Starting phenix.real_space_refine on Thu Jun 5 23:50:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0t_41784/06_2025/8u0t_41784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0t_41784/06_2025/8u0t_41784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u0t_41784/06_2025/8u0t_41784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0t_41784/06_2025/8u0t_41784.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0t_41784/06_2025/8u0t_41784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0t_41784/06_2025/8u0t_41784.cif" } resolution = 3.2 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= 0.094 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4377 2.51 5 N 1134 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6761 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5342 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 34, 'TRANS': 640} Chain breaks: 1 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 16, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1292 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' ZN': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" 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 Time building chain proxies: 4.51, per 1000 atoms: 0.67 Number of scatterers: 6761 At special positions: 0 Unit cell: (101, 96, 115, 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 38 16.00 O 1211 8.00 N 1134 7.00 C 4377 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=2.22 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=2.06 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 351 " distance=2.06 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.13 Simple disulfide: pdb=" SG CYS B 469 " - pdb=" SG CYS B 477 " distance=2.05 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 NAG-ASN " NAG A 801 " - " ASN A 90 " " NAG A 802 " - " ASN A 546 " " NAG A 803 " - " ASN A 53 " " NAG A 804 " - " ASN A 299 " " NAG A 805 " - " ASN A 329 " " NAG A 806 " - " ASN A 432 " " NAG A 807 " - " ASN A 82 " " NAG B 601 " - " ASN B 333 " " NAG B 602 " - " ASN B 360 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 904.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 808 " pdb="ZN ZN A 808 " - pdb=" NE2 HIS A 374 " 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 56.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.390A pdb=" N ASN A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.729A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.193A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.701A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.637A pdb=" N GLY A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.585A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.505A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.648A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 249 removed outlier: 4.385A pdb=" N GLU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.895A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.888A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 411 removed outlier: 3.882A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.603A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.862A 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 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.656A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.873A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.665A pdb=" N LYS A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.715A pdb=" N PHE A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.981A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 659 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.939A pdb=" N TRP B 343 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.023A pdb=" N ARG B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 491 through 494 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.580A pdb=" N GLU A 140 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.099A 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: 6.095A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 618 through 620 removed outlier: 7.046A pdb=" N SER A 680 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A 675 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 344 through 348 Processing sheet with id=AA6, first strand: chain 'B' and resid 441 through 443 Processing sheet with id=AA7, first strand: chain 'B' and resid 462 through 463 326 hydrogen bonds defined for protein. 