Starting phenix.real_space_refine on Wed May 14 08:30:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdy_37467/05_2025/8wdy_37467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdy_37467/05_2025/8wdy_37467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wdy_37467/05_2025/8wdy_37467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdy_37467/05_2025/8wdy_37467.map" model { file = "/net/cci-nas-00/data/ceres_data/8wdy_37467/05_2025/8wdy_37467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdy_37467/05_2025/8wdy_37467.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6322 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4188 2.51 5 N 1073 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6548 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1549 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 4.47, per 1000 atoms: 0.68 Number of scatterers: 6548 At special positions: 0 Unit cell: (74.8, 85.85, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1249 8.00 N 1073 7.00 C 4188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 D 1 " - " NAG D 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 908.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 374 " 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: 1490 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 53.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.527A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.567A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.200A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.026A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.510A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.671A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 249 removed outlier: 4.009A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.795A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.608A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.887A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.742A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.503A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.577A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.537A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.741A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.787A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.652A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.859A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.012A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.251A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.116A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.896A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 278 hydrogen bonds defined for protein. 789 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: 1.61 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2059 1.34 - 1.47: 1746 1.47 - 1.59: 2868 1.59 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6731 Sorted by residual: bond pdb=" CE1 HIS A 34 " pdb=" NE2 HIS A 34 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" C HIS A 34 " pdb=" N GLU A 35 " ideal model delta sigma weight residual 1.334 1.288 0.046 1.20e-02 6.94e+03 1.50e+01 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.15e+01 bond pdb=" N HIS A 34 " pdb=" CA HIS A 34 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.17e-02 7.31e+03 1.14e+01 ... (remaining 6726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 8940 2.35 - 4.70: 182 4.70 - 7.06: 25 7.06 - 9.41: 4 9.41 - 11.76: 1 Bond angle restraints: 9152 Sorted by residual: angle pdb=" N HIS A 34 " pdb=" CA HIS A 34 " pdb=" C HIS A 34 " ideal model delta sigma weight residual 112.72 100.96 11.76 1.28e+00 6.10e-01 8.44e+01 angle pdb=" C HIS A 34 " pdb=" N GLU A 35 " pdb=" CA GLU A 35 " ideal model delta sigma weight residual 120.79 129.77 -8.98 1.39e+00 5.18e-01 4.18e+01 angle pdb=" N THR A 92 " pdb=" CA THR A 92 " pdb=" C THR A 92 " ideal model delta sigma weight residual 113.41 106.00 7.41 1.22e+00 6.72e-01 3.69e+01 angle pdb=" O ASN A 33 " pdb=" C ASN A 33 " pdb=" N HIS A 34 " ideal model delta sigma weight residual 122.59 115.99 6.60 1.33e+00 5.65e-01 2.46e+01 angle pdb=" N GLU A 87 " pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 113.50 107.53 5.97 1.23e+00 6.61e-01 2.35e+01 ... (remaining 9147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 3860 24.77 - 49.53: 195 49.53 - 74.30: 29 74.30 - 99.06: 