Starting phenix.real_space_refine on Thu Jul 2 04:24:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wum_66264/07_2026/9wum_66264.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wum_66264/07_2026/9wum_66264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wum_66264/07_2026/9wum_66264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wum_66264/07_2026/9wum_66264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wum_66264/07_2026/9wum_66264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wum_66264/07_2026/9wum_66264.map" } resolution = 3.48 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= 0.001 sd= 0.030 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 18 5.16 5 C 4062 2.51 5 N 1045 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6441 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4610 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 33, 'TRANS': 559} Chain: "C" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1351 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 11, 'TRANS': 166} Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 158 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.37, per 1000 atoms: 0.21 Number of scatterers: 6441 At special positions: 0 Unit cell: (75.65, 91.8, 119, 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 18 16.00 O 1316 8.00 N 1045 7.00 C 4062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 64 " distance=2.02 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 21 " 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 Atom "HETATM 6425 O5 NAG C 303 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 701 " - " ASN A 47 " " NAG A 702 " - " ASN A 64 " " NAG A 703 " - " ASN A 109 " " NAG A 704 " - " ASN A 233 " " NAG A 705 " - " ASN A 246 " " NAG A 706 " - " ASN A 260 " " NAG A 707 " - " ASN A 293 " " NAG A 708 " - " ASN A 304 " " NAG A 709 " - " ASN A 389 " " NAG A 710 " - " ASN A 424 " " NAG A 711 " - " ASN A 435 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 149 " " NAG C 303 " - " ASN C 114 " " NAG C 304 " - " ASN C 103 " " NAG D 1 " - " ASN A 74 " " NAG E 1 " - " ASN A 124 " " NAG F 1 " - " ASN A 449 " " NAG G 1 " - " ASN A 573 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 365.6 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1462 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 20.8% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.739A pdb=" N LEU A 45 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.592A pdb=" N ILE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS A 84 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 183 removed outlier: 3.557A pdb=" N ILE A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 183 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.692A pdb=" N PHE A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.528A pdb=" N PHE A 256 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.956A pdb=" N GLY A 303 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 305 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.952A pdb=" N LEU A 329 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.726A pdb=" N LEU A 398 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.796A pdb=" N ILE A 468 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY A 469 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.575A pdb=" N LEU A 540 " --> pdb=" O PRO A 537 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 543 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 removed outlier: 4.315A pdb=" N GLY A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 566 " --> pdb=" O PRO A 562 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 567' Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.791A pdb=" N LEU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.509A pdb=" N GLY C 89 " --> pdb=" O MET C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.814A pdb=" N GLY C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 139 " --> pdb=" O THR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 removed outlier: 3.638A pdb=" N THR C 161 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 163 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 164 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.786A pdb=" N LEU C 188 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 61 removed outlier: 7.014A pdb=" N THR A 59 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 141 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 