Starting phenix.real_space_refine on Tue Feb 3 20:34:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0t_41784/02_2026/8u0t_41784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0t_41784/02_2026/8u0t_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_41784/02_2026/8u0t_41784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0t_41784/02_2026/8u0t_41784.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0t_41784/02_2026/8u0t_41784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0t_41784/02_2026/8u0t_41784.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.094 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: {'ASP:plan': 16, 'GLU:plan': 14, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 3, '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, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2} 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: 1.50, per 1000 atoms: 0.22 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: 0.50 Conformation dependent library (CDL) restraints added in 165.6 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: 0.29 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: 0.84 Time building geometry restraints manager: 0.66 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (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 ARG 0.009 0.001 ARG A 161 TYR 0.025 0.004 TYR A 516 PHE 0.015 0.003 PHE A 523 TRP 0.020 0.004 TRP A 163 HIS 0.017 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.01337 ( 6956) covalent geometry : angle 1.40088 ( 9470) SS BOND : bond 0.09034 ( 6) SS BOND : angle 7.83215 ( 12) hydrogen bonds : bond 0.22993 ( 326) hydrogen bonds : angle 7.99954 ( 915) metal coordination : bond 0.42543 ( 1) link_NAG-ASN : bond 0.06930 ( 9) link_NAG-ASN : angle 3.00185 ( 27) *********************** 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 : 0.155 Fit side-chains REVERT: A 259 THR cc_start: 0.7832 (m) cc_final: 0.7268 (p) REVERT: A 474 MET cc_start: 0.8037 (mmm) cc_final: 0.7835 (mmp) REVERT: B 396 ASP cc_start: 0.8115 (m-30) cc_final: 0.7878 (m-30) outliers start: 3 outliers final: 1 residues processed: 145 average time/residue: 0.0699 time to fit residues: 13.6552 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 : 0.258 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 401 HIS ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.182537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148131 restraints weight = 7727.979| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.02 r_work: 0.3490 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6972 Z= 0.155 Angle : 0.623 12.719 9509 Z= 0.326 Chirality : 0.054 0.871 1033 Planarity : 0.005 0.034 1200 Dihedral : 4.992 32.645 1115 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.56 % Allowed : 8.24 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.29), residues: 839 helix: 0.43 (0.26), residues: 405 sheet: 0.82 (0.63), residues: 58 loop : -0.23 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 652 TYR 0.022 0.002 TYR A 385 PHE 0.018 0.002 PHE A 327 TRP 0.013 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6956) covalent geometry : angle 0.59088 ( 9470) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.58505 ( 12) hydrogen bonds : bond 0.05779 ( 326) hydrogen bonds : angle 5.13717 ( 915) metal coordination : bond 0.00065 ( 1) link_NAG-ASN : bond 0.00568 ( 9) link_NAG-ASN : angle 3.60204 ( 27) *********************** 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: 10 poor density : 92 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 THR cc_start: 0.8493 (m) cc_final: 0.8044 (p) REVERT: A 292 ASP cc_start: 0.8390 (t0) cc_final: 0.8176 (t0) REVERT: A 408 MET cc_start: 0.8660 (mmt) cc_final: 0.8295 (mmt) REVERT: B 396 ASP cc_start: 0.8712 (m-30) cc_final: 0.8477 (m-30) REVERT: B 446 ARG cc_start: 0.8368 (ttt-90) cc_final: 0.8106 (ttt-90) REVERT: B 489 THR cc_start: 0.8186 (p) cc_final: 0.7778 (p) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.0562 time to fit residues: 7.9331 Evaluate side-chains 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 151 ILE 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 71 optimal weight: 0.2980 chunk 51 optimal weight: 0.0980 chunk 66 optimal weight: 0.3980 chunk 60 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 