Starting phenix.real_space_refine on Wed Sep 17 06:56:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dzz_8943/09_2025/6dzz_8943.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzz_8943/09_2025/6dzz_8943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dzz_8943/09_2025/6dzz_8943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzz_8943/09_2025/6dzz_8943.map" model { file = "/net/cci-nas-00/data/ceres_data/6dzz_8943/09_2025/6dzz_8943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzz_8943/09_2025/6dzz_8943.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.036 sd= 1.351 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 34 5.16 5 C 4046 2.51 5 N 965 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6141 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4314 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'HJM': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.28 Number of scatterers: 6141 At special positions: 0 Unit cell: (81.477, 79.008, 115.22, 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 34 16.00 O 1096 8.00 N 965 7.00 C 4046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 320.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 48.3% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.726A pdb=" N LYS A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 112 removed outlier: 4.029A pdb=" N TYR A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.676A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 removed outlier: 3.744A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 159 through 176 removed outlier: 3.673A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.614A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.975A pdb=" N TYR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.540A pdb=" N LEU A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 4.265A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 310 through 314 removed outlier: 4.079A pdb=" N LYS A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.924A pdb=" N SER A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 removed outlier: 3.864A pdb=" N LEU A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 4.325A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 414 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 441 removed outlier: 3.630A pdb=" N ALA A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.517A pdb=" N THR A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.758A pdb=" N ASP A 452 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.719A pdb=" N VAL A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 490 through 495 removed outlier: 3.535A pdb=" N TYR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.567A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 removed outlier: 3.756A pdb=" N PHE A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 526 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.848A pdb=" N ILE A 539 " --> pdb=" O TRP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 559 removed outlier: 3.692A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET A 558 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 4.040A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.530A pdb=" N THR A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.952A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.800A pdb=" N TYR B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.747A pdb=" N THR C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 25 removed outlier: 3.752A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 97 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.059A pdb=" N ASP B 76 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 113 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.942A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 113 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 60 " --> pdb=" O PHE C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 207 hydrogen bonds defined for protein. 