Starting phenix.real_space_refine on Thu Jul 24 15:07:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aqu_15590/07_2025/8aqu_15590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqu_15590/07_2025/8aqu_15590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2025/8aqu_15590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2025/8aqu_15590.map" model { file = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2025/8aqu_15590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2025/8aqu_15590.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4049 2.51 5 N 1062 2.21 5 O 1192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4744 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 557} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1554 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.63, per 1000 atoms: 0.73 Number of scatterers: 6340 At special positions: 0 Unit cell: (96.4503, 81.9309, 113.044, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1192 8.00 N 1062 7.00 C 4049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 C 1 " - " NAG C 2 " NAG-ASN " NAG B 526 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 961.1 milliseconds 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 49.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.512A pdb=" N ALA A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 88 removed outlier: 4.859A pdb=" N SER A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N GLN A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N GLU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 5.539A pdb=" N LYS A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 removed outlier: 4.652A pdb=" N GLN A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.872A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 4.471A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 4.636A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.727A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.634A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Proline residue: A 280 - end of helix No H-bonds generated for 'chain 'A' and resid 275 through 282' Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.977A pdb=" N ASN A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.723A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.943A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.011A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ARG A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Proline residue: A 389 - end of helix removed outlier: 5.879A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 419 removed outlier: 3.839A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.607A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.865A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.268A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 removed outlier: 4.980A pdb=" N SER A 502 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N PHE A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N HIS A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.529A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 575 removed outlier: 4.000A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Proline residue: A 565 - end of helix removed outlier: 6.348A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.949A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Proline residue: A 590 - end of helix removed outlier: 5.375A pdb=" N ASP A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.865A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.425A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.236A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 421' 177 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2039 1.35 - 1.47: 1681 1.47 - 1.59: 2737 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 6515 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C1 NAG B 526 " pdb=" O5 NAG B 526 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.440 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C2 NAG B 526 " pdb=" N2 NAG B 526 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.59e+00 ... (remaining 6510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 8592 1.60 - 3.20: 211 3.20 - 4.79: 35 4.79 - 6.39: 8 6.39 - 7.99: 1 Bond angle restraints: 8847 Sorted by residual: angle pdb=" C ALA A 107 " pdb=" CA ALA A 107 " pdb=" CB ALA A 107 " ideal model delta sigma weight residual 115.89 110.49 5.40 1.32e+00 5.74e-01 1.67e+01 angle pdb=" N GLU A 471 " pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 114.56 109.81 4.75 1.27e+00 6.20e-01 1.40e+01 angle pdb=" N VAL A 318 " pdb=" CA VAL A 318 " pdb=" C VAL A 318 " ideal model delta sigma weight residual 111.81 109.20 2.61 8.60e-01 1.35e+00 9.24e+00 angle pdb=" C THR A 55 " pdb=" N GLU A 56 " pdb=" CA GLU A 56 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.65e+00 angle pdb=" C ARG B 457 " pdb=" N LYS B 458 " pdb=" CA LYS B 458 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.39e+00 ... (remaining 8842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 3621 22.87 - 45.74: 232 45.74 - 68.61: 22 68.61 - 91.48: 12 91.48 - 114.35: 17 Dihedral angle restraints: 3904 sinusoidal: 1614 harmonic: 2290 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -29.20 -56.80 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C5 NAG C 2 " ideal model delta sinusoidal sigma weight residual -62.96 51.39 -114.35 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C3 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sinusoidal sigma weight residual -55.55 55.41 -110.96 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 3901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 592 0.035 - 0.070: 253 0.070 - 0.105: 76 0.105 - 0.139: 9 0.139 - 0.174: 2 Chirality restraints: 932 Sorted by residual: chirality pdb=" C2 NAG B 526 " pdb=" C1 NAG B 526 " pdb=" C3 NAG B 526 " pdb=" N2 NAG B 526 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA PRO B 337 " pdb=" N PRO B 337 " pdb=" C PRO B 337 " pdb=" CB PRO B 337 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 929 not shown) Planarity restraints: 1147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO B 337 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 56 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C GLU A 56 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A 56 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 134 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 135 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.025 5.00e-02 4.00e+02 ... (remaining 1144 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1190 2.77 - 3.30: 6104 3.30 - 3.84: 9943 3.84 - 4.37: 11280 4.37 - 4.90: 19334 Nonbonded interactions: 47851 Sorted by model distance: nonbonded pdb=" O SER A 77 " pdb=" NE2 GLN A 81 " model vdw 2.240 3.120 nonbonded pdb=" O ARG A 273 " pdb=" OG1 THR A 445 " model vdw 2.240 3.040 nonbonded pdb=" O ASN A 53 " pdb=" ND2 ASN A 58 " model vdw 2.260 3.120 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.311 3.040 nonbonded pdb=" NH1 ARG B 454 " pdb=" O ASP B 467 " model vdw 2.311 3.120 ... (remaining 47846 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 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: 3.270 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.050 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6524 Z= 0.141 Angle : 0.618 7.988 8868 Z= 0.340 Chirality : 0.040 0.174 932 Planarity : 0.005 0.073 1145 Dihedral : 16.844 114.347 2414 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.31), residues: 773 helix: 0.63 (0.33), residues: 274 sheet: -2.59 (0.83), residues: 37 loop : -1.94 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.002 0.001 HIS A 378 PHE 0.017 0.001 PHE B 497 TYR 0.015 0.001 TYR B 495 ARG 0.002 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 2) link_NAG-ASN : angle 1.70237 ( 6) link_BETA1-4 : bond 0.01081 ( 1) link_BETA1-4 : angle 1.62660 ( 3) hydrogen bonds : bond 0.05443 ( 177) hydrogen bonds : angle 5.20105 ( 531) SS BOND : bond 0.00545 ( 6) SS BOND : angle 0.84512 ( 12) covalent geometry : bond 0.00269 ( 6515) covalent geometry : angle 0.61611 ( 8847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LEU cc_start: 0.6302 (pp) cc_final: 0.6079 (mp) REVERT: A 455 MET cc_start: 0.7447 (ppp) cc_final: 0.7055 (ppp) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.1907 time to fit residues: 32.5273 Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 0.0020 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 265 HIS A 345 HIS A 388 GLN A 442 GLN A 526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.236370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.203569 restraints weight = 