165 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 240 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE A 264 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 287 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 311 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 335 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 359 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 383 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 407 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 431 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 501 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 525 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 4.030A pdb=" N GLY A 77 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 100 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 99 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN A 124 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY A 101 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N SER A 126 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU A 123 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER A 149 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLY A 125 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 148 " --> pdb=" O GLU A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 5.536A pdb=" N GLY A 249 " --> pdb=" O THR A 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 295 through 297 removed outlier: 5.704A pdb=" N GLY A 296 " --> pdb=" O THR A 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 368 removed outlier: 5.445A pdb=" N GLY A 368 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 390 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER A 415 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY A 392 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS A 417 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE A 414 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 439 " --> pdb=" O PHE A 414 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY A 416 " --> pdb=" O THR A 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 463 removed outlier: 5.814A pdb=" N GLY A 462 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE A 484 " --> pdb=" O ASP A 507 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 533 through 534 removed outlier: 5.108A pdb=" N GLY A 534 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY A 559 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE A 556 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR A 580 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY A 558 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLY A 582 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 579 " --> pdb=" O ASN A 601 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS A 603 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLY A 581 " --> pdb=" O CYS A 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 39 through 40 removed outlier: 5.867A pdb=" N GLY C 82 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE C 104 " --> pdb=" O ASN C 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 64 removed outlier: 6.874A pdb=" N THR C 63 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C 71 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLU C 98 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL C 73 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 97 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 121 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU C 145 " --> pdb=" O ASP C 170 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 123 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: 0.70 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1101 1.32 - 1.45: 1674 1.45 - 1.58: 3756 1.58 - 1.71: 1 1.71 - 1.84: 24 Bond restraints: 6556 Sorted by residual: bond pdb=" CG ASN C 114 " pdb=" ND2 ASN C 114 " ideal model delta sigma weight residual 1.328 1.478 -0.150 2.10e-02 2.27e+03 5.13e+01 bond pdb=" CG ASN A 435 " pdb=" ND2 ASN A 435 " ideal model delta sigma weight residual 1.328 1.470 -0.142 2.10e-02 2.27e+03 4.56e+01 bond pdb=" CA HIS B 22 " pdb=" C HIS B 22 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.21e-02 6.83e+03 2.96e+01 bond pdb=" N TRP A 519 " pdb=" CA TRP A 519 " ideal model delta sigma weight residual 1.456 1.387 0.070 1.28e-02 6.10e+03 2.95e+01 bond pdb=" CA SER A 518 " pdb=" C SER A 518 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.26e-02 