585 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: 0.84 Time building geometry restraints manager: 0.70 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: 1783 1.34 - 1.46: 1438 1.46 - 1.58: 3054 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 6326 Sorted by residual: bond pdb=" C2 HJM A 701 " pdb=" C8 HJM A 701 " ideal model delta sigma weight residual 1.490 1.593 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C7 HJM A 701 " pdb=" N1 HJM A 701 " ideal model delta sigma weight residual 1.472 1.566 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C9 HJM A 701 " pdb=" N1 HJM A 701 " ideal model delta sigma weight residual 1.467 1.558 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C18 HJM A 701 " pdb=" C19 HJM A 701 " ideal model delta sigma weight residual 1.407 1.492 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O HJM A 701 " pdb=" C18 HJM A 701 " ideal model delta sigma weight residual 1.374 1.430 -0.056 2.00e-02 2.50e+03 7.83e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 8412 2.38 - 4.75: 155 4.75 - 7.13: 36 7.13 - 9.50: 8 9.50 - 11.88: 3 Bond angle restraints: 8614 Sorted by residual: angle pdb=" C ASP A 216 " pdb=" N ASN A 217 " pdb=" CA ASN A 217 " ideal model delta sigma weight residual 122.46 129.63 -7.17 1.41e+00 5.03e-01 2.58e+01 angle pdb=" N GLY A 338 " pdb=" CA GLY A 338 " pdb=" C GLY A 338 " ideal model delta sigma weight residual 112.34 120.92 -8.58 2.04e+00 2.40e-01 1.77e+01 angle pdb=" C GLY B 121 " pdb=" N SER B 122 " pdb=" CA SER B 122 " ideal model delta sigma weight residual 120.63 127.40 -6.77 1.61e+00 3.86e-01 1.77e+01 angle pdb=" C ASN A 569 " pdb=" N TYR A 570 " pdb=" CA TYR A 570 " ideal model delta sigma weight residual 121.80 131.99 -10.19 2.44e+00 1.68e-01 1.74e+01 angle pdb=" N SER B 122 " pdb=" CA SER B 122 " pdb=" C SER B 122 " ideal model delta sigma weight residual 112.34 117.67 -5.33 1.30e+00 5.92e-01 1.68e+01 ... (remaining 8609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 3664 35.47 - 70.93: 25 70.93 - 106.40: 8 106.40 - 141.86: 0 141.86 - 177.33: 3 Dihedral angle restraints: 3700 sinusoidal: 1491 harmonic: 2209 Sorted by residual: dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 112 " pdb=" CB CYS C 112 " ideal model delta sinusoidal sigma weight residual 93.00 132.33 -39.33 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" C16 HJM A 701 " pdb=" O HJM A 701 " pdb=" C18 HJM A 701 " pdb=" C20 HJM A 701 " ideal model delta sinusoidal sigma weight residual -178.78 -1.45 -177.33 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 HJM A 701 " pdb=" O HJM A 701 " pdb=" C18 HJM A 701 " pdb=" C20 HJM A 701 " ideal model delta sinusoidal sigma weight residual 1.28 173.41 -172.13 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 3697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 843 0.073 - 0.146: 105 0.146 - 0.219: 7 0.219 - 0.292: 2 0.292 - 0.365: 2 Chirality restraints: 959 Sorted by residual: chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C2 HJM A 701 " pdb=" C1 HJM A 701 " pdb=" C5 HJM A 701 " pdb=" C8 HJM A 701 " both_signs ideal model delta sigma weight residual False -2.62 -2.28 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE C 99 " pdb=" CA ILE C 99 " pdb=" CG1 ILE C 99 " pdb=" CG2 ILE C 99 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 956 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O HJM A 701 " -0.042 2.00e-02 2.50e+03 7.19e-02 1.55e+02 pdb=" C11 HJM A 701 " 0.051 2.00e-02 2.50e+03 pdb=" C12 HJM A 701 " 0.086 2.00e-02 2.50e+03 pdb=" C13 HJM A 701 " -0.014 2.00e-02 2.50e+03 pdb=" C15 HJM A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C16 HJM A 701 " -0.129 2.00e-02 2.50e+03 pdb=" C17 HJM A 701 " 0.068 2.00e-02 2.50e+03 pdb=" C18 HJM A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C19 HJM A 701 " 0.105 2.00e-02 2.50e+03 pdb=" C2 HJM A 701 " -0.018 2.00e-02 2.50e+03 pdb=" C8 HJM A 701 " 0.013 2.00e-02 2.50e+03 pdb=" N2 HJM A 701 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 498 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 499 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 560 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO A 561 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.034 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 