9212.518| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 3.48 r_work: 0.4114 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6524 Z= 0.124 Angle : 0.621 9.679 8868 Z= 0.301 Chirality : 0.043 0.234 932 Planarity : 0.005 0.074 1145 Dihedral : 11.467 106.092 915 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.04 % Allowed : 9.91 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.31), residues: 773 helix: 0.23 (0.31), residues: 295 sheet: -2.28 (0.84), residues: 36 loop : -1.95 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 PHE 0.017 0.001 PHE A 452 TYR 0.039 0.002 TYR A 535 ARG 0.005 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 2) link_NAG-ASN : angle 1.73234 ( 6) link_BETA1-4 : bond 0.01264 ( 1) link_BETA1-4 : angle 2.23602 ( 3) hydrogen bonds : bond 0.03471 ( 177) hydrogen bonds : angle 4.91279 ( 531) SS BOND : bond 0.00653 ( 6) SS BOND : angle 1.59003 ( 12) covalent geometry : bond 0.00268 ( 6515) covalent geometry : angle 0.61586 ( 8847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6731 (tt0) REVERT: A 236 LEU cc_start: 0.4443 (OUTLIER) cc_final: 0.3913 (mt) REVERT: A 270 MET cc_start: 0.2600 (tpt) cc_final: 0.2032 (tpt) REVERT: A 455 MET cc_start: 0.7511 (ppp) cc_final: 0.7170 (ppp) outliers start: 7 outliers final: 4 residues processed: 93 average time/residue: 0.1856 time to fit residues: 23.6836 Evaluate side-chains 86 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.225527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.192520 restraints weight = 9395.090| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 4.68 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6524 Z= 0.212 Angle : 0.693 9.872 8868 Z= 0.346 Chirality : 0.044 0.258 932 Planarity : 0.005 0.070 1145 Dihedral : 8.191 89.774 914 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.44 % Favored : 90.43 % Rotamer: Outliers : 3.25 % Allowed : 12.72 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.30), residues: 773 helix: -0.21 (0.30), residues: 300 sheet: -2.31 (0.74), residues: 47 loop : -2.27 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 436 HIS 0.004 0.001 HIS A 378 PHE 0.016 0.002 PHE B 347 TYR 0.022 0.002 TYR B 453 ARG 0.004 0.001 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 2) link_NAG-ASN : angle 1.85161 ( 6) link_BETA1-4 : bond 0.01365 ( 1) link_BETA1-4 : angle 2.80162 ( 3) hydrogen bonds : bond 0.04202 ( 177) hydrogen bonds : angle 5.24709 ( 531) SS BOND : bond 0.00721 ( 6) SS BOND : angle 1.21103 ( 12) covalent geometry : bond 0.00481 ( 6515) covalent geometry : angle 0.68921 ( 8847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 158 TYR cc_start: 0.2516 (OUTLIER) cc_final: 0.2029 (m-80) REVERT: A 229 THR cc_start: 0.2448 (t) cc_final: 0.1878 (m) REVERT: A 236 LEU cc_start: 0.4363 (OUTLIER) cc_final: 0.3873 (mt) REVERT: A 270 MET cc_start: 0.2114 (tpt) cc_final: 0.1769 (tpt) REVERT: A 455 MET cc_start: 0.6988 (ppp) cc_final: 0.6517 (ppp) outliers start: 22 outliers final: 13 residues processed: 103 average time/residue: 0.1663 time to fit residues: 24.0680 Evaluate side-chains 94 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 24 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.227237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.192855 restraints weight = 9389.662| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 4.00 r_work: 0.3975 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6524 Z= 0.128 Angle : 0.621 9.732 8868 Z= 0.302 Chirality : 0.042 0.250 932 Planarity : 0.005 0.065 1145 Dihedral : 7.665 85.881 914 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.11 % Allowed : 14.20 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.30), residues: 773 helix: -0.02 (0.31), residues: 306 sheet: -2.04 (0.74), residues: 49 loop : -2.17 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.009 0.001 PHE A 369 TYR 0.014 0.001 TYR A 535 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 2) link_NAG-ASN : angle 1.57353 ( 6) link_BETA1-4 : bond 0.01095 ( 1) link_BETA1-4 : angle 3.60182 ( 3) hydrogen bonds : bond 0.03523 ( 177) hydrogen bonds : angle 5.13331 ( 531) SS BOND : bond 0.00524 ( 6) SS BOND : angle 1.46332 ( 12) covalent geometry : bond 0.00288 ( 6515) covalent geometry : angle 0.61494 ( 8847) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.778 Fit side-chains REVERT: A 229 THR cc_start: 0.2211 (t) cc_final: 0.1426 (m) REVERT: A 236 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.4095 (mt) REVERT: A 270 MET cc_start: 0.1974 (tpt) cc_final: 0.1552 (tpt) REVERT: A 455 MET cc_start: 0.6776 (ppp) cc_final: 0.6243 (ppp) REVERT: B 418 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7784 (tt) outliers start: 21 outliers final: 12 residues processed: 96 average time/residue: 0.1452 time to fit residues: 19.8896 Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 0.4980 chunk 41 optimal weight: 0.0970 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** 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 = 0.4638 r_free = 0.4638 target = 0.228477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.194332 restraints weight = 9364.562| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.96 r_work: 0.3996 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6524 Z= 0.113 Angle : 0.593 9.720 8868 Z= 0.289 Chirality : 0.041 0.248 932 Planarity : 0.005 0.063 1145 Dihedral : 7.214 80.244 914 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.85 % Allowed : 14.64 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.30), residues: 773 helix: 0.05 (0.31), residues: 309 sheet: -2.12 (0.75), residues: 47 loop : -2.12 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 459 HIS 0.003 0.001 HIS A 378 PHE 0.009 0.001 PHE A 369 TYR 0.010 0.001 TYR A 535 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 2) link_NAG-ASN : angle 1.62047 ( 6) link_BETA1-4 : bond 0.01047 ( 1) link_BETA1-4 : angle 3.76762 ( 3) hydrogen bonds : bond 0.03369 ( 177) hydrogen bonds : angle 4.96276 ( 531) SS BOND : bond 0.00571 ( 6) SS BOND : angle 1.27853 ( 12) covalent geometry : bond 0.00249 ( 6515) covalent geometry : angle 0.58613 ( 8847) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.743 Fit side-chains REVERT: A 229 THR cc_start: 0.2307 (t) cc_final: 0.1529 (m) REVERT: A 236 LEU cc_start: 0.4571 (OUTLIER) cc_final: 0.4120 (mt) REVERT: A 270 MET cc_start: 0.1951 (tpt) cc_final: 0.1532 (tpt) REVERT: A 455 MET cc_start: 0.6742 (ppp) cc_final: 0.6222 (ppp) REVERT: B 418 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7685 (tt) outliers start: 26 outliers final: 14 residues processed: 107 average time/residue: 0.1517 time to fit residues: 23.5820 Evaluate side-chains 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.227058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.192958 restraints weight = 9318.413| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 3.94 r_work: 0.3979 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6524 Z= 0.125 Angle : 0.618 9.761 8868 Z= 0.301 Chirality : 0.042 0.251 932 Planarity : 0.005 0.061 1145 Dihedral : 7.041 76.143 914 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.14 % Allowed : 14.94 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.31), residues: 773 helix: 0.12 (0.31), residues: 310 sheet: -1.92 (0.75), residues: 47 loop : -2.08 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 378 PHE 0.010 0.001 PHE A 369 TYR 0.009 0.001 TYR B 453 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 1.68150 ( 6) link_BETA1-4 : bond 0.00960 ( 1) link_BETA1-4 : angle 4.04032 ( 3) hydrogen bonds : bond 0.03438 ( 177) hydrogen bonds : angle 5.07760 ( 531) SS BOND : bond 0.00759 ( 6) SS BOND : angle 1.13961 ( 12) covalent geometry : bond 0.00279 ( 6515) covalent geometry : angle 0.61098 ( 8847) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.642 Fit side-chains REVERT: A 236 LEU cc_start: 0.4484 (OUTLIER) cc_final: 0.4084 (mt) REVERT: A 270 MET cc_start: 0.1956 (tpt) cc_final: 0.1562 (tpt) REVERT: A 455 MET cc_start: 0.6766 (ppp) cc_final: 0.6238 (ppp) REVERT: A 579 MET cc_start: 0.6647 (mtm) cc_final: 0.6409 (mtt) REVERT: A 592 PHE cc_start: 0.5732 (OUTLIER) cc_final: 0.4983 (t80) REVERT: B 418 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7687 (tt) outliers start: 28 outliers final: 17 residues processed: 103 average time/residue: 0.1377 time to fit residues: 20.5393 Evaluate side-chains 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** 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 = 0.4596 r_free = 0.4596 target = 0.223756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.181576 restraints weight = 9318.346| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.99 r_work: 0.3981 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6524 Z= 0.155 Angle : 0.665 