6.30e+03 2.28e+01 ... (remaining 6551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 8787 3.83 - 7.66: 102 7.66 - 11.49: 18 11.49 - 15.33: 5 15.33 - 19.16: 2 Bond angle restraints: 8914 Sorted by residual: angle pdb=" N THR B 12 " pdb=" CA THR B 12 " pdb=" C THR B 12 " ideal model delta sigma weight residual 111.28 130.44 -19.16 1.09e+00 8.42e-01 3.09e+02 angle pdb=" N LYS C 140 " pdb=" CA LYS C 140 " pdb=" C LYS C 140 " ideal model delta sigma weight residual 111.36 125.29 -13.93 1.09e+00 8.42e-01 1.63e+02 angle pdb=" N SER A 518 " pdb=" CA SER A 518 " pdb=" C SER A 518 " ideal model delta sigma weight residual 110.23 127.39 -17.16 1.45e+00 4.76e-01 1.40e+02 angle pdb=" N TYR A 168 " pdb=" CA TYR A 168 " pdb=" C TYR A 168 " ideal model delta sigma weight residual 110.23 122.87 -12.64 1.45e+00 4.76e-01 7.60e+01 angle pdb=" N ASP C 67 " pdb=" CA ASP C 67 " pdb=" C ASP C 67 " ideal model delta sigma weight residual 110.50 98.49 12.01 1.41e+00 5.03e-01 7.26e+01 ... (remaining 8909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 3626 15.64 - 31.29: 450 31.29 - 46.93: 147 46.93 - 62.57: 46 62.57 - 78.21: 4 Dihedral angle restraints: 4273 sinusoidal: 2007 harmonic: 2266 Sorted by residual: dihedral pdb=" CB CYS A 375 " pdb=" SG CYS A 375 " pdb=" SG CYS A 401 " pdb=" CB CYS A 401 " ideal model delta sinusoidal sigma weight residual 93.00 166.23 -73.23 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS C 57 " pdb=" SG CYS C 57 " pdb=" SG CYS C 64 " pdb=" CB CYS C 64 " ideal model delta sinusoidal sigma weight residual 93.00 131.15 -38.15 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" C ILE A 516 " pdb=" N ILE A 516 " pdb=" CA ILE A 516 " pdb=" CB ILE A 516 " ideal model delta harmonic sigma weight residual -122.00 -133.25 11.25 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 4270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 1063 0.141 - 0.283: 31 0.283 - 0.424: 8 0.424 - 0.566: 0 0.566 - 0.707: 1 Chirality restraints: 1103 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 124 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CA ILE A 516 " pdb=" N ILE A 516 " pdb=" C ILE A 516 " pdb=" CB ILE A 516 " both_signs ideal model delta sigma weight residual False 2.43 2.06 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA TYR A 168 " pdb=" N TYR A 168 " pdb=" C TYR A 168 " pdb=" CB TYR A 168 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 1100 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 303 " -0.215 2.00e-02 2.50e+03 1.77e-01 3.93e+02 pdb=" C7 NAG C 303 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG C 303 " -0.154 2.00e-02 2.50e+03 pdb=" N2 NAG C 303 " 0.289 2.00e-02 2.50e+03 pdb=" O7 NAG C 303 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 435 " 0.088 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN A 435 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 435 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 435 " -0.197 2.00e-02 2.50e+03 pdb=" C1 NAG A 711 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 114 " -0.010 2.00e-02 2.50e+03 6.21e-02 4.82e+01 pdb=" CG ASN C 114 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 114 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN C 114 " -0.106 2.00e-02 2.50e+03 pdb=" C1 NAG C 303 " 0.072 2.00e-02 2.50e+03 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1097 2.76 - 3.30: 5954 3.30 - 3.83: 10194 3.83 - 4.37: 11956 4.37 - 4.90: 20241 Nonbonded interactions: 49442 Sorted by model distance: nonbonded pdb=" N GLU A 563 " pdb=" OE1 GLU A 563 " model vdw 2.226 3.120 nonbonded pdb=" OG SER A 290 " pdb=" ND2 ASN B 9 " model vdw 2.245 3.120 nonbonded pdb=" O ASN A 246 " pdb=" OD1 ASN A 246 " model vdw 2.282 3.040 nonbonded pdb=" O LEU C 169 " pdb=" OG SER C 193 " model vdw 2.317 3.040 nonbonded pdb=" O LEU A 569 " pdb=" OH TYR A 592 " model vdw 2.356 3.040 ... (remaining 49437 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.220 Find NCS groups from input model: 0.020 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.007 0.150 6585 Z= 0.448 Angle : 1.296 45.297 8995 Z= 0.725 Chirality : 0.065 0.707 1103 Planarity : 0.009 0.177 1131 Dihedral : 15.178 78.212 2793 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.56 % Allowed : 22.91 % Favored : 75.53 % Cbeta Deviations : 0.27 % 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 are not related in a simple way. whole: -1.49 (0.32), residues: 787 helix: -1.84 (0.52), residues: 100 sheet: -3.34 (0.42), residues: 136 loop : -0.08 (0.29), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.023 0.001 TYR A 168 PHE 0.015 0.001 PHE A 75 TRP 0.039 0.002 TRP A 55 HIS 0.005 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.45 ( 6556) covalent geometry : angle 1.10617 / 0.69 ( 8914) SS BOND : bond 0.00491 / 0.33 ( 6) SS BOND : angle 6.84974 / 4.35 ( 12) hydrogen bonds : bond 0.32521 / 20.63 ( 82) hydrogen bonds : angle 9.10191 / 7.07 ( 123) link_BETA1-4 : bond 0.00380 / 0.19 ( 4) link_BETA1-4 : angle 3.90891 / 1.81 ( 12) link_NAG-ASN : bond 0.00701 / 0.46 ( 19) link_NAG-ASN : angle 7.78716 / 6.80 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 139 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6813 (pp) outliers start: 11 outliers final: 3 residues processed: 76 average time/residue: 0.0699 time to fit residues: 7.2292 Evaluate side-chains 66 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 598 ASN C 47 GLN ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.161314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127960 restraints weight = 8570.817| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.79 r_work: 0.3376 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6585 Z= 0.115 Angle : 0.762 13.557 8995 Z= 0.348 Chirality : 0.048 0.307 1103 Planarity : 0.005 0.087 1131 Dihedral : 9.273 58.737 1316 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.82 % Allowed : 21.22 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -1.55 (0.32), residues: 787 helix: -1.89 (0.48), residues: 101 sheet: -3.30 (0.40), residues: 140 loop : -0.11 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.010 0.001 TYR A 386 PHE 0.013 0.001 PHE A 572 TRP 0.023 0.002 TRP A 55 HIS 0.002 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6556) covalent geometry : angle 0.67382 / 0.33 ( 8914) SS BOND : bond 0.00245 / 0.14 ( 6) SS BOND : angle 1.58770 / 1.00 ( 12) hydrogen bonds : bond 0.05128 / 3.25 ( 82) hydrogen bonds : angle 6.41507 / 4.97 ( 123) link_BETA1-4 : bond 0.00518 / 0.26 ( 4) link_BETA1-4 : angle 3.47483 / 1.69 ( 12) link_NAG-ASN : bond 0.00622 / 0.41 ( 19) link_NAG-ASN : angle 4.17827 / 3.23 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.6235 (t80) REVERT: C 87 GLN cc_start: 0.7143 (mp10) cc_final: 0.6904 (mm-40) REVERT: C 193 SER cc_start: 0.7441 (t) cc_final: 0.7170 (p) outliers start: 27 outliers final: 13 residues processed: 87 average time/residue: 0.0630 time to fit residues: 7.7080 Evaluate side-chains 74 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 overall best weight: 1.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 GLN C 83 GLN ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121308 restraints weight = 8668.895| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.84 r_work: 0.3285 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6585 Z= 0.169 Angle : 0.789 16.863 8995 Z= 0.361 Chirality : 0.050 0.340 1103 Planarity : 0.005 0.076 1131 Dihedral : 8.984 57.908 1311 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.67 % Allowed : 20.65 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -1.72 (0.31), residues: 787 helix: -1.84 (0.51), residues: 102 sheet: -3.39 (0.39), residues: 139 loop : -0.28 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.015 0.002 TYR A 115 PHE 0.018 0.002 PHE A 314 TRP 0.027 0.002 TRP A 55 HIS 0.004 0.002 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6556) covalent geometry : angle 0.70639 / 0.34 ( 8914) SS BOND : bond 0.00357 / 0.24 ( 6) SS BOND : angle 2.33385 / 1.44 ( 12) hydrogen bonds : bond 0.04503 / 2.70 ( 82) hydrogen bonds : angle 6.22982 / 4.78 ( 123) link_BETA1-4 : bond 0.00340 / 0.17 ( 4) link_BETA1-4 : angle 3.01854 / 1.53 ( 12) link_NAG-ASN : bond 0.00557 / 0.36 ( 19) link_NAG-ASN : angle 4.15252 / 3.30 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.5584 (p90) REVERT: C 87 GLN cc_start: 0.7131 (mp10) cc_final: 0.6898 (mm-40) REVERT: C 193 SER cc_start: 0.7547 (t) cc_final: 0.7305 (p) outliers start: 33 outliers final: 16 residues processed: 91 average time/residue: 0.0663 time to fit residues: 8.3334 Evaluate side-chains 73 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain C residue 135 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 598 ASN C 47 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128299 restraints weight = 8661.226| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.78 r_work: 0.3367 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6585 