4 2.35 - 2.99: 2788 2.99 - 3.63: 8594 3.63 - 4.26: 13473 4.26 - 4.90: 21533 Nonbonded interactions: 46392 Sorted by model distance: nonbonded pdb=" OH TYR A 107 " pdb=" OE2 GLU A 493 " model vdw 1.715 3.040 nonbonded pdb=" OH TYR A 107 " pdb=" CD GLU A 493 " model vdw 1.910 3.270 nonbonded pdb=" OH TYR A 107 " pdb=" OE1 GLU A 493 " model vdw 2.001 3.040 nonbonded pdb=" CZ TYR A 107 " pdb=" OE2 GLU A 493 " model vdw 2.262 3.260 nonbonded pdb=" O5' LMT A 704 " pdb=" O6' LMT A 704 " model vdw 2.358 2.432 ... (remaining 46387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.090 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 6331 Z= 0.249 Angle : 0.851 11.877 8626 Z= 0.428 Chirality : 0.052 0.365 959 Planarity : 0.008 0.072 1050 Dihedral : 11.997 177.328 2289 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.16 % Allowed : 1.40 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.28 (0.22), residues: 762 helix: -4.59 (0.10), residues: 301 sheet: -2.47 (0.50), residues: 94 loop : -2.71 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 234 TYR 0.015 0.002 TYR C 73 PHE 0.035 0.001 PHE A 454 TRP 0.022 0.002 TRP B 130 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 6326) covalent geometry : angle 0.84645 ( 8614) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.93679 ( 6) hydrogen bonds : bond 0.33019 ( 207) hydrogen bonds : angle 9.64043 ( 585) link_BETA1-4 : bond 0.00886 ( 1) link_BETA1-4 : angle 1.48718 ( 3) link_NAG-ASN : bond 0.00546 ( 1) link_NAG-ASN : angle 4.85078 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8563 (t80) cc_final: 0.8339 (t80) REVERT: A 145 ASN cc_start: 0.8176 (m110) cc_final: 0.7690 (m-40) REVERT: A 272 LYS cc_start: 0.6303 (mmtt) cc_final: 0.5992 (pttt) REVERT: A 326 TRP cc_start: 0.7372 (m-10) cc_final: 0.7098 (m-10) REVERT: A 385 TYR cc_start: 0.8146 (t80) cc_final: 0.7512 (t80) REVERT: A 558 MET cc_start: 0.4587 (tpt) cc_final: 0.3420 (mtt) REVERT: B 50 TYR cc_start: 0.4382 (t80) cc_final: 0.4068 (t80) REVERT: B 101 GLN cc_start: 0.6951 (mt0) cc_final: 0.6228 (tm-30) REVERT: B 102 LEU cc_start: 0.8568 (mt) cc_final: 0.8270 (tt) REVERT: B 108 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 127 MET cc_start: 0.5917 (mtp) cc_final: 0.5629 (mtm) REVERT: B 129 TYR cc_start: 0.7339 (m-10) cc_final: 0.6536 (m-80) REVERT: C 22 ILE cc_start: 0.7416 (mt) cc_final: 0.7206 (mp) REVERT: C 112 CYS cc_start: 0.4762 (t) cc_final: 0.4471 (t) REVERT: C 116 LYS cc_start: 0.7015 (tttt) cc_final: 0.6421 (mttt) outliers start: 1 outliers final: 1 residues processed: 218 average time/residue: 0.0831 time to fit residues: 23.5975 Evaluate side-chains 133 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 202 ASN A 254 GLN B 25 GLN C 51 ASN C 100 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.140826 restraints weight = 13165.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.144821 restraints weight = 6907.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.147507 restraints weight = 4365.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.149326 restraints weight = 3130.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.150525 restraints weight = 2445.783| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6331 Z= 0.121 Angle : 0.680 12.673 8626 Z= 0.332 Chirality : 0.043 0.271 959 Planarity : 0.006 0.050 1050 Dihedral : 10.452 145.096 974 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.26 % Allowed : 10.39 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.26), residues: 762 helix: -2.61 (0.22), residues: 332 sheet: -2.17 (0.51), residues: 92 loop : -2.38 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 104 TYR 0.019 0.001 TYR A 495 PHE 0.035 0.001 PHE A 454 TRP 0.015 0.001 TRP A 282 HIS 0.007 0.002 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6326) covalent geometry : angle 0.67475 ( 8614) SS BOND : bond 0.00594 ( 3) SS BOND : angle 1.89332 ( 6) hydrogen bonds : bond 0.04684 ( 207) hydrogen bonds : angle 5.35464 ( 585) link_BETA1-4 : bond 0.00760 ( 1) link_BETA1-4 : angle 0.38483 ( 3) link_NAG-ASN : bond 0.00464 ( 1) link_NAG-ASN : angle 3.70761 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8471 (t80) cc_final: 0.8045 (t80) REVERT: A 526 LYS cc_start: 0.7693 (mttt) cc_final: 0.7290 (ttmm) REVERT: A 558 MET cc_start: 0.4380 (tpt) cc_final: 0.3366 (mtt) REVERT: A 597 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8755 (pt) REVERT: B 50 TYR cc_start: 0.4471 (t80) cc_final: 0.3723 (t80) REVERT: B 101 GLN cc_start: 0.7240 (mt0) cc_final: 0.6816 (pt0) REVERT: B 102 LEU cc_start: 0.8274 (mt) cc_final: 0.8056 (tt) REVERT: B 129 TYR cc_start: 0.7402 (m-10) cc_final: 0.6914 (m-10) REVERT: C 22 ILE cc_start: 0.7345 (mt) cc_final: 0.7089 (mp) REVERT: C 44 ARG cc_start: 0.6306 (mmt-90) cc_final: 0.5213 (mmm160) REVERT: C 86 PHE cc_start: 0.5578 (m-80) cc_final: 0.5325 (m-10) REVERT: C 116 LYS cc_start: 0.7031 (tttt) cc_final: 0.6361 (ptpt) outliers start: 21 outliers final: 15 residues processed: 144 average time/residue: 0.0738 time to fit residues: 14.3938 Evaluate side-chains 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.156442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.138301 restraints weight = 13404.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.142101 restraints weight = 7114.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.144699 restraints weight = 4574.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.146351 restraints weight = 3300.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.147686 restraints weight = 2618.753| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6331 Z= 0.129 Angle : 0.629 10.413 8626 Z= 0.311 Chirality : 0.042 0.276 959 Planarity : 0.005 0.054 1050 Dihedral : 9.233 156.257 974 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.58 % Allowed : 11.16 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.83 (0.29), residues: 762 helix: -1.63 (0.25), residues: 342 sheet: -1.70 (0.53), residues: 90 loop : -2.07 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.014 0.001 TYR A 385 PHE 0.023 0.001 PHE A 454 TRP 0.014 0.001 TRP B 130 HIS 0.002 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6326) covalent geometry : angle 0.62322 ( 8614) SS BOND : bond 0.00074 ( 3) SS BOND : angle 2.08616 ( 6) hydrogen bonds : bond 0.03960 ( 207) hydrogen bonds : angle 4.64329 ( 585) link_BETA1-4 : bond 0.00429 ( 1) link_BETA1-4 : angle 0.62268 ( 3) link_NAG-ASN : bond 0.00253 ( 1) link_NAG-ASN : angle 3.58011 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6342 (mpp) REVERT: A 526 LYS cc_start: 0.7820 (mttt) cc_final: 0.7372 (ttmm) REVERT: A 548 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 558 MET cc_start: 0.4475 (tpt) cc_final: 0.3543 (mtt) REVERT: B 129 TYR cc_start: 0.7531 (m-10) cc_final: 0.6723 (m-80) REVERT: C 69 LYS cc_start: 0.7250 (tmtt) cc_final: 0.6989 (tmtt) REVERT: C 71 LEU cc_start: 0.8584 (tp) cc_final: 0.8375 (mt) REVERT: C 116 LYS cc_start: 0.7219 (tttt) cc_final: 0.6515 (ptpt) outliers start: 36 outliers final: 27 residues processed: 136 average time/residue: 0.0820 time to fit residues: 15.0095 Evaluate side-chains 131 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 537 TRP Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 62 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 101 GLN ** C 62 GLN ** 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 = 0.4211 r_free = 0.4211 target = 0.158065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.140170 restraints weight = 13741.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.144060 restraints weight = 7240.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.146692 restraints weight = 4601.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.148488 restraints weight = 3288.