Starting phenix.real_space_refine on Wed Feb 12 00:30:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0t_41784/02_2025/8u0t_41784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0t_41784/02_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_41784/02_2025/8u0t_41784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0t_41784/02_2025/8u0t_41784.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0t_41784/02_2025/8u0t_41784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0t_41784/02_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-5592/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: 4.79, per 1000 atoms: 0.71 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: 1.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.86 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: 1.85 Time building geometry restraints manager: 1.70 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- 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 : 0.013 0.207 6956 Z= 0.845 Angle : 1.401 22.949 9470 Z= 0.945 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 *********************** 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 : 0.704 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: 0.1873 time to fit residues: 35.9669 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 : 0.720 ------------------------------------------------------------------------------- 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: 0.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4091 r_free = 0.4091 target = 0.182133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147128 restraints weight = 7659.309| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.26 r_work: 0.3478 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6956 Z= 0.234 Angle : 0.597 7.550 9470 Z= 0.321 Chirality : 0.052 0.777 1033 Planarity : 0.005 0.033 1200 Dihedral : 5.008 32.124 1115 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.92 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 (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: 0.14 (0.29), residues: 839 helix: 0.44 (0.26), residues: 404 sheet: 0.80 (0.64), residues: 58 loop : -0.27 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.018 0.002 PHE A 369 TYR 0.024 0.002 TYR A 385 ARG 0.004 0.001 ARG A 652 *********************** 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 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 THR cc_start: 0.8363 (m) cc_final: 0.7924 (p) REVERT: A 355 ASP cc_start: 0.8488 (t0) cc_final: 0.8186 (t0) REVERT: A 408 MET cc_start: 0.8547 (mmt) cc_final: 0.8191 (mmt) REVERT: B 396 ASP cc_start: 0.8564 (m-30) cc_final: 0.8320 (m-30) REVERT: B 446 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.8089 (ttt-90) REVERT: B 489 THR cc_start: 0.8140 (p) cc_final: 0.7609 (p) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.1698 time to fit residues: 24.0658 Evaluate side-chains 91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 203 TRP 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: 0.5980 chunk 8 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.179932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145601 restraints weight = 7747.066| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.96 r_work: 0.3457 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6956 Z= 0.240 Angle : 0.585 13.061 9470 Z= 0.303 Chirality : 0.047 0.493 1033 Planarity : 0.005 0.043 1200 Dihedral : 4.811 31.947 1113 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.18 % Allowed : 9.18 % Favored : 88.65 % 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: 0.38 (0.29), residues: 839 helix: 0.85 (0.26), residues: 405 sheet: 0.63 (0.66), residues: 58 loop : -0.39 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.002 PHE A 573 TYR 0.023 0.002 TYR A 654 ARG 0.007 0.001 ARG A 169 *********************** 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 101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7669 (tt0) cc_final: 0.7315 (mm-30) REVERT: A 259 THR cc_start: 0.8718 (m) cc_final: 0.8217 (p) REVERT: A 288 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6581 (mmtt) REVERT: A 322 HIS cc_start: 0.8244 (m-70) cc_final: 0.8007 (m-70) REVERT: A 408 MET cc_start: 0.8693 (mmt) cc_final: 0.8356 (mmt) REVERT: B 396 ASP cc_start: 0.8734 (m-30) cc_final: 0.8463 (m-30) REVERT: B 446 ARG cc_start: 0.8406 (ttt-90) cc_final: 0.8057 (ttt-90) REVERT: B 489 THR cc_start: 0.8243 (p) cc_final: 0.7862 (p) outliers start: 14 outliers final: 7 residues processed: 95 average time/residue: 0.1720 time to fit residues: 22.8791 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 : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 246 THR 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 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: 0.9980 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 overall best weight: 0.7978 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.178331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143917 restraints weight = 7830.446| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.00 r_work: 0.3436 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 6956 Z= 0.260 Angle : 0.565 14.333 9470 Z= 0.294 Chirality : 0.047 0.476 1033 Planarity : 0.005 0.039 1200 Dihedral : 4.406 36.015 1113 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.02 % Allowed : 10.58 % Favored : 87.40 % 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: 0.43 (0.29), residues: 839 helix: 0.90 (0.26), residues: 407 sheet: 0.78 (0.66), residues: 58 loop : -0.39 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.017 0.002 PHE A 369 TYR 0.025 0.002 TYR A 385 ARG 