Z= 0.107 Angle : 0.718 14.902 8995 Z= 0.324 Chirality : 0.047 0.311 1103 Planarity : 0.004 0.066 1131 Dihedral : 8.285 56.452 1310 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.68 % Allowed : 21.78 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -1.66 (0.32), residues: 787 helix: -1.72 (0.53), residues: 102 sheet: -3.44 (0.39), residues: 140 loop : -0.22 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.010 0.001 TYR A 386 PHE 0.014 0.001 PHE A 572 TRP 0.028 0.002 TRP A 55 HIS 0.001 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6556) covalent geometry : angle 0.63998 / 0.30 ( 8914) SS BOND : bond 0.00384 / 0.28 ( 6) SS BOND : angle 2.28567 / 1.37 ( 12) hydrogen bonds : bond 0.03385 / 2.10 ( 82) hydrogen bonds : angle 5.61702 / 4.31 ( 123) link_BETA1-4 : bond 0.00392 / 0.20 ( 4) link_BETA1-4 : angle 2.76407 / 1.40 ( 12) link_NAG-ASN : bond 0.00580 / 0.37 ( 19) link_NAG-ASN : angle 3.81118 / 3.02 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.5637 (p90) REVERT: A 190 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8592 (mtt90) REVERT: A 360 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: C 87 GLN cc_start: 0.7116 (mp10) cc_final: 0.6880 (mm-40) REVERT: C 193 SER cc_start: 0.7557 (t) cc_final: 0.7324 (p) outliers start: 26 outliers final: 19 residues processed: 81 average time/residue: 0.0825 time to fit residues: 8.9106 Evaluate side-chains 80 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 174 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129078 restraints weight = 8665.895| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.78 r_work: 0.3380 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6585 Z= 0.102 Angle : 0.712 14.105 8995 Z= 0.320 Chirality : 0.046 0.307 1103 Planarity : 0.004 0.060 1131 Dihedral : 7.801 55.505 1310 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % Rotamer: Outliers : 4.95 % Allowed : 20.93 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -1.48 (0.32), residues: 787 helix: -1.43 (0.56), residues: 95 sheet: -3.42 (0.40), residues: 140 loop : -0.12 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.010 0.001 TYR A 386 PHE 0.013 0.001 PHE A 572 TRP 0.022 0.002 TRP A 55 HIS 0.001 0.000 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 6556) covalent geometry : angle 0.63797 / 0.30 ( 8914) SS BOND : bond 0.00258 / 0.18 ( 6) SS BOND : angle 2.64675 / 1.61 ( 12) hydrogen bonds : bond 0.03180 / 1.99 ( 82) hydrogen bonds : angle 5.45505 / 4.15 ( 123) link_BETA1-4 : bond 0.00345 / 0.18 ( 4) link_BETA1-4 : angle 2.60490 / 1.33 ( 12) link_NAG-ASN : bond 0.00508 / 0.30 ( 19) link_NAG-ASN : angle 3.66840 / 2.92 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5578 (p90) REVERT: A 190 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8580 (mtt90) REVERT: A 360 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: A 593 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.4740 (pm20) REVERT: C 193 SER cc_start: 0.7539 (t) cc_final: 0.7316 (p) outliers start: 35 outliers final: 22 residues processed: 87 average time/residue: 0.0802 time to fit residues: 9.2252 Evaluate side-chains 84 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 166 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122918 restraints weight = 8702.763| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.91 r_work: 0.3292 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6585 Z= 0.147 Angle : 0.731 13.173 8995 Z= 0.333 Chirality : 0.048 0.333 1103 Planarity : 0.005 0.059 1131 Dihedral : 7.807 57.799 1310 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.73 % Favored : 93.14 % Rotamer: Outliers : 4.24 % Allowed : 21.07 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -1.83 (0.31), residues: 787 helix: -1.93 (0.50), residues: 108 sheet: -3.45 (0.41), residues: 134 loop : -0.38 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.013 0.002 TYR A 386 PHE 0.016 0.002 PHE A 314 TRP 0.024 0.002 TRP A 55 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 6556) covalent geometry : angle 0.65635 / 0.32 ( 8914) SS BOND : bond 0.00138 / 0.07 ( 6) SS BOND : angle 1.96876 / 1.16 ( 12) hydrogen bonds : bond 0.03526 / 2.13 ( 82) hydrogen bonds : angle 5.62934 / 4.29 ( 123) link_BETA1-4 : bond 0.00306 / 0.16 ( 4) link_BETA1-4 : angle 2.50797 / 1.31 ( 12) link_NAG-ASN : bond 0.00505 / 0.30 ( 19) link_NAG-ASN : angle 3.84429 / 3.01 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: A 593 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.4746 (pm20) REVERT: C 193 SER cc_start: 0.7587 (t) cc_final: 0.7373 (p) outliers start: 30 outliers final: 23 residues processed: 86 average time/residue: 0.0735 time to fit residues: 8.8339 Evaluate side-chains 85 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 174 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 ASN C 47 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123040 restraints weight = 8665.346| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.92 r_work: 0.3314 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6585 Z= 0.113 Angle : 0.720 14.630 8995 Z= 0.327 Chirality : 0.047 0.320 1103 Planarity : 0.004 0.055 1131 Dihedral : 7.732 56.951 1310 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % Rotamer: Outliers : 4.24 % Allowed : 22.07 % Favored : 73.69 % 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 are not related in a simple way. whole: -1.83 (0.31), residues: 787 helix: -1.94 (0.50), residues: 108 sheet: -3.47 (0.41), residues: 134 loop : -0.37 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.010 0.001 TYR A 386 PHE 0.013 0.001 PHE A 572 TRP 0.023 0.002 TRP A 55 HIS 0.001 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 6556) covalent geometry : angle 0.66182 / 0.31 ( 8914) SS BOND : bond 0.00140 / 0.08 ( 6) SS BOND : angle 2.95180 / 1.79 ( 12) hydrogen bonds : bond 0.03177 / 1.96 ( 82) hydrogen bonds : angle 5.49915 / 4.18 ( 123) link_BETA1-4 : bond 0.00322 / 0.16 ( 4) link_BETA1-4 : angle 2.43501 / 1.27 ( 12) link_NAG-ASN : bond 0.00513 / 0.31 ( 19) link_NAG-ASN : angle 3.21184 / 2.45 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8507 (mtt90) REVERT: A 360 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: A 593 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.4752 (pm20) outliers start: 30 outliers final: 22 residues processed: 83 average time/residue: 0.0783 time to fit residues: 8.9284 Evaluate side-chains 83 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN C 47 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121590 restraints weight = 8605.606| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.84 r_work: 0.3274 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6585 Z= 0.158 Angle : 0.731 12.636 8995 Z= 0.338 Chirality : 0.048 0.332 1103 Planarity : 0.005 0.055 1131 Dihedral : 7.940 57.979 1310 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.50 % Favored : 92.38 % Rotamer: Outliers : 4.67 % Allowed : 21.07 % Favored : 74.26 % 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 are not related in a simple way. whole: -1.98 (0.31), residues: 787 helix: -2.15 (0.47), residues: 109 sheet: -3.50 (0.41), residues: 134 loop : -0.47 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.013 0.002 TYR A 386 PHE 0.016 0.002 PHE A 314 TRP 0.024 0.002 TRP A 55 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 6556) covalent geometry : angle 0.67703 / 0.32 ( 8914) SS BOND : bond 0.00166 / 0.10 ( 6) SS BOND : angle 2.59030 / 1.54 ( 12) hydrogen bonds : bond 0.03616 / 2.19 ( 82) hydrogen bonds : angle 5.84855 / 4.42 ( 123) link_BETA1-4 : bond 0.00312 / 0.16 ( 4) link_BETA1-4 : angle 2.41008 / 1.27 ( 12) link_NAG-ASN : bond 0.00510 / 0.31 ( 19) link_NAG-ASN : angle 3.17733 / 2.43 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 PHE cc_start: 0.6259 (OUTLIER) cc_final: 0.5541 (p90) REVERT: A 190 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8477 (mtt90) REVERT: A 305 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8173 (pp) REVERT: A 360 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: A 593 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.4841 (pm20) outliers start: 33 outliers final: 23 residues processed: 84 average time/residue: 0.0711 time to fit residues: 8.2257 Evaluate side-chains 84 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 174 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN C 47 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.154519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122521 restraints weight = 8678.788| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.72 r_work: 0.3314 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6585 Z= 0.120 Angle : 0.698 12.505 8995 Z= 0.322 Chirality : 0.047 0.323 1103 Planarity : 0.004 0.053 1131 Dihedral : 7.820 57.200 1310 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.97 % Favored : 93.90 % Rotamer: Outliers : 4.24 % Allowed : 22.35 % Favored : 73.41 % 