10.705 8868 Z= 0.321 Chirality : 0.042 0.253 932 Planarity : 0.005 0.059 1145 Dihedral : 6.935 71.572 914 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.11 % Allowed : 17.31 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.31), residues: 773 helix: 0.05 (0.31), residues: 302 sheet: -1.89 (0.77), residues: 47 loop : -2.09 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.003 0.001 HIS A 505 PHE 0.011 0.001 PHE A 369 TYR 0.013 0.001 TYR B 453 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 1.91716 ( 6) link_BETA1-4 : bond 0.00797 ( 1) link_BETA1-4 : angle 4.28322 ( 3) hydrogen bonds : bond 0.03779 ( 177) hydrogen bonds : angle 5.10971 ( 531) SS BOND : bond 0.00599 ( 6) SS BOND : angle 1.27452 ( 12) covalent geometry : bond 0.00351 ( 6515) covalent geometry : angle 0.65753 ( 8847) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.689 Fit side-chains REVERT: A 158 TYR cc_start: 0.3079 (m-80) cc_final: 0.2823 (m-10) REVERT: A 236 LEU cc_start: 0.4488 (OUTLIER) cc_final: 0.4104 (mt) REVERT: A 241 HIS cc_start: 0.3405 (m90) cc_final: 0.3104 (t-170) REVERT: A 270 MET cc_start: 0.1708 (tpt) cc_final: 0.1339 (tpt) REVERT: A 455 MET cc_start: 0.6869 (ppp) cc_final: 0.6308 (ppp) REVERT: A 579 MET cc_start: 0.6761 (mtm) cc_final: 0.6474 (mtt) REVERT: A 592 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.4914 (t80) REVERT: B 418 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7760 (tt) outliers start: 21 outliers final: 15 residues processed: 99 average time/residue: 0.1383 time to fit residues: 19.8572 Evaluate side-chains 94 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 71 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** 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 = 0.4581 r_free = 0.4581 target = 0.222295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.188470 restraints weight = 9334.930| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 4.25 r_work: 0.3923 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6524 Z= 0.165 Angle : 0.677 12.549 8868 Z= 0.328 Chirality : 0.043 0.257 932 Planarity : 0.005 0.059 1145 Dihedral : 6.777 64.372 914 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 2.96 % Allowed : 17.75 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.30), residues: 773 helix: -0.02 (0.31), residues: 302 sheet: -2.10 (0.78), residues: 47 loop : -2.16 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 436 HIS 0.003 0.001 HIS A 378 PHE 0.011 0.002 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 2) link_NAG-ASN : angle 2.06926 ( 6) link_BETA1-4 : bond 0.00930 ( 1) link_BETA1-4 : angle 4.63471 ( 3) hydrogen bonds : bond 0.03829 ( 177) hydrogen bonds : angle 5.28463 ( 531) SS BOND : bond 0.00671 ( 6) SS BOND : angle 1.38067 ( 12) covalent geometry : bond 0.00378 ( 6515) covalent geometry : angle 0.66823 ( 8847) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.693 Fit side-chains REVERT: A 236 LEU cc_start: 0.4527 (OUTLIER) cc_final: 0.4126 (mt) REVERT: A 241 HIS cc_start: 0.3416 (m90) cc_final: 0.2965 (t-170) REVERT: A 270 MET cc_start: 0.2311 (tpt) cc_final: 0.1977 (tpt) REVERT: A 455 MET cc_start: 0.6905 (ppp) cc_final: 0.6369 (ppp) REVERT: A 571 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5494 (mt-10) REVERT: A 592 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.5071 (t80) REVERT: B 418 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.7808 (tt) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.1508 time to fit residues: 20.2384 Evaluate side-chains 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.0050 chunk 37 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** 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 = 0.4607 r_free = 0.4607 target = 0.225438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.191452 restraints weight = 9393.513| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 4.05 r_work: 0.3968 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6524 Z= 0.118 Angle : 0.654 11.722 8868 Z= 0.310 Chirality : 0.042 0.251 932 Planarity : 0.005 0.058 1145 Dihedral : 6.371 58.837 914 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.66 % Allowed : 18.49 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.31), residues: 773 helix: 0.09 (0.31), residues: 307 sheet: -2.14 (0.79), residues: 47 loop : -2.17 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.009 