GLN B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.182940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148311 restraints weight = 7733.908| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.02 r_work: 0.3493 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2762 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= 0.128 Angle : 0.602 16.668 9509 Z= 0.303 Chirality : 0.047 0.557 1033 Planarity : 0.004 0.039 1200 Dihedral : 4.676 32.969 1113 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.71 % Allowed : 9.18 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.29), residues: 839 helix: 0.90 (0.26), residues: 405 sheet: 0.75 (0.66), residues: 58 loop : -0.26 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 169 TYR 0.023 0.001 TYR A 654 PHE 0.012 0.001 PHE A 438 TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6956) covalent geometry : angle 0.56940 ( 9470) SS BOND : bond 0.00950 ( 6) SS BOND : angle 2.44507 ( 12) hydrogen bonds : bond 0.04781 ( 326) hydrogen bonds : angle 4.75531 ( 915) metal coordination : bond 0.00163 ( 1) link_NAG-ASN : bond 0.00592 ( 9) link_NAG-ASN : angle 3.36937 ( 27) *********************** 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 104 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8574 (m) cc_final: 0.8097 (p) REVERT: A 288 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6510 (mmtt) REVERT: A 322 HIS cc_start: 0.8170 (m-70) cc_final: 0.7914 (m-70) REVERT: A 408 MET cc_start: 0.8637 (mmt) cc_final: 0.8301 (mmt) REVERT: A 474 MET cc_start: 0.8263 (mmp) cc_final: 0.7874 (mmp) REVERT: B 396 ASP cc_start: 0.8733 (m-30) cc_final: 0.8466 (m-30) REVERT: B 446 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.8059 (ttt-90) outliers start: 11 outliers final: 4 residues processed: 97 average time/residue: 0.0771 time to fit residues: 10.2118 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 : 0.241 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.0170 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.180038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145966 restraints weight = 7763.105| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.95 r_work: 0.3462 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6972 Z= 0.139 Angle : 0.686 20.711 9509 Z= 0.340 Chirality : 0.046 0.469 1033 Planarity : 0.005 0.040 1200 Dihedral : 4.640 42.759 1113 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.87 % Allowed : 9.49 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 839 helix: 1.07 (0.26), residues: 407 sheet: 0.63 (0.66), residues: 58 loop : -0.41 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 169 TYR 0.022 0.002 TYR A 385 PHE 0.014 0.001 PHE A 369 TRP 0.010 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6956) covalent geometry : angle 0.62391 ( 9470) SS BOND : bond 0.00301 ( 6) SS BOND : angle 5.92066 ( 12) hydrogen bonds : bond 0.04737 ( 326) hydrogen bonds : angle 4.75430 ( 915) metal coordination : bond 0.00274 ( 1) link_NAG-ASN : bond 0.00455 ( 9) link_NAG-ASN : angle 3.70583 ( 27) *********************** 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: 12 poor density : 85 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7193 (tt0) REVERT: A 259 THR cc_start: 0.8746 (m) cc_final: 0.8234 (p) REVERT: A 322 HIS cc_start: 0.8241 (m-70) cc_final: 0.7968 (m-70) REVERT: A 408 MET cc_start: 0.8701 (mmt) cc_final: 0.8386 (mmt) REVERT: A 474 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7835 (mmp) REVERT: B 396 ASP cc_start: 0.8741 (m-30) cc_final: 0.8473 (m-30) REVERT: B 446 ARG cc_start: 0.8374 (ttt-90) cc_final: 0.7983 (ttt-90) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.0684 time to fit residues: 8.9532 Evaluate side-chains 92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.154024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116392 restraints weight = 7835.917| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.30 r_work: 0.3082 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6972 Z= 0.165 Angle : 0.677 17.643 9509 Z= 0.339 Chirality : 0.046 0.426 1033 Planarity : 0.005 0.040 1200 Dihedral : 4.651 41.187 1113 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.49 % Allowed : 10.