915 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: 1.78 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 5 1.19 - 1.36: 2136 1.36 - 1.52: 2887 1.52 - 1.68: 1866 1.68 - 1.85: 62 Bond restraints: 6956 Sorted by residual: bond pdb=" C GLU A 402 " pdb=" O GLU A 402 " ideal model delta sigma weight residual 1.236 1.029 0.207 1.29e-02 6.01e+03 2.57e+02 bond pdb=" CA GLU A 402 " pdb=" CB GLU A 402 " ideal model delta sigma weight residual 1.529 1.326 0.203 1.63e-02 3.76e+03 1.55e+02 bond pdb=" C GLU A 406 " pdb=" O GLU A 406 " ideal model delta sigma weight residual 1.237 1.141 0.095 1.19e-02 7.06e+03 6.40e+01 bond pdb=" CD ARG A 134 " pdb=" NE ARG A 134 " ideal model delta sigma weight residual 1.458 1.566 -0.108 1.40e-02 5.10e+03 6.00e+01 bond pdb=" N ASN A 546 " pdb=" CA ASN A 546 " ideal model delta sigma weight residual 1.459 1.550 -0.091 1.32e-02 5.74e+03 4.77e+01 ... (remaining 6951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 9322 4.59 - 9.18: 141 9.18 - 13.77: 5 13.77 - 18.36: 0 18.36 - 22.95: 2 Bond angle restraints: 9470 Sorted by residual: angle pdb=" CD1 LEU B 475 " pdb=" CG LEU B 475 " pdb=" CD2 LEU B 475 " ideal model delta sigma weight residual 110.80 133.75 -22.95 2.20e+00 2.07e-01 1.09e+02 angle pdb=" CD1 LEU A 351 " pdb=" CG LEU A 351 " pdb=" CD2 LEU A 351 " ideal model delta sigma weight residual 110.80 133.46 -22.66 2.20e+00 2.07e-01 1.06e+02 angle pdb=" C ARG A 134 " pdb=" N PRO A 135 " pdb=" CA PRO A 135 " ideal model delta sigma weight residual 119.84 131.49 -11.65 1.25e+00 6.40e-01 8.69e+01 angle pdb=" N SER B 363 " pdb=" CA SER B 363 " pdb=" C SER B 363 " ideal model delta sigma weight residual 113.23 102.21 11.02 1.24e+00 6.50e-01 7.90e+01 angle pdb=" C ASN A 137 " pdb=" N PRO A 138 " pdb=" CA PRO A 138 " ideal model delta sigma weight residual 119.19 127.76 -8.57 1.06e+00 8.90e-01 6.54e+01 ... (remaining 9465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 3949 17.01 - 34.02: 190 34.02 - 51.04: 35 51.04 - 68.05: 11 68.05 - 85.06: 5 Dihedral angle restraints: 4190 sinusoidal: 1696 harmonic: 2494 Sorted by residual: dihedral pdb=" CB CYS B 469 " pdb=" SG CYS B 469 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual -86.00 -171.06 85.06 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 31.49 61.51 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" C GLU A 402 " pdb=" N GLU A 402 " pdb=" CA GLU A 402 " pdb=" CB GLU A 402 " ideal model delta harmonic sigma weight residual -122.60 -106.82 -15.78 0 2.50e+00 1.60e-01 3.98e+01 ... (remaining 4187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 942 0.137 - 0.274: 71 0.274 - 0.412: 17 0.412 - 0.549: 1 0.549 - 0.686: 2 Chirality restraints: 1033 Sorted by residual: chirality pdb=" CG LEU A 351 " pdb=" CB LEU A 351 " pdb=" CD1 LEU A 351 " pdb=" CD2 LEU A 351 " both_signs ideal model delta sigma weight residual False -2.59 -1.90 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CG LEU B 475 " pdb=" CB LEU B 475 " pdb=" CD1 LEU B 475 " pdb=" CD2 LEU B 475 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ASN A 136 " pdb=" N ASN A 136 " pdb=" C ASN A 136 " pdb=" CB ASN A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 1030 not shown) Planarity restraints: 1209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 82 " -0.083 2.00e-02 2.50e+03 8.13e-02 8.27e+01 pdb=" CG ASN A 82 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN A 82 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 82 " 0.117 2.00e-02 2.50e+03 pdb=" C1 NAG A 807 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 