0.005 0.000 ARG A 169 *********************** 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 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7676 (tt0) cc_final: 0.7372 (mm-30) REVERT: A 259 THR cc_start: 0.8796 (m) cc_final: 0.8299 (p) REVERT: A 408 MET cc_start: 0.8719 (mmt) cc_final: 0.8385 (mmt) REVERT: A 474 MET cc_start: 0.8265 (mmp) cc_final: 0.7843 (mmp) REVERT: B 396 ASP cc_start: 0.8722 (m-30) cc_final: 0.8453 (m-30) REVERT: B 446 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8034 (ttt-90) REVERT: B 489 THR cc_start: 0.8307 (p) cc_final: 0.7908 (p) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.1672 time to fit residues: 22.6295 Evaluate side-chains 92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 246 THR 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 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.178608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144050 restraints weight = 7704.258| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.97 r_work: 0.3435 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 6956 Z= 0.230 Angle : 0.537 13.775 9470 Z= 0.278 Chirality : 0.045 0.397 1033 Planarity : 0.004 0.040 1200 Dihedral : 4.332 38.642 1113 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.87 % Allowed : 11.35 % Favored : 86.78 % 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: 0.51 (0.30), residues: 839 helix: 0.97 (0.26), residues: 407 sheet: 0.86 (0.66), residues: 58 loop : -0.36 (0.34), residues: 374 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 0.014 0.001 PHE A 369 TYR 0.023 0.002 TYR A 385 ARG 0.006 0.000 ARG A 169 *********************** 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 94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7646 (tt0) cc_final: 0.7351 (mm-30) REVERT: A 259 THR cc_start: 0.8803 (m) cc_final: 0.8280 (p) REVERT: A 269 ASP cc_start: 0.8165 (t0) cc_final: 0.7836 (t0) REVERT: A 408 MET cc_start: 0.8706 (mmt) cc_final: 0.8390 (mmt) REVERT: A 474 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7844 (mmp) REVERT: B 396 ASP cc_start: 0.8724 (m-30) cc_final: 0.8448 (m-30) REVERT: B 446 ARG cc_start: 0.8449 (ttt-90) cc_final: 0.8057 (ttt-90) outliers start: 12 outliers final: 8 residues processed: 87 average time/residue: 0.1797 time to fit residues: 21.8694 Evaluate side-chains 91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 246 THR 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 387 TYR Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.154780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117538 restraints weight = 7827.099| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.30 r_work: 0.3115 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6956 Z= 0.192 Angle : 0.509 13.182 9470 Z= 0.263 Chirality : 0.043 0.334 1033 Planarity : 0.004 0.039 1200 Dihedral : 4.107 36.377 1113 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 11.20 % Favored : 86.78 % 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: 0.68 (0.30), residues: 839 helix: 1.15 (0.26), residues: 407 sheet: 0.84 (0.65), residues: 58 loop : -0.32 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 203 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE A 369 TYR 0.022 0.001 TYR A 654 ARG 0.004 0.000 ARG A 169 *********************** 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 99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8752 (m) cc_final: 0.8180 (p) REVERT: A 269 ASP cc_start: 0.8120 (t0) cc_final: 0.7836 (t0) REVERT: A 408 MET cc_start: 0.8436 (mmt) cc_final: 0.8120 (mmt) REVERT: A 474 MET cc_start: 0.8382 (mmp) cc_final: 0.7962 (mmp) REVERT: B 396 ASP cc_start: 0.8645 (m-30) cc_final: 0.8329 (m-30) REVERT: B 446 ARG cc_start: 0.8356 (ttt-90) cc_final: 0.8091 (ttt-90) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.1733 time to fit residues: 22.4921 Evaluate side-chains 94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 246 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 55 optimal weight: 0.1980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120452 restraints weight = 7730.860| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.09 r_work: 0.3135 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6956 Z= 0.171 Angle : 0.490 13.537 9470 Z= 0.253 Chirality : 0.043 0.304 1033 Planarity : 0.004 0.038 1200 Dihedral : 3.846 34.113 1113 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 : 0.00 % 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: 0.82 (0.30), residues: 839 helix: 1.28 (0.26), residues: 409 sheet: 0.78 (0.63), residues: 58 loop : -0.25 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 203 HIS 0.003 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.024 0.001 TYR A 654 ARG 0.005 0.000 ARG A 169 *********************** 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 98 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8752 (m) cc_final: 0.8165 (p) REVERT: A 269 ASP cc_start: 0.8093 (t0) cc_final: 0.7812 (t0) REVERT: A 323 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7424 (mtm) REVERT: A 376 MET cc_start: 0.8391 (mmm) cc_final: 0.8131 (mmm) REVERT: A 408 MET cc_start: 0.8410 (mmt) cc_final: 0.8101 (mmt) REVERT: A 474 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7954 (mmp) REVERT: A 480 MET cc_start: 0.8780 (ptm) cc_final: 0.8576 (mtp) REVERT: B 396 ASP cc_start: 0.8644 (m-30) cc_final: 0.8312 (m-30) REVERT: B 446 ARG cc_start: 0.8351 (ttt-90) cc_final: 0.8063 (ttt-90) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1816 time to fit residues: 23.5264 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 : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 323 MET 