Starting phenix.real_space_refine on Fri Aug 22 17:44:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ka8_37006/08_2025/8ka8_37006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ka8_37006/08_2025/8ka8_37006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ka8_37006/08_2025/8ka8_37006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ka8_37006/08_2025/8ka8_37006.map" model { file = "/net/cci-nas-00/data/ceres_data/8ka8_37006/08_2025/8ka8_37006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ka8_37006/08_2025/8ka8_37006.cif" } resolution = 2.96 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= 0.000 sd= 0.011 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 36 5.16 5 C 4131 2.51 5 N 1072 2.21 5 O 1241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6481 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4854 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} 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 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.00, per 1000 atoms: 0.31 Number of scatterers: 6481 At special positions: 0 Unit cell: (77.44, 99.44, 119.68, 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 36 16.00 O 1241 8.00 N 1072 7.00 C 4131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 82 " " NAG B 1 " - " ASN A 546 " " NAG C 1 " - " ASN E 343 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 376.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 51.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 removed outlier: 4.069A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.858A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.719A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 192 removed outlier: 4.223A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 4.052A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.893A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 279 removed outlier: 3.652A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.869A pdb=" N ILE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.887A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.873A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.621A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.847A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.508A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 removed outlier: 4.811A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.546A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.598A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.532A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.546A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.529A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.910A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 removed outlier: 5.880A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.779A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.034A 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 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.627A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 268 hydrogen bonds defined for protein. 774 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: 0.96 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2083 1.35 - 1.47: 1736 1.47 - 1.59: 2780 1.59 - 1.72: 0 1.72 - 1.84: 56 Bond restraints: 6655 Sorted by residual: bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C HIS A 401 " pdb=" N GLU A 402 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.34e-02 5.57e+03 1.90e+00 ... (remaining 6650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8860 2.02 - 4.04: 155 4.04 - 6.06: 23 6.06 - 8.09: 2 8.09 - 10.11: 1 Bond angle restraints: 9041 Sorted by residual: angle pdb=" N ASP E 389 " pdb=" CA ASP E 389 " pdb=" C ASP E 389 " ideal model delta sigma weight residual 114.04 110.30 3.74 1.24e+00 6.50e-01 9.10e+00 angle pdb=" CA LEU A 558 " pdb=" CB LEU A 558 " pdb=" CG LEU A 558 " ideal model delta sigma weight residual 116.30 126.41 -10.11 3.50e+00 8.16e-02 8.34e+00 angle pdb=" C ALA A 170 " pdb=" N GLU A 171 " pdb=" CA GLU A 171 " ideal model delta sigma weight residual 122.26 117.77 4.49 1.59e+00 3.96e-01 7.98e+00 angle pdb=" C PHE A 400 " pdb=" N HIS A 401 " pdb=" CA HIS A 401 " ideal model delta sigma weight residual 121.54 116.58 4.96 1.91e+00 2.74e-01 6.75e+00 angle pdb=" CA CYS E 432 " pdb=" CB CYS E 432 " pdb=" SG CYS E 432 " ideal model delta sigma weight residual 114.40 120.31 -5.91 2.30e+00 1.89e-01 6.60e+00 ... (remaining 9036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 3646 18.07 - 36.13: 302 36.13 - 54.20: 53 54.20 - 72.26: 13 72.26 - 90.33: 5 Dihedral angle restraints: 4019 sinusoidal: 1702 harmonic: 2317 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -176.33 90.33 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 53.18 39.82 1 1.00e+01 1.00e-02 2.23e+01 dihedral pdb=" CA ASN E 360 " pdb=" C ASN E 360 " pdb=" N CYS E 361 " pdb=" CA CYS E 361 " ideal model delta harmonic sigma weight residual 180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 4016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 758 0.049 - 0.099: 161 0.099 - 0.148: 36 0.148 - 0.197: 3 0.197 - 0.246: 1 Chirality restraints: 959 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CG LEU E 492 " pdb=" CB LEU E 492 " pdb=" CD1 LEU E 492 " pdb=" CD2 LEU E 492 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 956 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 82 " 0.023 2.00e-02 2.50e+03 2.17e-02 5.88e+00 pdb=" CG ASN A 82 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 82 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 82 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO A 415 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 397 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C ASN A 397 " 0.033 2.00e-02 2.50e+03 pdb=" O ASN A 397 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 398 " -0.011 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 53 2.59 - 3.17: 5269 3.17 - 3.75: 9414 3.75 - 4.32: 12872 4.32 - 4.90: 22110 Nonbonded interactions: 49718 Sorted by model distance: nonbonded pdb=" NE2 HIS A 374 " pdb=" OE1 GLU A 402 " model vdw 2.017 3.120 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.102 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASN E 360 " pdb=" OG1 THR E 523 " model vdw 2.161 