11 99.06 - 123.83: 1 Dihedral angle restraints: 4096 sinusoidal: 1774 harmonic: 2322 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 27.76 65.24 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CA GLU A 145 " pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual 0.00 -28.16 28.16 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 60.87 -123.83 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 4093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 832 0.060 - 0.119: 136 0.119 - 0.178: 13 0.178 - 0.238: 5 0.238 - 0.297: 1 Chirality restraints: 987 Sorted by residual: chirality pdb=" CA HIS A 34 " pdb=" N HIS A 34 " pdb=" C HIS A 34 " pdb=" CB HIS A 34 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA TYR B 501 " pdb=" N TYR B 501 " pdb=" C TYR B 501 " pdb=" CB TYR B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA TYR B 453 " pdb=" N TYR B 453 " pdb=" C TYR B 453 " pdb=" CB TYR B 453 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 984 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 34 " 0.042 2.00e-02 2.50e+03 9.01e-02 8.11e+01 pdb=" C HIS A 34 " -0.156 2.00e-02 2.50e+03 pdb=" O HIS A 34 " 0.059 2.00e-02 2.50e+03 pdb=" N GLU A 35 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 484 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ALA B 484 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA B 484 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY B 485 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 85 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C LEU A 85 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 85 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN A 86 " -0.020 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 42 2.58 - 3.16: 5172 3.16 - 3.74: 9722 3.74 - 4.32: 13544 4.32 - 4.90: 22870 Nonbonded interactions: 51350 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 905 " model vdw 2.000 2.230 nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.173 3.040 nonbonded pdb=" OG SER A 425 " pdb=" OD1 ASP A 427 " model vdw 2.186 3.040 nonbonded pdb=" NE2 GLN A 42 " pdb=" NH2 ARG B 498 " model vdw 2.234 3.200 nonbonded pdb=" OG1 THR A 20 " pdb=" OE1 GLU A 23 " model vdw 2.269 3.040 ... (remaining 51345 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 6750 Z= 0.285 Angle : 0.770 11.760 9196 Z= 0.479 Chirality : 0.047 0.297 987 Planarity : 0.005 0.090 1173 Dihedral : 14.720 123.825 2585 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 1.44 % Allowed : 0.87 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.31), residues: 787 helix: 1.05 (0.28), residues: 383 sheet: 1.83 (0.79), residues: 44 loop : -1.02 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.035 0.001 PHE A 592 TYR 0.044 0.001 TYR B 453 ARG 0.002 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 7) link_NAG-ASN : angle 2.30085 ( 21) link_BETA1-4 : bond 0.00430 ( 2) link_BETA1-4 : angle 0.78761 ( 6) hydrogen bonds : bond 0.16713 ( 278) hydrogen bonds : angle 6.07163 ( 789) link_BETA1-6 : bond 0.00395 ( 1) link_BETA1-6 : angle 1.33646 ( 3) metal coordination : bond 0.20327 ( 2) SS BOND : bond 0.00562 ( 7) SS BOND : angle 1.26862 ( 14) covalent geometry : bond 0.00415 ( 6731) covalent geometry : angle 0.76156 ( 9152) *********************** 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 198 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.7107 (tmm) cc_final: 0.6699 (tmm) REVERT: B 406 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7314 (mt-10) REVERT: B 509 ARG cc_start: 0.8448 (mtt180) cc_final: 0.8230 (mtt-85) outliers start: 10 outliers final: 3 residues processed: 191 average time/residue: 1.0782 time to fit residues: 217.0708 Evaluate side-chains 166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 61 ASN A 64 ASN A 598 GLN B 437 ASN B 487 ASN B 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114733 restraints weight = 8962.525| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.94 r_work: 0.3431 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6750 Z= 0.154 Angle : 0.566 10.868 9196 Z= 0.283 Chirality : 0.043 0.234 987 Planarity : 0.004 0.051 1173 Dihedral : 8.564 108.731 1070 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 10.97 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 787 helix: 1.30 (0.28), residues: 377 sheet: 1.72 (0.75), residues: 44 loop : -0.97 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.001 