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.149690 restraints weight = 2550.991| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6331 Z= 0.108 Angle : 0.615 12.049 8626 Z= 0.295 Chirality : 0.042 0.265 959 Planarity : 0.004 0.046 1050 Dihedral : 8.013 128.139 974 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.50 % Allowed : 14.11 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.30), residues: 762 helix: -1.10 (0.27), residues: 341 sheet: -1.29 (0.54), residues: 90 loop : -1.91 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.012 0.001 TYR A 385 PHE 0.019 0.001 PHE A 454 TRP 0.012 0.001 TRP A 282 HIS 0.002 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6326) covalent geometry : angle 0.61092 ( 8614) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.71979 ( 6) hydrogen bonds : bond 0.03325 ( 207) hydrogen bonds : angle 4.36171 ( 585) link_BETA1-4 : bond 0.00297 ( 1) link_BETA1-4 : angle 0.48889 ( 3) link_NAG-ASN : bond 0.00428 ( 1) link_NAG-ASN : angle 3.26655 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LYS cc_start: 0.7873 (mttt) cc_final: 0.7359 (tmtt) REVERT: A 548 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7605 (t80) REVERT: A 558 MET cc_start: 0.4617 (tpt) cc_final: 0.3672 (mtt) REVERT: C 44 ARG cc_start: 0.5644 (mmm160) cc_final: 0.4836 (mmm160) REVERT: C 116 LYS cc_start: 0.7098 (tttt) cc_final: 0.6494 (ptpt) outliers start: 29 outliers final: 20 residues processed: 121 average time/residue: 0.0764 time to fit residues: 12.5137 Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 254 GLN ** C 62 GLN ** 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 = 0.4168 r_free = 0.4168 target = 0.154097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.136020 restraints weight = 13728.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139829 restraints weight = 7216.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.142428 restraints weight = 4613.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.144225 restraints weight = 3324.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.145392 restraints weight = 2594.290| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6331 Z= 0.120 Angle : 0.612 11.651 8626 Z= 0.299 Chirality : 0.043 0.277 959 Planarity : 0.004 0.049 1050 Dihedral : 6.050 59.565 974 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.27 % Allowed : 13.95 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.30), residues: 762 helix: -0.69 (0.28), residues: 339 sheet: -1.22 (0.52), residues: 91 loop : -1.75 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.013 0.001 TYR A 289 PHE 0.016 0.001 PHE A 454 TRP 0.015 0.001 TRP B 130 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6326) covalent geometry : angle 0.60741 ( 8614) SS BOND : bond 0.00119 ( 3) SS BOND : angle 1.57509 ( 6) hydrogen bonds : bond 0.03226 ( 207) hydrogen bonds : angle 4.17060 ( 585) link_BETA1-4 : bond 0.00328 ( 1) link_BETA1-4 : angle 0.60563 ( 3) link_NAG-ASN : bond 0.00183 ( 1) link_NAG-ASN : angle 3.48187 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6359 (mpp) REVERT: A 526 LYS cc_start: 0.7877 (mttt) cc_final: 0.7318 (tmtt) REVERT: A 548 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7652 (t80) REVERT: A 558 MET cc_start: 0.4526 (tpt) cc_final: 0.3583 (mtt) REVERT: B 76 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: B 102 LEU cc_start: 0.7690 (tt) cc_final: 0.7481 (tt) REVERT: B 125 PHE cc_start: 0.4884 (p90) cc_final: 0.4640 (p90) REVERT: C 44 ARG cc_start: 0.5654 (mmm160) cc_final: 0.5002 (mmm160) REVERT: C 86 PHE cc_start: 0.6275 (m-80) cc_final: 0.5898 (m-80) REVERT: C 116 LYS cc_start: 0.7242 (tttt) cc_final: 0.6484 (ptpt) outliers start: 34 outliers final: 25 residues processed: 126 average time/residue: 0.0706 time to fit residues: 12.2939 Evaluate side-chains 126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 537 TRP Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.153173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135184 restraints weight = 13510.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.138978 restraints weight = 7105.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.141487 restraints weight = 4547.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.143239 restraints weight = 3298.