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 839 helix: 1.00 (0.26), residues: 407 sheet: 0.82 (0.66), residues: 58 loop : -0.45 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.025 0.002 TYR A 385 PHE 0.023 0.002 PHE A 327 TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6956) covalent geometry : angle 0.62847 ( 9470) SS BOND : bond 0.00182 ( 6) SS BOND : angle 5.48868 ( 12) hydrogen bonds : bond 0.05214 ( 326) hydrogen bonds : angle 4.78397 ( 915) metal coordination : bond 0.00126 ( 1) link_NAG-ASN : bond 0.00405 ( 9) link_NAG-ASN : angle 3.05695 ( 27) *********************** 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 98 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6899 (tt0) REVERT: A 259 THR cc_start: 0.8812 (m) cc_final: 0.8266 (p) REVERT: A 288 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6664 (mmtp) REVERT: A 408 MET cc_start: 0.8474 (mmt) cc_final: 0.8126 (mmt) REVERT: A 474 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7914 (mmp) REVERT: B 396 ASP cc_start: 0.8640 (m-30) cc_final: 0.8304 (m-30) REVERT: B 446 ARG cc_start: 0.8327 (ttt-90) cc_final: 0.7804 (ttt-90) outliers start: 16 outliers final: 8 residues processed: 91 average time/residue: 0.0693 time to fit residues: 8.8552 Evaluate side-chains 91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 50 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 0.0040 chunk 67 optimal weight: 0.2980 chunk 63 optimal weight: 0.2980 chunk 58 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 overall best weight: 0.3192 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.159074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121548 restraints weight = 7811.629| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.20 r_work: 0.3148 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3647 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= 0.107 Angle : 0.586 14.920 9509 Z= 0.295 Chirality : 0.043 0.324 1033 Planarity : 0.004 0.036 1200 Dihedral : 4.213 39.489 1113 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.56 % Allowed : 11.98 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.30), residues: 839 helix: 1.26 (0.26), residues: 408 sheet: 0.83 (0.64), residues: 58 loop : -0.29 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.022 0.001 TYR A 654 PHE 0.016 0.001 PHE A 327 TRP 0.009 0.001 TRP A 69 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 6956) covalent geometry : angle 0.54423 ( 9470) SS BOND : bond 0.00144 ( 6) SS BOND : angle 5.02441 ( 12) hydrogen bonds : bond 0.04047 ( 326) hydrogen bonds : angle 4.70511 ( 915) metal coordination : bond 0.00293 ( 1) link_NAG-ASN : bond 0.00331 ( 9) link_NAG-ASN : angle 2.40796 ( 27) *********************** 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 100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6826 (tt0) REVERT: A 154 THR cc_start: 0.9113 (p) cc_final: 0.8910 (p) REVERT: A 259 THR cc_start: 0.8638 (m) cc_final: 0.8038 (p) REVERT: A 288 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6573 (mmtp) REVERT: A 408 MET cc_start: 0.8319 (mmt) cc_final: 0.7997 (mmt) REVERT: A 474 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7791 (mmp) REVERT: A 531 ARG cc_start: 0.8330 (ttt-90) cc_final: 0.7834 (ttp-170) REVERT: B 396 ASP cc_start: 0.8504 (m-30) cc_final: 0.8174 (m-30) REVERT: B 446 ARG cc_start: 0.8331 (ttt-90) cc_final: 0.8099 (ttt-90) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.0771 time to fit residues: 10.2127 Evaluate side-chains 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 474 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 82 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.155839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117652 restraints weight = 7738.849| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.14 r_work: 0.3100 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3726 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= 0.135 Angle : 0.622 15.165 9509 Z= 0.312 Chirality : 0.044 0.322 1033 Planarity : 0.004 0.039 1200 Dihedral : 4.053 38.214 1113 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.87 % Allowed : 12.