PHE A 400 TYR 0.017 0.001 TYR A 202 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 7) link_NAG-ASN : angle 2.34419 ( 21) link_BETA1-4 : bond 0.00490 ( 2) link_BETA1-4 : angle 0.95940 ( 6) hydrogen bonds : bond 0.04759 ( 278) hydrogen bonds : angle 4.46919 ( 789) link_BETA1-6 : bond 0.00305 ( 1) link_BETA1-6 : angle 1.26053 ( 3) metal coordination : bond 0.00569 ( 2) SS BOND : bond 0.00610 ( 7) SS BOND : angle 1.25552 ( 14) covalent geometry : bond 0.00348 ( 6731) covalent geometry : angle 0.55273 ( 9152) *********************** 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 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6846 (mp0) cc_final: 0.6456 (mp0) REVERT: A 364 VAL cc_start: 0.8332 (m) cc_final: 0.8109 (t) REVERT: A 431 ASP cc_start: 0.7622 (p0) cc_final: 0.7409 (p0) REVERT: A 455 MET cc_start: 0.7655 (tmm) cc_final: 0.7308 (tmm) REVERT: A 496 THR cc_start: 0.8794 (m) cc_final: 0.8555 (t) REVERT: B 343 ASN cc_start: 0.7731 (t0) cc_final: 0.7380 (t0) outliers start: 10 outliers final: 3 residues processed: 172 average time/residue: 1.0733 time to fit residues: 194.8174 Evaluate side-chains 166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 67 optimal weight: 0.0270 chunk 45 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 409 GLN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115401 restraints weight = 9065.361| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.94 r_work: 0.3440 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6750 Z= 0.112 Angle : 0.514 8.193 9196 Z= 0.254 Chirality : 0.041 0.221 987 Planarity : 0.004 0.039 1173 Dihedral : 7.703 105.503 1065 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 13.13 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.31), residues: 787 helix: 1.53 (0.28), residues: 371 sheet: 1.33 (0.75), residues: 44 loop : -0.94 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.007 0.001 PHE A 72 TYR 0.016 0.001 TYR A 202 ARG 0.002 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 7) link_NAG-ASN : angle 2.06944 ( 21) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 0.91555 ( 6) hydrogen bonds : bond 0.04097 ( 278) hydrogen bonds : angle 4.14106 ( 789) link_BETA1-6 : bond 0.00349 ( 1) link_BETA1-6 : angle 1.10507 ( 3) metal coordination : bond 0.00283 ( 2) SS BOND : bond 0.00596 ( 7) SS BOND : angle 1.22773 ( 14) covalent geometry : bond 0.00246 ( 6731) covalent geometry : angle 0.50251 ( 9152) *********************** 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 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8056 (t) REVERT: A 455 MET cc_start: 0.7629 (tmm) cc_final: 0.7288 (tmm) REVERT: B 343 ASN cc_start: 0.7657 (t0) cc_final: 0.7273 (t0) outliers start: 14 outliers final: 8 residues processed: 165 average time/residue: 1.1125 time to fit residues: 193.4159 Evaluate side-chains 168 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113758 restraints weight = 9124.701| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.93 r_work: 0.3409 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6750 Z= 0.164 Angle : 0.558 9.961 9196 Z= 0.274 Chirality : 0.043 0.217 987 Planarity : 0.004 0.038 1173 Dihedral : 7.361 98.998 1065 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 2.45 % Allowed : 13.42 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.31), residues: 787 helix: 1.51 (0.28), residues: 371 sheet: 1.11 (0.74), residues: 44 loop : -0.93 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 400 TYR 0.015 0.001 TYR A 202 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 7) link_NAG-ASN : angle 2.13170 ( 21) link_BETA1-4 : bond 0.00376 ( 2) link_BETA1-4 : angle 0.90680 ( 6) hydrogen bonds : bond 0.04677 ( 278) hydrogen bonds : angle 4.07397 ( 789) link_BETA1-6 : bond 0.00461 ( 1) link_BETA1-6 : angle 1.11544 ( 3) metal coordination : bond 0.00627 ( 2) SS BOND : bond 0.00603 ( 7) SS BOND : angle 1.22115 ( 14) covalent geometry : bond 0.00381 ( 6731) covalent geometry : angle 0.54695 ( 9152) *********************** 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 180 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8351 (tmm) cc_final: 0.8106 (ttp) REVERT: A 364 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8126 (t) REVERT: A 383 MET cc_start: 0.8487 (mtp) cc_final: 0.8220 (mtp) REVERT: A 455 MET cc_start: 0.7702 (tmm) cc_final: 0.7219 (tmm) REVERT: A 564 