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.144457 restraints weight = 2585.228| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6331 Z= 0.116 Angle : 0.610 10.915 8626 Z= 0.298 Chirality : 0.042 0.272 959 Planarity : 0.004 0.047 1050 Dihedral : 5.485 59.341 974 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.81 % Allowed : 15.50 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.30), residues: 762 helix: -0.39 (0.28), residues: 338 sheet: -1.03 (0.53), residues: 91 loop : -1.65 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.011 0.001 TYR A 385 PHE 0.015 0.001 PHE A 454 TRP 0.010 0.001 TRP A 541 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6326) covalent geometry : angle 0.60535 ( 8614) SS BOND : bond 0.00092 ( 3) SS BOND : angle 1.55525 ( 6) hydrogen bonds : bond 0.03147 ( 207) hydrogen bonds : angle 4.04867 ( 585) link_BETA1-4 : bond 0.00374 ( 1) link_BETA1-4 : angle 0.61091 ( 3) link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 3.37025 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.6710 (mp0) cc_final: 0.6355 (mp0) REVERT: A 475 PHE cc_start: 0.6362 (m-80) cc_final: 0.6077 (m-80) REVERT: A 526 LYS cc_start: 0.7876 (mttt) cc_final: 0.7277 (tmtt) REVERT: A 528 MET cc_start: 0.7773 (pmm) cc_final: 0.7539 (pmm) REVERT: A 548 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7626 (t80) REVERT: A 558 MET cc_start: 0.4652 (tpt) cc_final: 0.3660 (mtt) REVERT: B 125 PHE cc_start: 0.5056 (p90) cc_final: 0.4778 (p90) REVERT: C 44 ARG cc_start: 0.5627 (mmm160) cc_final: 0.5090 (mmm160) REVERT: C 116 LYS cc_start: 0.7127 (tttt) cc_final: 0.6476 (ptpt) outliers start: 31 outliers final: 24 residues processed: 125 average time/residue: 0.0682 time to fit residues: 11.8312 Evaluate side-chains 128 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 537 TRP Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN B 101 GLN C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.151921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.134013 restraints weight = 13566.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.137736 restraints weight = 7134.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.140326 restraints weight = 4576.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.142099 restraints weight = 3297.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.143230 restraints weight = 2574.344| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6331 Z= 0.117 Angle : 0.618 10.188 8626 Z= 0.298 Chirality : 0.042 0.281 959 Planarity : 0.004 0.044 1050 Dihedral : 5.445 59.249 974 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 6.05 % Allowed : 15.50 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.31), residues: 762 helix: -0.23 (0.28), residues: 337 sheet: -0.92 (0.52), residues: 91 loop : -1.58 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.020 0.001 TYR A 110 PHE 0.014 0.001 PHE A 454 TRP 0.011 0.001 TRP A 541 HIS 0.003 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6326) covalent geometry : angle 0.61361 ( 8614) SS BOND : bond 0.00133 ( 3) SS BOND : angle 1.54204 ( 6) hydrogen bonds : bond 0.03086 ( 207) hydrogen bonds : angle 4.06409 ( 585) link_BETA1-4 : bond 0.00340 ( 1) link_BETA1-4 : angle 0.58619 ( 3) link_NAG-ASN : bond 0.00226 ( 1) link_NAG-ASN : angle 3.47706 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6290 (mpp) REVERT: A 215 GLU cc_start: 0.6724 (mp0) cc_final: 0.6350 (mp0) REVERT: A 526 LYS cc_start: 0.7933 (mttt) cc_final: 0.7328 (tmtt) REVERT: A 528 MET cc_start: 0.7763 (pmm) cc_final: 0.7476 (pmm) REVERT: A 548 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7590 (t80) REVERT: A 558 MET cc_start: 0.4823 (tpt) cc_final: 0.3835 (mtt) REVERT: B 101 GLN cc_start: 0.7623 (pt0) cc_final: 0.7372 (tm-30) REVERT: B 125 PHE cc_start: 0.5016 (p90) cc_final: 0.4788 (p90) REVERT: C 44 ARG cc_start: 0.5466 (mmm160) cc_final: 0.4799 (mmm160) REVERT: C 116 LYS cc_start: 0.7141 (tttt) cc_final: 0.6538 (ptpt) outliers start: 39 outliers final: 31 residues processed: 132 average time/residue: 0.0756 time to fit residues: 13.4480 Evaluate side-chains 136 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 13 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.155162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.137287 restraints weight = 13679.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.141163 restraints weight = 7149.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.143823 restraints weight = 4501.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.145616 restraints weight = 3209.