0.001 PHE A 369 TYR 0.011 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 2) link_NAG-ASN : angle 1.92061 ( 6) link_BETA1-4 : bond 0.00583 ( 1) link_BETA1-4 : angle 4.87841 ( 3) hydrogen bonds : bond 0.03493 ( 177) hydrogen bonds : angle 5.01322 ( 531) SS BOND : bond 0.00582 ( 6) SS BOND : angle 1.20808 ( 12) covalent geometry : bond 0.00264 ( 6515) covalent geometry : angle 0.64541 ( 8847) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.639 Fit side-chains REVERT: A 152 MET cc_start: 0.0543 (ttt) cc_final: -0.0375 (ptp) REVERT: A 236 LEU cc_start: 0.4242 (OUTLIER) cc_final: 0.3870 (mt) REVERT: A 241 HIS cc_start: 0.3548 (m90) cc_final: 0.3108 (t-170) REVERT: A 270 MET cc_start: 0.2100 (tpt) cc_final: 0.1756 (tpt) REVERT: A 455 MET cc_start: 0.6906 (ppp) cc_final: 0.6328 (ppp) REVERT: A 592 PHE cc_start: 0.5683 (OUTLIER) cc_final: 0.4876 (t80) REVERT: B 418 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7670 (tt) outliers start: 18 outliers final: 15 residues processed: 95 average time/residue: 0.1460 time to fit residues: 19.8402 Evaluate side-chains 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.0980 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 397 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 = 0.4614 r_free = 0.4614 target = 0.226136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.192537 restraints weight = 9409.782| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 4.11 r_work: 0.3973 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6524 Z= 0.112 Angle : 0.642 13.029 8868 Z= 0.302 Chirality : 0.042 0.251 932 Planarity : 0.005 0.058 1145 Dihedral : 5.948 55.577 914 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.51 % Allowed : 18.49 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.31), residues: 773 helix: 0.11 (0.31), residues: 314 sheet: -2.05 (0.79), residues: 47 loop : -2.13 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 459 HIS 0.003 0.001 HIS A 378 PHE 0.010 0.001 PHE A 369 TYR 0.009 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 2) link_NAG-ASN : angle 1.96763 ( 6) link_BETA1-4 : bond 0.00643 ( 1) link_BETA1-4 : angle 5.00597 ( 3) hydrogen bonds : bond 0.03399 ( 177) hydrogen bonds : angle 5.04045 ( 531) SS BOND : bond 0.00539 ( 6) SS BOND : angle 1.16309 ( 12) covalent geometry : bond 0.00253 ( 6515) covalent geometry : angle 0.63211 ( 8847) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.0530 (ttt) cc_final: -0.0347 (ptp) REVERT: A 236 LEU cc_start: 0.4139 (OUTLIER) cc_final: 0.3806 (mt) REVERT: A 241 HIS cc_start: 0.3416 (m90) cc_final: 0.2996 (t-170) REVERT: A 270 MET cc_start: 0.1891 (tpt) cc_final: 0.1618 (tpt) REVERT: A 455 MET cc_start: 0.6872 (ppp) cc_final: 0.6287 (ppp) REVERT: A 592 PHE cc_start: 0.5586 (OUTLIER) cc_final: 0.4740 (t80) REVERT: B 418 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7646 (tt) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.1561 time to fit residues: 20.6120 Evaluate side-chains 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 34 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** 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 = 0.4613 r_free = 0.4613 target = 0.225726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.191943 restraints weight = 9480.770| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 4.09 r_work: 0.3977 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 6524 Z= 0.223 Angle : 1.080 58.962 8868 Z= 0.610 Chirality : 0.049 0.786 932 Planarity : 0.005 0.058 1145 Dihedral : 6.030 55.594 914 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.37 % Allowed : 18.64 % Favored : 78.99 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.31), residues: 773 helix: 0.10 (0.31), residues: 314 sheet: -2.05 (0.79), residues: 47 loop : -2.13 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 378 PHE 0.010 0.001 PHE A 369 TYR 0.009 0.001 TYR A 385 ARG 0.003 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 1.96840 ( 6) link_BETA1-4 : bond 0.00188 ( 1) link_BETA1-4 : angle 5.03360 ( 3) hydrogen bonds : bond 0.03816 ( 177) hydrogen bonds : angle 5.07866 ( 531) SS BOND : bond 0.00541 ( 6) SS BOND : angle 1.18344 ( 12) covalent geometry : bond 0.00419 ( 6515) covalent geometry : angle 1.07477 ( 8847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3915.48 seconds wall clock time: 68 minutes 40.87 seconds (4120.87 seconds total)