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: B 343 ASN cc_start: 0.7675 (t0) cc_final: 0.7256 (t0) outliers start: 17 outliers final: 9 residues processed: 169 average time/residue: 1.0835 time to fit residues: 192.9690 Evaluate side-chains 169 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 370 ASN B 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114185 restraints weight = 9092.036| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.94 r_work: 0.3421 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6750 Z= 0.135 Angle : 0.545 9.387 9196 Z= 0.267 Chirality : 0.042 0.211 987 Planarity : 0.004 0.037 1173 Dihedral : 7.011 92.216 1065 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.73 % Allowed : 14.86 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.31), residues: 787 helix: 1.57 (0.28), residues: 373 sheet: 0.95 (0.75), residues: 44 loop : -0.88 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 PHE 0.008 0.001 PHE A 315 TYR 0.014 0.001 TYR A 202 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 7) link_NAG-ASN : angle 2.18201 ( 21) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 0.92206 ( 6) hydrogen bonds : bond 0.04326 ( 278) hydrogen bonds : angle 3.96667 ( 789) link_BETA1-6 : bond 0.00436 ( 1) link_BETA1-6 : angle 1.17374 ( 3) metal coordination : bond 0.00439 ( 2) SS BOND : bond 0.00577 ( 7) SS BOND : angle 1.18560 ( 14) covalent geometry : bond 0.00309 ( 6731) covalent geometry : angle 0.53300 ( 9152) *********************** 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 169 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6973 (mp0) cc_final: 0.6647 (mp0) REVERT: A 189 GLU cc_start: 0.7941 (tp30) cc_final: 0.7649 (tp30) REVERT: A 190 MET cc_start: 0.8364 (tmm) cc_final: 0.8079 (ttp) REVERT: A 364 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8125 (t) REVERT: A 383 MET cc_start: 0.8436 (mtp) cc_final: 0.8108 (mtp) REVERT: A 455 MET cc_start: 0.7676 (tmm) cc_final: 0.7280 (tmm) REVERT: A 564 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 343 ASN cc_start: 0.7690 (t0) cc_final: 0.7250 (t0) REVERT: B 355 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7480 (ttt-90) outliers start: 12 outliers final: 6 residues processed: 160 average time/residue: 1.1533 time to fit residues: 194.0286 Evaluate side-chains 160 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.0000 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 598 GLN B 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115251 restraints weight = 9053.956| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.93 r_work: 0.3438 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6750 Z= 0.107 Angle : 0.534 10.264 9196 Z= 0.258 Chirality : 0.041 0.221 987 Planarity : 0.004 0.037 1173 Dihedral : 6.707 86.132 1065 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 2.02 % Allowed : 15.01 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.31), residues: 787 helix: 1.66 (0.28), residues: 373 sheet: 0.86 (0.75), residues: 44 loop : -0.80 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE A 315 TYR 0.013 0.001 TYR A 202 ARG 0.001 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 7) link_NAG-ASN : angle 2.14965 ( 21) link_BETA1-4 : bond 0.00409 ( 2) link_BETA1-4 : angle 0.92899 ( 6) hydrogen bonds : bond 0.03847 ( 278) hydrogen bonds : angle 3.93548 ( 789) link_BETA1-6 : bond 0.00407 ( 1) link_BETA1-6 : angle 1.19639 ( 3) metal coordination : bond 0.00350 ( 2) SS BOND : bond 0.00538 ( 7) SS BOND : angle 1.14627 ( 14) covalent geometry : bond 0.00234 ( 6731) covalent geometry : angle 0.52251 ( 9152) *********************** 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 173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6931 (mp0) cc_final: 0.6613 (mp0) REVERT: A 189 GLU cc_start: 0.7944 (tp30) cc_final: 0.7649 (tp30) REVERT: A 190 MET cc_start: 0.8338 (tmm) cc_final: 0.8055 (ttp) REVERT: A 383 MET cc_start: 0.8360 (mtp) cc_final: 0.7949 (mtp) REVERT: A 455 MET cc_start: 0.7619 (tmm) cc_final: 0.7251 (tmm) outliers start: 14 outliers final: 9 residues processed: 162 average time/residue: 1.1206 time to fit residues: 190.9352 Evaluate side-chains 162 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 58 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 102 GLN A 598 GLN B 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114366 restraints weight = 9012.344| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.91 