299 " 0.027 2.00e-02 2.50e+03 5.64e-02 3.19e+01 pdb=" C ASN A 299 " -0.098 2.00e-02 2.50e+03 pdb=" O ASN A 299 " 0.037 2.00e-02 2.50e+03 pdb=" N GLN A 300 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 402 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C GLU A 402 " 0.089 2.00e-02 2.50e+03 pdb=" O GLU A 402 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 403 " -0.029 2.00e-02 2.50e+03 ... (remaining 1206 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1952 2.81 - 3.33: 6011 3.33 - 3.86: 10777 3.86 - 4.38: 13352 4.38 - 4.90: 21852 Nonbonded interactions: 53944 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 808 " model vdw 2.291 2.230 nonbonded pdb=" O THR B 489 " pdb=" OG1 THR B 489 " model vdw 2.439 3.040 nonbonded pdb=" N SER B 363 " pdb=" N SER B 364 " model vdw 2.483 2.560 nonbonded pdb=" O ARG A 115 " pdb=" N SER A 118 " model vdw 2.492 3.120 nonbonded pdb=" N GLN A 139 " pdb=" N GLU A 140 " model vdw 2.525 2.560 ... (remaining 53939 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.380 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.015 0.425 6972 Z= 0.815 Angle : 1.434 22.949 9509 Z= 0.954 Chirality : 0.089 0.686 1033 Planarity : 0.007 0.093 1200 Dihedral : 10.776 80.773 2568 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.74 % Favored : 97.14 % Rotamer: Outliers : 0.47 % Allowed : 3.11 % Favored : 96.42 % Cbeta Deviations : 0.25 % 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: -1.05 (0.27), residues: 839 helix: -0.93 (0.23), residues: 397 sheet: 0.79 (0.62), residues: 59 loop : -0.50 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 163 HIS 0.017 0.002 HIS A 374 PHE 0.015 0.003 PHE A 523 TYR 0.025 0.004 TYR A 516 ARG 0.009 0.001 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.06930 ( 9) link_NAG-ASN : angle 3.00185 ( 27) hydrogen bonds : bond 0.22993 ( 326) hydrogen bonds : angle 7.99954 ( 915) metal coordination : bond 0.42543 ( 1) SS BOND : bond 0.09034 ( 6) SS BOND : angle 7.83215 ( 12) covalent geometry : bond 0.01337 ( 6956) covalent geometry : angle 1.40088 ( 9470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.959 Fit side-chains REVERT: A 259 THR cc_start: 0.7826 (m) cc_final: 0.7264 (p) REVERT: B 396 ASP cc_start: 0.8112 (m-30) cc_final: 0.7872 (m-30) outliers start: 3 outliers final: 1 residues processed: 145 average time/residue: 0.2279 time to fit residues: 45.1016 Evaluate side-chains 89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.0050 chunk 49 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS ** A 616 GLN ** 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 = 0.4113 r_free = 0.4113 target = 0.184134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149763 restraints weight = 7649.760| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.18 r_work: 0.3497 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6972 Z= 0.143 Angle : 0.613 12.922 9509 Z= 0.321 Chirality : 0.052 0.835 1033 Planarity : 0.005 0.033 1200 Dihedral : 4.944 32.403 1115 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.40 % Allowed : 8.71 % Favored : 89.89 % 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: 0.23 (0.29), residues: 839 helix: 0.50 (0.26), residues: 405 sheet: 0.85 (0.64), residues: 58 loop : -0.21 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.019 0.002 PHE A 327 TYR 0.019 0.002 TYR A 385 ARG 0.003 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 9) link_NAG-ASN : angle 3.64744 ( 27) hydrogen bonds : bond 0.05601 ( 326) hydrogen bonds : angle 5.09838 ( 915) metal coordination : bond 0.00162 ( 1) SS BOND : bond 0.00647 ( 6) SS BOND : angle 1.54203 ( 12) covalent geometry : bond 0.00300 ( 6956) covalent geometry : angle 0.57971 ( 9470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 THR cc_start: 0.8306 (m) cc_final: 0.7847 (p) REVERT: A 292 ASP cc_start: 0.8344 (t0) cc_final: 0.8136 (t0) REVERT: A 408 MET cc_start: 0.8529 (mmt) cc_final: 0.8176 (mmt) REVERT: B 396 ASP cc_start: 0.8533 (m-30) cc_final: 0.8283 (m-30) REVERT: B 446 ARG cc_start: 0.8328 (ttt-90) cc_final: 0.8069 (ttt-90) REVERT: B 489 THR cc_start: 0.8158 (p) cc_final: 0.7827 (p) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.1845 time to fit residues: 26.5211 Evaluate side-chains 89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 492 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.0670 chunk 79 optimal weight: 8.9990 chunk 41 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 616 GLN B 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.182540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148203 restraints weight = 7712.699| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.00 r_work: 0.3490 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6972 Z= 0.133 Angle : 0.594 14.567 9509 Z= 0.301 Chirality : 0.047 0.530 1033 Planarity : 0.004 0.040 1200 Dihedral : 4.655 33.650 1113 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.02 % Allowed : 9.18 % Favored : 88.80 % 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: 0.55 (0.29), residues: 839 helix: 0.96 (0.26), residues: 405 sheet: 0.79 (0.67), residues: 58 loop : -0.27 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.014 0.001 PHE A 369 TYR 0.023 0.002 TYR A 654 ARG 0.007 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 9) link_NAG-ASN : angle 3.18947 ( 27) hydrogen bonds : bond 0.04870 ( 326) hydrogen bonds : angle 4.76559 ( 915) metal coordination : bond 0.00147 ( 1) SS BOND : bond 0.00939 ( 6) SS BOND : angle 2.29522 ( 12) covalent geometry : bond 0.00303 ( 6956) covalent geometry : angle 0.56453 ( 9470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8602 (m) cc_final: 0.8130 (p) REVERT: A 288 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6514 (mmtt) REVERT: A 408 MET cc_start: 0.8648 (mmt) cc_final: 0.8302 (mmt) REVERT: B 396 ASP cc_start: 0.8708 (m-30) cc_final: 0.8452 (m-30) REVERT: B 446 ARG cc_start: 0.8369 (ttt-90) cc_final: 0.8050 (ttt-90) outliers start: 13 outliers final: 5 residues processed: 96 average time/residue: 0.1839 time to fit residues: 24.4483 Evaluate side-chains 90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.177289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143813 restraints weight = 7719.639| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.92 r_work: 0.3467 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6972 Z= 0.143 Angle : 0.693 19.976 9509 Z= 0.343 Chirality : 0.046 0.432 1033 Planarity : 0.005 0.039 1200 Dihedral : 4.589 41.163 1113 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.56 % Allowed : 10.26 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.54 (0.29), residues: 839 helix: 1.05 (0.26), residues: 407 sheet: 0.66 (0.66), residues: 58 loop : -0.38 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.017 0.001 PHE A 369 TYR 0.023 0.002 TYR A 385 ARG 0.009 0.001 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 9) link_NAG-ASN : angle 3.66885 ( 27) hydrogen bonds : bond 0.04883 ( 326) hydrogen bonds : angle 4.71980 ( 915) metal coordination : bond 0.00196 ( 1) SS BOND : bond 0.00313 ( 6) SS BOND : angle 6.03199 ( 12) covalent geometry : bond 0.00332 ( 6956) covalent geometry : angle 0.63113 ( 9470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8058 (t0) cc_final: 0.7816 (m-30) REVERT: A 49 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7208 (tt0) REVERT: A 259 THR cc_start: 0.8764 (m) cc_final: 0.8251 (p) REVERT: A 408 MET cc_start: 0.8690 (mmt) cc_final: 0.8365 (mmt) REVERT: B 396 ASP cc_start: 0.8733 (m-30) cc_final: 0.8463 (m-30) REVERT: B 446 ARG cc_start: 0.8382 (ttt-90) cc_final: 0.7988 (ttt-90) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1660 time to fit residues: 21.9089 Evaluate side-chains 89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119074 restraints weight = 7736.578| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.25 r_work: 0.3119 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6972 Z= 0.133 Angle : 0.641 17.631 