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.146781 restraints weight = 2488.579| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6331 Z= 0.100 Angle : 0.606 10.801 8626 Z= 0.291 Chirality : 0.041 0.264 959 Planarity : 0.004 0.040 1050 Dihedral : 5.356 59.397 974 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.50 % Allowed : 16.74 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.31), residues: 762 helix: -0.03 (0.29), residues: 339 sheet: -0.65 (0.53), residues: 91 loop : -1.48 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.016 0.001 TYR A 110 PHE 0.013 0.001 PHE A 454 TRP 0.010 0.001 TRP A 282 HIS 0.002 0.000 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6326) covalent geometry : angle 0.60266 ( 8614) SS BOND : bond 0.00199 ( 3) SS BOND : angle 1.53806 ( 6) hydrogen bonds : bond 0.02909 ( 207) hydrogen bonds : angle 3.87543 ( 585) link_BETA1-4 : bond 0.00328 ( 1) link_BETA1-4 : angle 0.56797 ( 3) link_NAG-ASN : bond 0.00398 ( 1) link_NAG-ASN : angle 3.08159 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6039 (mpp) REVERT: A 215 GLU cc_start: 0.6639 (mp0) cc_final: 0.6327 (mp0) REVERT: A 475 PHE cc_start: 0.6426 (m-80) cc_final: 0.6170 (m-80) REVERT: A 526 LYS cc_start: 0.7853 (mttt) cc_final: 0.7264 (tmtt) REVERT: A 528 MET cc_start: 0.7784 (pmm) cc_final: 0.7479 (pmm) REVERT: A 548 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7608 (t80) REVERT: A 558 MET cc_start: 0.4642 (tpt) cc_final: 0.3654 (mtt) REVERT: B 76 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: B 125 PHE cc_start: 0.4862 (p90) cc_final: 0.4444 (p90) REVERT: C 44 ARG cc_start: 0.5280 (mmm160) cc_final: 0.5007 (mmm160) REVERT: C 116 LYS cc_start: 0.6877 (tttt) cc_final: 0.6227 (ptpt) outliers start: 29 outliers final: 21 residues processed: 122 average time/residue: 0.0700 time to fit residues: 11.7819 Evaluate side-chains 126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN B 25 GLN B 58 GLN C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.148992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130569 restraints weight = 13839.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.134264 restraints weight = 7463.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.136838 restraints weight = 4860.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.138528 restraints weight = 3573.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.139740 restraints weight = 2848.162| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6331 Z= 0.202 Angle : 0.743 10.081 8626 Z= 0.365 Chirality : 0.046 0.301 959 Planarity : 0.005 0.042 1050 Dihedral : 5.895 59.959 972 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.81 % Allowed : 16.12 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.30), residues: 762 helix: -0.17 (0.28), residues: 334 sheet: -0.96 (0.48), residues: 101 loop : -1.57 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 104 TYR 0.021 0.002 TYR A 110 PHE 0.029 0.002 PHE A 341 TRP 0.020 0.002 TRP A 151 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 6326) covalent geometry : angle 0.73740 ( 8614) SS BOND : bond 0.00363 ( 3) SS BOND : angle 1.87607 ( 6) hydrogen bonds : bond 0.03580 ( 207) hydrogen bonds : angle 4.37287 ( 585) link_BETA1-4 : bond 0.00153 ( 1) link_BETA1-4 : angle 0.74565 ( 3) link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 4.04878 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6478 (mpp) REVERT: A 318 GLN cc_start: 0.6152 (tp40) cc_final: 0.5520 (tp40) REVERT: A 465 PHE cc_start: 0.7245 (p90) cc_final: 0.6965 (p90) REVERT: A 526 LYS cc_start: 0.8015 (mttt) cc_final: 0.7401 (tmtt) REVERT: A 548 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7661 (t80) REVERT: A 558 MET cc_start: 0.4743 (tpt) cc_final: 0.3751 (mtt) REVERT: B 69 ARG cc_start: 0.8050 (ptt90) cc_final: 0.7734 (ptt90) REVERT: B 76 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.6910 (m-30) REVERT: B 101 GLN cc_start: 0.7498 (tm-30) cc_final: 0.6928 (tm-30) REVERT: C 44 ARG cc_start: 0.5414 (mmm160) cc_final: 0.5178 (mmm160) REVERT: C 116 LYS cc_start: 0.7398 (tttt) cc_final: 0.6503 (ptpt) outliers start: 31 outliers final: 24 residues processed: 133 average time/residue: 0.0701 time to fit residues: 12.8151 Evaluate side-chains 131 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.0060 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 0.0070 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.152056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.134201 restraints weight = 13690.