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.30), residues: 839 helix: 1.26 (0.26), residues: 406 sheet: 0.83 (0.64), residues: 58 loop : -0.38 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.022 0.002 TYR A 654 PHE 0.019 0.001 PHE A 369 TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6956) covalent geometry : angle 0.58476 ( 9470) SS BOND : bond 0.00195 ( 6) SS BOND : angle 5.06776 ( 12) hydrogen bonds : bond 0.04612 ( 326) hydrogen bonds : angle 4.71810 ( 915) metal coordination : bond 0.00153 ( 1) link_NAG-ASN : bond 0.00343 ( 9) link_NAG-ASN : angle 2.17017 ( 27) *********************** 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 97 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6772 (tt0) REVERT: A 154 THR cc_start: 0.9098 (p) cc_final: 0.8872 (p) REVERT: A 259 THR cc_start: 0.8689 (m) cc_final: 0.8102 (p) REVERT: A 269 ASP cc_start: 0.8118 (t0) cc_final: 0.7915 (t0) REVERT: A 408 MET cc_start: 0.8361 (mmt) cc_final: 0.8036 (mmt) REVERT: A 474 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7816 (mmp) REVERT: A 531 ARG cc_start: 0.8320 (ttt-90) cc_final: 0.7747 (ttp-170) REVERT: B 396 ASP cc_start: 0.8489 (m-30) cc_final: 0.8152 (m-30) REVERT: B 446 ARG cc_start: 0.8335 (ttt-90) cc_final: 0.8066 (ttt-90) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.0744 time to fit residues: 9.3993 Evaluate side-chains 92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 579 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 13 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.156600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118373 restraints weight = 7816.086| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.12 r_work: 0.3110 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3826 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= 0.128 Angle : 0.605 14.717 9509 Z= 0.304 Chirality : 0.044 0.308 1033 Planarity : 0.004 0.040 1200 Dihedral : 3.957 37.205 1113 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.87 % Allowed : 12.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.30), residues: 839 helix: 1.27 (0.26), residues: 406 sheet: 0.83 (0.64), residues: 58 loop : -0.38 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.023 0.001 TYR A 654 PHE 0.015 0.001 PHE A 369 TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6956) covalent geometry : angle 0.57029 ( 9470) SS BOND : bond 0.00217 ( 6) SS BOND : angle 4.93261 ( 12) hydrogen bonds : bond 0.04438 ( 326) hydrogen bonds : angle 4.69153 ( 915) metal coordination : bond 0.00115 ( 1) link_NAG-ASN : bond 0.00393 ( 9) link_NAG-ASN : angle 2.05782 ( 27) *********************** 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 94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6880 (tt0) REVERT: A 154 THR cc_start: 0.9096 (p) cc_final: 0.8871 (p) REVERT: A 259 THR cc_start: 0.8672 (m) cc_final: 0.8082 (p) REVERT: A 269 ASP cc_start: 0.8121 (t0) cc_final: 0.7880 (t0) REVERT: A 408 MET cc_start: 0.8340 (mmt) cc_final: 0.8034 (mmt) REVERT: A 474 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7753 (mmp) REVERT: A 531 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.7763 (ttp-170) REVERT: B 396 ASP cc_start: 0.8499 (m-30) cc_final: 0.8175 (m-30) REVERT: B 446 ARG cc_start: 0.8347 (ttt-90) cc_final: 0.8076 (ttt-90) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.0734 time to fit residues: 9.0380 Evaluate side-chains 92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 579 MET 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: 0.7980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.0030 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.156171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119850 restraints weight = 7806.321| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.15 r_work: 0.3159 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 6972 Z= 0.112 Angle : 0.587 14.420 9509 Z= 0.295 Chirality : 0.043 0.289 1033 Planarity : 0.004 0.038 1200 Dihedral : 3.836 36.575 1113 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.87 % Allowed : 12.75 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.30), residues: 839 helix: 1.32 (0.26), residues: 408 sheet: 0.86 (0.63), residues: 58 loop : -0.27 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.025 0.001 TYR A 654 PHE 0.021 0.001 PHE A 327 TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6956) covalent geometry : angle 0.55298 ( 9470) SS BOND : bond 0.00137 ( 6) SS BOND : angle 4.82636 ( 12) hydrogen