r_work: 0.3424 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6750 Z= 0.135 Angle : 0.560 11.094 9196 Z= 0.271 Chirality : 0.042 0.223 987 Planarity : 0.004 0.037 1173 Dihedral : 6.465 77.887 1065 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 15.30 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.31), residues: 787 helix: 1.70 (0.28), residues: 373 sheet: 0.82 (0.74), residues: 44 loop : -0.81 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.008 0.001 PHE A 315 TYR 0.014 0.001 TYR A 497 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 7) link_NAG-ASN : angle 2.29297 ( 21) link_BETA1-4 : bond 0.00434 ( 2) link_BETA1-4 : angle 0.95201 ( 6) hydrogen bonds : bond 0.04224 ( 278) hydrogen bonds : angle 3.96692 ( 789) link_BETA1-6 : bond 0.00310 ( 1) link_BETA1-6 : angle 1.10876 ( 3) metal coordination : bond 0.00425 ( 2) SS BOND : bond 0.00554 ( 7) SS BOND : angle 1.15833 ( 14) covalent geometry : bond 0.00312 ( 6731) covalent geometry : angle 0.54727 ( 9152) *********************** 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 173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7939 (tp30) cc_final: 0.7606 (tp30) REVERT: A 190 MET cc_start: 0.8336 (tmm) cc_final: 0.8057 (ttp) REVERT: A 383 MET cc_start: 0.8372 (mtp) cc_final: 0.8076 (mtp) REVERT: A 455 MET cc_start: 0.7653 (tmm) cc_final: 0.7251 (tmm) REVERT: A 564 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7479 (mp0) outliers start: 15 outliers final: 11 residues processed: 162 average time/residue: 1.0907 time to fit residues: 185.8500 Evaluate side-chains 169 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 102 GLN A 598 GLN B 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113893 restraints weight = 9106.691| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.94 r_work: 0.3413 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6750 Z= 0.145 Angle : 0.557 9.352 9196 Z= 0.272 Chirality : 0.042 0.230 987 Planarity : 0.004 0.037 1173 Dihedral : 6.201 67.009 1065 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 15.58 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.31), residues: 787 helix: 1.74 (0.28), residues: 367 sheet: 0.71 (0.73), residues: 44 loop : -0.81 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 PHE 0.007 0.001 PHE A 72 TYR 0.013 0.001 TYR A 202 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 7) link_NAG-ASN : angle 2.37584 ( 21) link_BETA1-4 : bond 0.00371 ( 2) link_BETA1-4 : angle 0.94354 ( 6) hydrogen bonds : bond 0.04341 ( 278) hydrogen bonds : angle 3.99724 ( 789) link_BETA1-6 : bond 0.00424 ( 1) link_BETA1-6 : angle 1.15891 ( 3) metal coordination : bond 0.00530 ( 2) SS BOND : bond 0.00562 ( 7) SS BOND : angle 1.15537 ( 14) covalent geometry : bond 0.00336 ( 6731) covalent geometry : angle 0.54358 ( 9152) *********************** 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 171 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7963 (tp30) cc_final: 0.7677 (tp30) REVERT: A 190 MET cc_start: 0.8352 (tmm) cc_final: 0.8086 (ttp) REVERT: A 227 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: A 455 MET cc_start: 0.7707 (tmm) cc_final: 0.7299 (tmm) REVERT: B 343 ASN cc_start: 0.7695 (t0) cc_final: 0.7431 (t0) outliers start: 15 outliers final: 12 residues processed: 159 average time/residue: 1.1139 time to fit residues: 186.3571 Evaluate side-chains 166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 578 ASN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115088 restraints weight = 9125.402| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.93 r_work: 0.3432 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6750 Z= 0.110 Angle : 0.567 12.784 9196 Z= 0.272 Chirality : 0.041 0.195 987 Planarity : 0.004 0.035 1173 Dihedral : 5.872 55.267 1065 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 2.02 % Allowed : 16.16 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.32), residues: 787 helix: 1.73 (0.28), residues: 373 sheet: 0.65 (0.73), residues: 44 loop : -0.75 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.007 0.001 PHE A 72 TYR 0.013 0.001 TYR A 497 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 7) link_NAG-ASN : angle 2.55399 ( 21) link_BETA1-4 : bond 0.00330 ( 2) link_BETA1-4 : angle 0.92771 ( 6) hydrogen bonds : bond 0.03768 ( 278) hydrogen bonds : angle 3.94749 ( 789) link_BETA1-6 : bond 0.00506 ( 