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.138073 restraints weight = 7160.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140658 restraints weight = 4551.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.142383 restraints weight = 3274.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.143660 restraints weight = 2568.844| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6331 Z= 0.112 Angle : 0.651 10.950 8626 Z= 0.317 Chirality : 0.042 0.262 959 Planarity : 0.005 0.091 1050 Dihedral : 5.514 57.840 972 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.57 % Allowed : 18.91 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.31), residues: 762 helix: 0.02 (0.28), residues: 349 sheet: -0.61 (0.51), residues: 96 loop : -1.44 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 462 TYR 0.012 0.001 TYR A 110 PHE 0.029 0.001 PHE A 531 TRP 0.016 0.001 TRP A 458 HIS 0.003 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6326) covalent geometry : angle 0.64687 ( 8614) SS BOND : bond 0.00231 ( 3) SS BOND : angle 1.68565 ( 6) hydrogen bonds : bond 0.03031 ( 207) hydrogen bonds : angle 4.00981 ( 585) link_BETA1-4 : bond 0.00454 ( 1) link_BETA1-4 : angle 0.81577 ( 3) link_NAG-ASN : bond 0.00250 ( 1) link_NAG-ASN : angle 3.29823 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6033 (mpp) REVERT: A 215 GLU cc_start: 0.6690 (mp0) cc_final: 0.6354 (mp0) REVERT: A 318 GLN cc_start: 0.6118 (tp40) cc_final: 0.5561 (tp40) REVERT: A 375 SER cc_start: 0.8882 (m) cc_final: 0.8323 (t) REVERT: A 465 PHE cc_start: 0.6981 (p90) cc_final: 0.6634 (p90) REVERT: A 526 LYS cc_start: 0.7944 (mttt) cc_final: 0.7358 (tmtt) REVERT: A 548 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7646 (t80) REVERT: A 558 MET cc_start: 0.4761 (tpt) cc_final: 0.3811 (mtt) REVERT: B 76 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.6892 (m-30) REVERT: C 44 ARG cc_start: 0.5462 (mmm160) cc_final: 0.5172 (mmm160) REVERT: C 105 ASP cc_start: 0.8156 (t0) cc_final: 0.7807 (t0) REVERT: C 116 LYS cc_start: 0.6785 (tttt) cc_final: 0.6231 (ptpt) outliers start: 23 outliers final: 19 residues processed: 123 average time/residue: 0.0753 time to fit residues: 12.5073 Evaluate side-chains 126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.151575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.133833 restraints weight = 13658.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.137643 restraints weight = 7207.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.140179 restraints weight = 4608.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.141775 restraints weight = 3329.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.143108 restraints weight = 2639.781| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6331 Z= 0.113 Angle : 0.645 10.516 8626 Z= 0.312 Chirality : 0.043 0.279 959 Planarity : 0.005 0.089 1050 Dihedral : 5.452 59.194 972 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.72 % Allowed : 19.53 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.31), residues: 762 helix: 0.23 (0.28), residues: 344 sheet: -0.54 (0.51), residues: 96 loop : -1.41 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.015 0.001 TYR A 110 PHE 0.026 0.001 PHE A 531 TRP 0.014 0.001 TRP A 458 HIS 0.005 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6326) covalent geometry : angle 0.64076 ( 8614) SS BOND : bond 0.00222 ( 3) SS BOND : angle 1.58170 ( 6) hydrogen bonds : bond 0.02897 ( 207) hydrogen bonds : angle 3.96255 ( 585) link_BETA1-4 : bond 0.00352 ( 1) link_BETA1-4 : angle 0.61982 ( 3) link_NAG-ASN : bond 0.00223 ( 1) link_NAG-ASN : angle 3.37053 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1223.54 seconds wall clock time: 21 minutes 52.48 seconds (1312.48 seconds total)