9509 Z= 0.320 Chirality : 0.045 0.401 1033 Planarity : 0.004 0.038 1200 Dihedral : 4.453 39.630 1113 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.56 % Allowed : 11.66 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.63 (0.29), residues: 839 helix: 1.12 (0.26), residues: 407 sheet: 0.79 (0.66), residues: 58 loop : -0.36 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.025 0.001 PHE A 327 TYR 0.021 0.002 TYR A 654 ARG 0.007 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 9) link_NAG-ASN : angle 2.83180 ( 27) hydrogen bonds : bond 0.04620 ( 326) hydrogen bonds : angle 4.70323 ( 915) metal coordination : bond 0.00053 ( 1) SS BOND : bond 0.00183 ( 6) SS BOND : angle 5.44675 ( 12) covalent geometry : bond 0.00306 ( 6956) covalent geometry : angle 0.59316 ( 9470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7932 (t0) cc_final: 0.7604 (m-30) REVERT: A 49 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6856 (tt0) REVERT: A 259 THR cc_start: 0.8774 (m) cc_final: 0.8207 (p) REVERT: A 269 ASP cc_start: 0.8274 (t0) cc_final: 0.7944 (t0) REVERT: A 288 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6494 (mmtt) REVERT: A 408 MET cc_start: 0.8443 (mmt) cc_final: 0.8127 (mmt) REVERT: A 474 MET cc_start: 0.8385 (mmp) cc_final: 0.7990 (mmp) REVERT: B 396 ASP cc_start: 0.8642 (m-30) cc_final: 0.8294 (m-30) REVERT: B 446 ARG cc_start: 0.8317 (ttt-90) cc_final: 0.8077 (ttt-90) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.1704 time to fit residues: 21.2817 Evaluate side-chains 90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 0.0060 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119974 restraints weight = 7785.206| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.07 r_work: 0.3150 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 6972 Z= 0.111 Angle : 0.589 14.506 9509 Z= 0.295 Chirality : 0.043 0.322 1033 Planarity : 0.004 0.036 1200 Dihedral : 4.157 39.692 1113 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.71 % Allowed : 11.35 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.83 (0.30), residues: 839 helix: 1.30 (0.26), residues: 408 sheet: 0.77 (0.64), residues: 58 loop : -0.24 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE A 327 TYR 0.022 0.001 TYR A 654 ARG 0.005 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 9) link_NAG-ASN : angle 2.32676 ( 27) hydrogen bonds : bond 0.04124 ( 326) hydrogen bonds : angle 4.64501 ( 915) metal coordination : bond 0.00072 ( 1) SS BOND : bond 0.00259 ( 6) SS BOND : angle 4.99741 ( 12) covalent geometry : bond 0.00248 ( 6956) covalent geometry : angle 0.54894 ( 9470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7827 (t0) cc_final: 0.7469 (m-30) REVERT: A 49 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6839 (tt0) REVERT: A 154 THR cc_start: 0.9105 (p) cc_final: 0.8897 (p) REVERT: A 259 THR cc_start: 0.8738 (m) cc_final: 0.8146 (p) REVERT: A 323 MET cc_start: 0.8060 (mtt) cc_final: 0.7636 (mtt) REVERT: A 408 MET cc_start: 0.8402 (mmt) cc_final: 0.8085 (mmt) REVERT: A 474 MET cc_start: 0.8443 (mmp) cc_final: 0.7912 (mmp) REVERT: A 557 MET cc_start: 0.9115 (tmm) cc_final: 0.8703 (ttp) REVERT: B 396 ASP cc_start: 0.8644 (m-30) cc_final: 0.8329 (m-30) REVERT: B 446 ARG cc_start: 0.8321 (ttt-90) cc_final: 0.8060 (ttt-90) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.1720 time to fit residues: 22.2811 Evaluate side-chains 88 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.1980 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 0.0770 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120242 restraints weight = 7683.095| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.14 r_work: 0.3137 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 6972 Z= 0.112 Angle : 0.582 14.809 9509 Z= 0.293 Chirality : 0.042 0.308 1033 Planarity : 0.004 0.037 1200 Dihedral : 4.014 38.039 1113 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.33 % Allowed : 11.20 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.87 (0.30), residues: 839 helix: 1.36 (0.26), residues: 408 sheet: 0.77 (0.64), residues: 58 loop : -0.26 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE A 369 TYR 0.021 0.001 TYR A 654 ARG 0.006 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 9) link_NAG-ASN : angle 2.12611 ( 27) hydrogen bonds : bond 0.04149 ( 326) hydrogen bonds : angle 4.59336 ( 915) metal coordination : bond 0.00043 ( 1) SS BOND : bond 0.00185 ( 6) SS BOND : angle 4.94480 ( 12) covalent geometry : bond 0.00250 ( 6956) covalent geometry : angle 0.54380 ( 9470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7571 (t0) cc_final: 0.7273 (m-30) REVERT: A 49 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6729 (tt0) REVERT: A 154 THR cc_start: 0.9078 (p) cc_final: 0.8869 (p) REVERT: A 259 THR cc_start: 0.8669 (m) cc_final: 0.8071 (p) REVERT: A 288 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6564 (mmtp) REVERT: A 408 MET cc_start: 0.8333 (mmt) cc_final: 0.8028 (mmt) REVERT: A 474 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7650 (mmp) REVERT: A 557 MET cc_start: 0.9084 (tmm) cc_final: 0.8686 (ttp) REVERT: B 396 ASP cc_start: 0.8508 (m-30) cc_final: 0.8190 (m-30) REVERT: B 446 ARG cc_start: 0.8309 (ttt-90) cc_final: 0.8032 (ttt-90) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.1819 time to fit residues: 24.0269 Evaluate side-chains 96 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117603 restraints weight = 7824.466| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.13 r_work: 0.3098 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6972 Z= 0.141 Angle : 0.624 15.348 9509 Z= 0.313 Chirality : 0.044 0.315 1033 Planarity : 0.004 0.040 1200 Dihedral : 3.961 36.711 1113 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.18 % Allowed : 11.98 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.30), residues: 839 helix: 1.30 (0.26), residues: 406 sheet: 0.81 (0.64), residues: 58 loop : -0.31 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.016 0.001 PHE A 369 TYR 0.024 0.002 TYR A 654 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 9) link_NAG-ASN : angle 2.05149 ( 27) hydrogen bonds : bond 0.04666 ( 326) hydrogen bonds : angle 4.66163 ( 915) metal coordination : bond 0.00173 ( 1) SS BOND : bond 0.00184 ( 6) SS BOND : angle 5.02136 ( 12) covalent geometry : bond 0.00331 ( 6956) covalent geometry : angle 0.58881 ( 9470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7726 (t0) cc_final: 0.7410 (m-30) REVERT: A 49 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6891 (tt0) REVERT: A 154 THR cc_start: 0.9117 (p) cc_final: 0.8874 (p) REVERT: A 259 THR cc_start: 0.8710 (m) cc_final: 0.8111 (p) REVERT: A 408 MET cc_start: 0.8367 (mmt) cc_final: 0.8045 (mmt) REVERT: A 474 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7832 (mmp) REVERT: B 396 ASP cc_start: 0.8509 (m-30) cc_final: 0.8190 (m-30) REVERT: B 446 ARG cc_start: 0.8327 (ttt-90) cc_final: 0.8044 (ttt-90) outliers start: 14 outliers final: 10 residues processed: 88 average time/residue: 0.1775 time to fit residues: 22.0329 Evaluate side-chains 92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 79 optimal weight: 0.0980 overall best weight: 0.2538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121790 restraints weight = 7754.622| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.20 r_work: 0.3173 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 6972 Z= 0.101 Angle : 0.561 14.191 9509 Z= 0.282 Chirality : 0.042 0.281 1033 Planarity : 0.004 0.037 1200 Dihedral : 3.659 35.512 1113 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.56 % Allowed : 12.29 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.04 (0.30), residues: 839 helix: 1.53 (0.26), residues: 407 sheet: 0.75 (0.64), residues: 58 loop : -0.18 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 69 HIS 0.002 0.000 HIS A 241 PHE 0.016 0.001 PHE A 327 TYR 0.024 0.001 TYR A 654 ARG 0.005 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 9) link_NAG-ASN : angle 1.80328 ( 27) hydrogen bonds : bond 0.03802 ( 326) hydrogen bonds : angle 4.54505 ( 915) metal coordination : bond 0.00236 ( 1) SS BOND : bond 0.00201 ( 6) SS BOND : angle 4.84034 ( 12) covalent geometry : bond 0.00220 ( 6956) covalent geometry : angle 0.52587 ( 9470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7504 (t0) cc_final: 0.7268 (m-30) REVERT: A 49 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6852 (tt0) REVERT: A 69 TRP cc_start: 0.8055 (t-100) cc_final: 0.7773 (t-100) REVERT: A 154 THR cc_start: 0.9052 (p) cc_final: 0.8843 (p) REVERT: A 259 THR cc_start: 0.8651 (m) cc_final: 0.8039 (p) REVERT: A 288 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6663 (mmtp) REVERT: A 408 MET cc_start: 0.8293 (mmt) cc_final: 0.8050 (mmt) REVERT: B 396 ASP cc_start: 0.8486 (m-30) cc_final: 0.8169 (m-30) REVERT: B 446 ARG cc_start: 0.8347 (ttt-90) cc_final: 0.8086 (ttt-90) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 0.1829 time to fit residues: 22.8712 Evaluate side-chains 90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 0.0670 chunk 80 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.178742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.145382 restraints weight = 7769.203| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.89 r_work: 0.3485 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6972 Z= 0.119 Angle : 0.586 14.789 9509 Z= 0.295 Chirality : 0.043 0.286 1033 Planarity : 0.004 0.038 1200 Dihedral : 3.655 35.091 1113 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.24 % Allowed : 13.22 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.97 (0.30), residues: 839 helix: 1.43 (0.26), residues: 415 sheet: 0.74 (0.65), residues: 57 loop : -0.22 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.036 0.001 PHE A 327 TYR 0.025 0.001 TYR A 654 ARG 0.005 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 9) link_NAG-ASN : angle 1.81382 ( 27) hydrogen bonds : bond 0.04232 ( 326) hydrogen bonds : angle 4.53811 ( 915) metal coordination : bond 0.00119 ( 1) SS BOND : bond 0.00137 ( 6) SS BOND : angle 4.85612 ( 12) covalent geometry : bond 0.00271 ( 6956) covalent geometry : angle 0.55244 ( 9470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7909 (t0) cc_final: 0.7672 (m-30) REVERT: A 259 THR cc_start: 0.8745 (m) cc_final: 0.8218 (p) REVERT: B 396 ASP cc_start: 0.8696 (m-30) cc_final: 0.8426 (m-30) REVERT: B 446 ARG cc_start: 0.8445 (ttt-90) cc_final: 0.8237 (ttt-90) outliers start: 8 outliers final: 8 residues processed: 86 average time/residue: 0.1772 time to fit residues: 21.2308 Evaluate side-chains 91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 0.0670 chunk 18 optimal weight: 0.0980 chunk 52 optimal weight: 0.0870 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.186921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153006 restraints weight = 7771.545| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.97 r_work: 0.3565 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 6972 Z= 0.097 Angle : 0.545 13.631 9509 Z= 0.275 Chirality : 0.041 0.252 1033 Planarity : 0.004 0.035 1200 Dihedral : 3.431 33.589 1113 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.40 % Allowed : 12.75 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.25 (0.30), residues: 839 helix: 1.68 (0.26), residues: 415 sheet: 0.78 (0.66), residues: 57 loop : -0.09 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.002 0.000 HIS A 241 PHE 0.034 0.001 PHE A 327 TYR 0.025 0.001 TYR A 654 ARG 0.005 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 9) link_NAG-ASN : angle 1.58004 ( 27) hydrogen bonds : bond 0.03468 ( 326) hydrogen bonds : angle 4.44421 ( 915) metal coordination : bond 0.00033 ( 1) SS BOND : bond 0.00125 ( 6) SS BOND : angle 4.61518 ( 12) covalent geometry : bond 0.00205 ( 6956) covalent geometry : angle 0.51409 ( 9470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5017.45 seconds wall clock time: 89 minutes 15.03 seconds (5355.03 seconds total)