1) link_BETA1-6 : angle 1.26472 ( 3) metal coordination : bond 0.00261 ( 2) SS BOND : bond 0.00506 ( 7) SS BOND : angle 1.10207 ( 14) covalent geometry : bond 0.00247 ( 6731) covalent geometry : angle 0.55285 ( 9152) *********************** 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 171 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7934 (tp30) cc_final: 0.7662 (tp30) REVERT: A 190 MET cc_start: 0.8333 (tmm) cc_final: 0.8064 (ttp) REVERT: A 227 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: A 383 MET cc_start: 0.8332 (mtp) cc_final: 0.8039 (mtp) REVERT: A 455 MET cc_start: 0.7624 (tmm) cc_final: 0.7254 (tmm) REVERT: A 564 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 600 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7981 (ptpp) REVERT: B 343 ASN cc_start: 0.7691 (t0) cc_final: 0.7434 (t0) outliers start: 14 outliers final: 9 residues processed: 161 average time/residue: 1.0965 time to fit residues: 185.7394 Evaluate side-chains 164 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN A 598 GLN B 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115135 restraints weight = 9139.462| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.93 r_work: 0.3426 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6750 Z= 0.121 Angle : 0.558 8.545 9196 Z= 0.273 Chirality : 0.041 0.246 987 Planarity : 0.004 0.036 1173 Dihedral : 5.678 53.230 1065 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 2.02 % Allowed : 16.45 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.32), residues: 787 helix: 1.83 (0.28), residues: 367 sheet: 0.60 (0.72), residues: 44 loop : -0.80 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.005 0.001 HIS A 374 PHE 0.008 0.001 PHE A 315 TYR 0.014 0.001 TYR A 50 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 7) link_NAG-ASN : angle 2.53701 ( 21) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 0.95018 ( 6) hydrogen bonds : bond 0.03948 ( 278) hydrogen bonds : angle 3.95075 ( 789) link_BETA1-6 : bond 0.00391 ( 1) link_BETA1-6 : angle 1.16146 ( 3) metal coordination : bond 0.00373 ( 2) SS BOND : bond 0.00521 ( 7) SS BOND : angle 1.12672 ( 14) covalent geometry : bond 0.00276 ( 6731) covalent geometry : angle 0.54373 ( 9152) ********************** 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 167 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7954 (tp30) cc_final: 0.7708 (tp30) REVERT: A 190 MET cc_start: 0.8346 (tmm) cc_final: 0.8080 (ttp) REVERT: A 227 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: A 383 MET cc_start: 0.8314 (mtp) cc_final: 0.7867 (mtp) REVERT: A 455 MET cc_start: 0.7662 (tmm) cc_final: 0.7292 (tmm) REVERT: A 564 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: A 600 LYS cc_start: 0.8279 (ptpp) cc_final: 0.7973 (ptpp) REVERT: B 343 ASN cc_start: 0.7711 (t0) cc_final: 0.7450 (t0) outliers start: 14 outliers final: 10 residues processed: 158 average time/residue: 1.1098 time to fit residues: 184.5828 Evaluate side-chains 165 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.0270 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN A 598 GLN B 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115524 restraints weight = 9227.171| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.95 r_work: 0.3439 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6750 Z= 0.105 Angle : 0.545 12.726 9196 Z= 0.265 Chirality : 0.040 0.224 987 Planarity : 0.004 0.035 1173 Dihedral : 5.440 53.019 1065 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 2.16 % Allowed : 16.02 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.32), residues: 787 helix: 1.78 (0.28), residues: 374 sheet: 0.55 (0.71), residues: 44 loop : -0.74 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.007 0.001 PHE A 315 TYR 0.016 0.001 TYR A 50 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 7) link_NAG-ASN : angle 2.51894 ( 21) link_BETA1-4 : bond 0.00413 ( 2) link_BETA1-4 : angle 0.95470 ( 6) hydrogen bonds : bond 0.03619 ( 278) hydrogen bonds : angle 3.92015 ( 789) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 1.19960 ( 3) metal coordination : bond 0.00220 ( 2) SS BOND : bond 0.00488 ( 7) SS BOND : angle 1.10909 ( 14) covalent geometry : bond 0.00234 ( 6731) covalent geometry : angle 0.53046 ( 9152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5747.70 seconds wall clock time: 99 minutes 19.29 seconds (5959.29 seconds total)