bonds : bond 0.04139 ( 326) hydrogen bonds : angle 4.63579 ( 915) metal coordination : bond 0.00107 ( 1) link_NAG-ASN : bond 0.00368 ( 9) link_NAG-ASN : angle 1.97359 ( 27) *********************** 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 99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6914 (tt0) REVERT: A 154 THR cc_start: 0.9075 (p) cc_final: 0.8848 (p) REVERT: A 227 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8009 (mp0) REVERT: A 259 THR cc_start: 0.8749 (m) cc_final: 0.8163 (p) REVERT: A 269 ASP cc_start: 0.8186 (t0) cc_final: 0.7904 (t0) REVERT: A 408 MET cc_start: 0.8403 (mmt) cc_final: 0.8127 (mmt) REVERT: A 474 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7862 (mmp) REVERT: A 531 ARG cc_start: 0.8501 (ttt-90) cc_final: 0.7894 (ttp-170) REVERT: B 396 ASP cc_start: 0.8646 (m-30) cc_final: 0.8315 (m-30) REVERT: B 446 ARG cc_start: 0.8394 (ttt-90) cc_final: 0.8126 (ttt-90) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.0802 time to fit residues: 10.2817 Evaluate side-chains 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 133 CYS 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 579 MET 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 49 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 67 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.181256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147326 restraints weight = 7732.140| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.93 r_work: 0.3484 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6972 Z= 0.117 Angle : 0.598 14.636 9509 Z= 0.299 Chirality : 0.043 0.287 1033 Planarity : 0.004 0.039 1200 Dihedral : 3.837 35.963 1113 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.71 % Allowed : 12.91 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 839 helix: 1.27 (0.26), residues: 413 sheet: 0.83 (0.63), residues: 58 loop : -0.25 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.026 0.001 TYR A 654 PHE 0.023 0.001 PHE A 327 TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6956) covalent geometry : angle 0.56424 ( 9470) SS BOND : bond 0.00161 ( 6) SS BOND : angle 4.82796 ( 12) hydrogen bonds : bond 0.04225 ( 326) hydrogen bonds : angle 4.60309 ( 915) metal coordination : bond 0.00147 ( 1) link_NAG-ASN : bond 0.00351 ( 9) link_NAG-ASN : angle 1.94554 ( 27) ********************** 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 96 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 THR cc_start: 0.8763 (m) cc_final: 0.8227 (p) REVERT: A 269 ASP cc_start: 0.8072 (t0) cc_final: 0.7793 (t0) REVERT: A 408 MET cc_start: 0.8620 (mmt) cc_final: 0.8348 (mmt) REVERT: A 474 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7697 (mmp) REVERT: A 531 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.8054 (ttp-170) REVERT: B 396 ASP cc_start: 0.8686 (m-30) cc_final: 0.8415 (m-30) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.0761 time to fit residues: 9.5212 Evaluate side-chains 95 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 579 MET 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 56 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.181058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147088 restraints weight = 7739.831| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.93 r_work: 0.3493 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6972 Z= 0.115 Angle : 0.589 14.485 9509 Z= 0.296 Chirality : 0.043 0.280 1033 Planarity : 0.004 0.039 1200 Dihedral : 3.786 35.462 1113 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.87 % Allowed : 12.44 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.30), residues: 839 helix: 1.28 (0.26), residues: 416 sheet: 0.82 (0.65), residues: 57 loop : -0.18 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.026 0.001 TYR A 654 PHE 0.025 0.001 PHE A 327 TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6956) covalent geometry : angle 0.55627 ( 9470) SS BOND : bond 0.00175 ( 6) SS BOND : angle 4.79340 ( 12) hydrogen bonds : bond 0.04160 ( 326) hydrogen bonds : angle 4.59092 ( 915) metal coordination : bond 0.00202 ( 1) link_NAG-ASN : bond 0.00348 ( 9) link_NAG-ASN : angle 1.88016 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.37 seconds wall clock time: 33 minutes 47.14 seconds (2027.14 seconds total)