (0.98), residues: 29 loop : -1.67 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 461 HIS 0.004 0.001 HIS A 374 PHE 0.024 0.001 PHE A 452 TYR 0.009 0.001 TYR A 510 ARG 0.003 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8797 (mt0) cc_final: 0.8537 (mt0) REVERT: B 421 TYR cc_start: 0.8577 (m-80) cc_final: 0.8030 (m-80) REVERT: B 440 ASN cc_start: 0.8642 (t0) cc_final: 0.8411 (t0) REVERT: B 518 LEU cc_start: 0.8526 (tp) cc_final: 0.8274 (tp) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.2190 time to fit residues: 30.0067 Evaluate side-chains 79 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6494 Z= 0.190 Angle : 0.631 11.721 8819 Z= 0.306 Chirality : 0.045 0.269 929 Planarity : 0.005 0.114 1142 Dihedral : 8.337 108.409 913 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.60 % Favored : 93.14 % Rotamer: Outliers : 0.15 % Allowed : 1.63 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.30 (0.30), residues: 773 helix: -0.04 (0.31), residues: 304 sheet: 1.14 (0.99), residues: 29 loop : -1.66 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 461 HIS 0.003 0.001 HIS A 374 PHE 0.024 0.001 PHE A 452 TYR 0.008 0.001 TYR A 454 ARG 0.008 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8602 (mm) cc_final: 0.8355 (mm) REVERT: A 60 GLN cc_start: 0.8868 (mt0) cc_final: 0.8587 (mt0) REVERT: A 557 MET cc_start: 0.5616 (mmt) cc_final: 0.5322 (mmt) REVERT: B 421 TYR cc_start: 0.8580 (m-80) cc_final: 0.8018 (m-80) REVERT: B 440 ASN cc_start: 0.8652 (t0) cc_final: 0.8406 (t0) REVERT: B 518 LEU cc_start: 0.8529 (tp) cc_final: 0.8277 (tp) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.2169 time to fit residues: 28.1539 Evaluate side-chains 76 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6494 Z= 0.187 Angle : 0.634 9.312 8819 Z= 0.309 Chirality : 0.045 0.284 929 Planarity : 0.005 0.113 1142 Dihedral : 8.242 107.740 913 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 0.15 % Allowed : 0.89 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.30), residues: 773 helix: -0.04 (0.31), residues: 304 sheet: 1.19 (1.00), residues: 29 loop : -1.63 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 461 HIS 0.003 0.001 HIS A 505 PHE 0.018 0.001 PHE A 452 TYR 0.009 0.001 TYR B 508 ARG 0.005 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8863 (mt0) cc_final: 0.8598 (mt0) REVERT: A 108 LEU cc_start: 0.7469 (tt) cc_final: 0.6431 (mp) REVERT: A 557 MET cc_start: 0.5744 (mmt) cc_final: 0.5429 (mmt) REVERT: B 390 LEU cc_start: 0.8981 (mt) cc_final: 0.8294 (tp) REVERT: B 421 TYR cc_start: 0.8557 (m-80) cc_final: 0.8005 (m-80) REVERT: B 440 ASN cc_start: 0.8654 (t0) cc_final: 0.8408 (t0) REVERT: B 518 LEU cc_start: 0.8547 (tp) cc_final: 0.8304 (tp) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2167 time to fit residues: 27.2591 Evaluate side-chains 77 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6494 Z= 0.182 Angle : 0.632 9.328 8819 Z= 0.306 Chirality : 0.045 0.282 929 Planarity : 0.005 0.112 1142 Dihedral : 8.083 106.427 913 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.08 % Favored : 93.79 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.35 (0.30), residues: 773 helix: -0.10 (0.31), residues: 304 sheet: 1.12 (0.99), residues: 29 loop : -1.68 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 461 HIS 0.002 0.001 HIS A 505 PHE 0.020 0.001 PHE A 452 TYR 0.010 0.001 TYR B 508 ARG 0.006 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8857 (mt0) cc_final: 0.8644 (mt0) REVERT: A 108 LEU cc_start: 0.7468 (tt) cc_final: 0.6475 (mp) REVERT: A 557 MET cc_start: 0.5659 (mmt) cc_final: 0.5385 (mmt) REVERT: B 390 LEU cc_start: 0.8974 (mt) cc_final: 0.8319 (tp) REVERT: B 421 TYR cc_start: 0.8547 (m-80) cc_final: 0.7984 (m-80) REVERT: B 440 ASN cc_start: 0.8660 (t0) cc_final: 0.8414 (t0) REVERT: B 518 LEU cc_start: 0.8592 (tp) cc_final: 0.8380 (tp) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.1981 time to fit residues: 26.0348 Evaluate side-chains 79 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 70 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6494 Z= 0.180 Angle : 0.648 9.360 8819 Z= 0.313 Chirality : 0.045 0.280 929 Planarity : 0.005 0.111 1142 Dihedral : 8.004 105.603 913 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.47 % Favored : 93.40 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.35 (0.30), residues: 773 helix: -0.13 (0.30), residues: 310 sheet: 1.18 (0.98), residues: 29 loop : -1.67 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 461 HIS 0.002 0.001 HIS A 505 PHE 0.016 0.001 PHE A 452 TYR 0.009 0.001 TYR B 508 ARG 0.009 0.000 ARG B 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8880 (mt0) cc_final: 0.8675 (mt0) REVERT: A 108 LEU cc_start: 0.7354 (tt) cc_final: 0.6453 (mp) REVERT: A 557 MET cc_start: 0.4907 (mmt) cc_final: 0.4669 (mmt) REVERT: B 390 LEU cc_start: 0.9009 (mt) cc_final: 0.8366 (tp) REVERT: B 421 TYR cc_start: 0.8556 (m-80) cc_final: 0.7996 (m-80) REVERT: B 440 ASN cc_start: 0.8622 (t0) cc_final: 0.8414 (t0) REVERT: B 518 LEU cc_start: 0.8587 (tp) cc_final: 0.8374 (tp) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1954 time to fit residues: 24.4749 Evaluate side-chains 83 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN B 394 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.143323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.130808 restraints weight = 33491.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.132597 restraints weight = 22994.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.133795 restraints weight = 16913.104| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6494 Z= 0.177 Angle : 0.620 9.403 8819 Z= 0.300 Chirality : 0.045 0.279 929 Planarity : 0.005 0.110 1142 Dihedral : 7.971 105.193 913 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.24 (0.30), residues: 773 helix: -0.07 (0.30), residues: 316 sheet: 1.12 (0.97), residues: 29 loop : -1.59 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 461 HIS 0.002 0.001 HIS A 374 PHE 0.018 0.001 PHE A 452 TYR 0.008 0.001 TYR A 510 ARG 0.009 0.000 ARG B 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.14 seconds wall clock time: 31 minutes 27.71 seconds (1887.71 seconds total)