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 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: 0.5980 chunk 54 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.178882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.145061 restraints weight = 7774.541| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.88 r_work: 0.3456 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6956 Z= 0.207 Angle : 0.523 13.666 9470 Z= 0.269 Chirality : 0.044 0.306 1033 Planarity : 0.004 0.040 1200 Dihedral : 3.734 21.123 1113 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.87 % Allowed : 11.35 % Favored : 86.78 % 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: 0.76 (0.30), residues: 839 helix: 1.25 (0.26), residues: 407 sheet: 0.79 (0.63), residues: 58 loop : -0.30 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 PHE 0.017 0.001 PHE A 369 TYR 0.025 0.002 TYR A 654 ARG 0.004 0.000 ARG A 169 *********************** 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 95 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8786 (m) cc_final: 0.8250 (p) REVERT: A 408 MET cc_start: 0.8623 (mmt) cc_final: 0.8348 (mmt) REVERT: A 474 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7826 (mmp) REVERT: B 396 ASP cc_start: 0.8719 (m-30) cc_final: 0.8443 (m-30) REVERT: B 446 ARG cc_start: 0.8430 (ttt-90) cc_final: 0.8198 (ttt-90) outliers start: 12 outliers final: 8 residues processed: 87 average time/residue: 0.1778 time to fit residues: 21.5884 Evaluate side-chains 90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 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 246 THR 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 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: 0.8980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 71 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 0.0030 overall best weight: 0.3328 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.178519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145358 restraints weight = 7653.402| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.83 r_work: 0.3497 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 6956 Z= 0.161 Angle : 0.490 13.426 9470 Z= 0.251 Chirality : 0.042 0.283 1033 Planarity : 0.004 0.038 1200 Dihedral : 3.571 21.784 1113 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.40 % Allowed : 11.98 % Favored : 86.63 % 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: 0.87 (0.30), residues: 839 helix: 1.27 (0.26), residues: 415 sheet: 0.77 (0.63), residues: 58 loop : -0.17 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.003 0.000 HIS A 241 PHE 0.012 0.001 PHE A 369 TYR 0.025 0.001 TYR A 654 ARG 0.004 0.000 ARG A 169 *********************** 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 95 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8715 (m) cc_final: 0.8186 (p) REVERT: A 474 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7752 (mmp) REVERT: B 396 ASP cc_start: 0.8674 (m-30) cc_final: 0.8405 (m-30) REVERT: B 446 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.8203 (ttt-90) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.1771 time to fit residues: 21.9893 Evaluate side-chains 92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 246 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.179811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146429 restraints weight = 7871.222| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.92 r_work: 0.3441 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6956 Z= 0.195 Angle : 0.513 13.484 9470 Z= 0.263 Chirality : 0.043 0.287 1033 Planarity : 0.004 0.040 1200 Dihedral : 3.606 25.136 1113 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.56 % Allowed : 12.13 % Favored : 86.31 % 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: 0.86 (0.30), residues: 839 helix: 1.25 (0.26), residues: 414 sheet: 0.84 (0.65), residues: 57 loop : -0.17 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.034 0.001 PHE A 327 TYR 0.026 0.001 TYR A 654 ARG 0.004 0.000 ARG A 169 ********************** 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 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 259 THR cc_start: 0.8675 (m) cc_final: 0.8026 (p) REVERT: A 408 MET cc_start: 0.8570 (mmt) cc_final: 0.8294 (mmm) REVERT: A 474 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7567 (mmp) REVERT: B 396 ASP cc_start: 0.8544 (m-30) cc_final: 0.8282 (m-30) REVERT: B 446 ARG cc_start: 0.8424 (ttt-90) cc_final: 0.8181 (ttt-90) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.2136 time to fit residues: 27.0357 Evaluate side-chains 89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 246 THR 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 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: 0.0050 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.180090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145204 restraints weight = 7797.987| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.21 r_work: 0.3465 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6956 Z= 0.189 Angle : 0.508 13.403 9470 Z= 0.262 Chirality : 0.043 0.284 1033 Planarity : 0.004 0.040 1200 Dihedral : 3.545 20.528 1113 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 : 0.00 % 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: 0.92 (0.30), residues: 839 helix: 1.31 (0.26), residues: 414 sheet: 0.86 (0.65), residues: 57 loop : -0.15 (0.34), residues: 368 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 0.034 0.001 PHE A 327 TYR 0.025 0.001 TYR A 654 ARG 0.004 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3969.16 seconds wall clock time: 71 minutes 11.11 seconds (4271.11 seconds total)