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 are not related in a simple way. whole: -1.96 (0.31), residues: 787 helix: -2.10 (0.48), residues: 108 sheet: -3.50 (0.41), residues: 134 loop : -0.46 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.011 0.001 TYR A 386 PHE 0.013 0.001 PHE A 572 TRP 0.023 0.002 TRP A 55 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6556) covalent geometry : angle 0.64762 / 0.31 ( 8914) SS BOND : bond 0.00135 / 0.08 ( 6) SS BOND : angle 2.10019 / 1.25 ( 12) hydrogen bonds : bond 0.03163 / 1.96 ( 82) hydrogen bonds : angle 5.65786 / 4.27 ( 123) link_BETA1-4 : bond 0.00346 / 0.17 ( 4) link_BETA1-4 : angle 2.34459 / 1.23 ( 12) link_NAG-ASN : bond 0.00514 / 0.31 ( 19) link_NAG-ASN : angle 3.02152 / 2.31 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8469 (mtt90) REVERT: A 305 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8186 (pp) REVERT: A 360 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8101 (mt-10) outliers start: 30 outliers final: 24 residues processed: 80 average time/residue: 0.0716 time to fit residues: 8.0091 Evaluate side-chains 85 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 174 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.0170 chunk 48 optimal weight: 0.7980 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120880 restraints weight = 8482.725| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.83 r_work: 0.3297 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6585 Z= 0.126 Angle : 0.701 12.013 8995 Z= 0.322 Chirality : 0.047 0.318 1103 Planarity : 0.005 0.053 1131 Dihedral : 7.781 56.989 1310 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.12 % Favored : 92.76 % Rotamer: Outliers : 3.54 % Allowed : 22.77 % Favored : 73.69 % 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 are not related in a simple way. whole: -1.96 (0.31), residues: 787 helix: -2.06 (0.48), residues: 108 sheet: -3.47 (0.41), residues: 134 loop : -0.48 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.011 0.001 TYR A 386 PHE 0.013 0.001 PHE A 572 TRP 0.022 0.002 TRP A 55 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6556) covalent geometry : angle 0.65378 / 0.31 ( 8914) SS BOND : bond 0.00145 / 0.09 ( 6) SS BOND : angle 1.96617 / 1.16 ( 12) hydrogen bonds : bond 0.03171 / 1.96 ( 82) hydrogen bonds : angle 5.65265 / 4.27 ( 123) link_BETA1-4 : bond 0.00324 / 0.16 ( 4) link_BETA1-4 : angle 2.30142 / 1.22 ( 12) link_NAG-ASN : bond 0.00499 / 0.29 ( 19) link_NAG-ASN : angle 2.95990 / 2.26 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8463 (mtt90) REVERT: A 305 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8190 (pp) REVERT: A 360 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: C 193 SER cc_start: 0.7421 (t) cc_final: 0.7164 (p) outliers start: 25 outliers final: 22 residues processed: 75 average time/residue: 0.0705 time to fit residues: 7.3301 Evaluate side-chains 79 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 401 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 174 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 64 optimal weight: 0.0370 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122715 restraints weight = 8479.696| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.77 r_work: 0.3334 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6585 Z= 0.099 Angle : 0.675 12.094 8995 Z= 0.310 Chirality : 0.047 0.307 1103 Planarity : 0.004 0.052 1131 Dihedral : 7.630 55.727 1310 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.54 % Rotamer: Outliers : 3.11 % Allowed : 23.06 % Favored : 73.83 % 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 are not related in a simple way. whole: -1.96 (0.31), residues: 787 helix: -1.99 (0.49), residues: 108 sheet: -3.62 (0.39), residues: 140 loop : -0.40 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 538 TYR 0.009 0.001 TYR A 386 PHE 0.012 0.001 PHE A 572 TRP 0.021 0.002 TRP A 55 HIS 0.001 0.000 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 6556) covalent geometry : angle 0.63164 / 0.30 ( 8914) SS BOND : bond 0.00132 / 0.07 ( 6) SS BOND : angle 1.66701 / 0.98 ( 12) hydrogen bonds : bond 0.02795 / 1.77 ( 82) hydrogen bonds : angle 5.39708 / 4.07 ( 123) link_BETA1-4 : bond 0.00340 / 0.17 ( 4) link_BETA1-4 : angle 2.22056 / 1.17 ( 12) link_NAG-ASN : bond 0.00501 / 0.29 ( 19) link_NAG-ASN : angle 2.81943 / 2.13 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.93 seconds wall clock time: 24 minutes 58.93 seconds (1498.93 seconds total)