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.216 3.040 ... (remaining 49713 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 8.940 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.050 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:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 6670 Z= 0.197 Angle : 0.665 10.108 9073 Z= 0.347 Chirality : 0.044 0.246 959 Planarity : 0.004 0.053 1169 Dihedral : 13.589 89.774 2514 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.71 % 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 aren not related in a simple way. whole: -0.68 (0.30), residues: 786 helix: 0.75 (0.28), residues: 369 sheet: 2.21 (0.95), residues: 35 loop : -2.01 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 306 TYR 0.026 0.001 TYR A 521 PHE 0.024 0.001 PHE A 327 TRP 0.014 0.001 TRP A 163 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6655) covalent geometry : angle 0.64268 ( 9041) SS BOND : bond 0.00557 ( 7) SS BOND : angle 1.91930 ( 14) hydrogen bonds : bond 0.14480 ( 268) hydrogen bonds : angle 5.61478 ( 774) metal coordination : bond 0.19961 ( 2) link_BETA1-4 : bond 0.00528 ( 2) link_BETA1-4 : angle 5.17234 ( 6) link_NAG-ASN : bond 0.00665 ( 4) link_NAG-ASN : angle 2.29405 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.262 Fit side-chains REVERT: A 34 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7361 (mp10) REVERT: A 78 LYS cc_start: 0.7667 (tppt) cc_final: 0.7416 (tppp) REVERT: A 166 GLU cc_start: 0.7973 (tp30) cc_final: 0.7572 (mm-30) REVERT: A 198 ASP cc_start: 0.7160 (p0) cc_final: 0.6956 (p0) REVERT: A 231 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7447 (ttpp) REVERT: A 310 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 313 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7882 (ttpp) REVERT: A 322 TYR cc_start: 0.8530 (m-80) cc_final: 0.8166 (m-80) REVERT: A 347 THR cc_start: 0.8329 (t) cc_final: 0.8117 (p) REVERT: A 401 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7599 (m-70) REVERT: A 483 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 557 MET cc_start: 0.7869 (tmm) cc_final: 0.7551 (tmm) REVERT: E 453 TYR cc_start: 0.8272 (p90) cc_final: 0.7972 (p90) REVERT: E 467 ASP cc_start: 0.7048 (p0) cc_final: 0.6792 (p0) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.5735 time to fit residues: 114.5124 Evaluate side-chains 150 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 0.9980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 368 ASN A 531 GLN E 354 ASN E 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106832 restraints weight = 9785.621| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.15 r_work: 0.3267 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6670 Z= 0.157 Angle : 0.653 8.520 9073 Z= 0.330 Chirality : 0.044 0.205 959 Planarity : 0.005 0.062 1169 Dihedral : 5.738 52.692 992 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.93 % Allowed : 12.81 % Favored : 83.26 % 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 aren not related in a simple way. whole: -0.39 (0.30), residues: 786 helix: 1.08 (0.28), residues: 368 sheet: 2.03 (0.90), residues: 37 loop : -1.96 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.016 0.002 TYR A 521 PHE 0.015 0.002 PHE A 327 TRP 0.016 0.002 TRP E 436 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6655) covalent geometry : angle 0.63062 ( 9041) SS BOND : bond 0.00593 ( 7) SS BOND : angle 1.53503 ( 14) hydrogen bonds : bond 0.05359 ( 268) hydrogen bonds : angle 4.33635 ( 774) metal coordination : bond 0.00060 ( 2) link_BETA1-4 : bond 0.00636 ( 2) link_BETA1-4 : angle 4.44966 ( 6) link_NAG-ASN : bond 0.00335 ( 4) link_NAG-ASN : angle 3.18257 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7941 (tppt) cc_final: 0.7735 (tppp) REVERT: A 198 ASP cc_start: 0.7736 (p0) cc_final: 0.7518 (p0) REVERT: A 208 GLU cc_start: 0.7955 (tp30) cc_final: 0.7664 (tt0) REVERT: A 215 TYR cc_start: 0.7909 (m-10) cc_final: 0.7549 (m-10) REVERT: A 231 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7945 (ttpp) REVERT: A 341 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.8002 (ptpp) REVERT: A 347 THR cc_start: 0.8541 (t) cc_final: 0.8167 (p) REVERT: A 401 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7672 (m-70) REVERT: A 406 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: A 465 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8476 (ttpt) REVERT: A 470 LYS cc_start: 0.8243 (mppt) cc_final: 0.8024 (mppt) REVERT: A 518 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.8230 (ptt90) REVERT: A 522 GLN cc_start: 0.7976 (tt0) cc_final: 0.7753 (tt0) REVERT: A 557 MET cc_start: 0.7892 (tmm) cc_final: 0.7672 (tmm) REVERT: A 564 GLU cc_start: 0.8210 (mt-10) cc_final: 0.8004 (mm-30) REVERT: E 459 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8185 (p) outliers start: 27 outliers final: 11 residues processed: 161 average time/residue: 0.5796 time to fit residues: 97.9146 Evaluate side-chains 157 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 459 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.0370 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 65 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN E 354 ASN ** E 394 ASN ** 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 = 0.3527 r_free = 0.3527 target = 0.115458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104926 restraints weight = 9648.661| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.13 r_work: 0.3251 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6670 Z= 0.165 Angle : 0.638 10.356 9073 Z= 0.321 Chirality : 0.043 0.176 959 Planarity : 0.005 0.058 1169 Dihedral : 5.272 53.423 992 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.80 % Allowed : 16.59 % Favored : 78.60 % 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 aren not related in a simple way. whole: -0.28 (0.30), residues: 786 helix: 1.20 (0.29), residues: 371 sheet: 1.86 (0.87), residues: 37 loop : -1.92 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 357 TYR 0.015 0.002 TYR A 183 PHE 0.012 0.002 PHE A 28 TRP 0.015 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6655) covalent geometry : angle 0.61961 ( 9041) SS BOND : bond 0.00552 ( 7) SS BOND : angle 1.57934 ( 14) hydrogen bonds : bond 0.05539 ( 268) hydrogen bonds : angle 4.26469 ( 774) metal coordination : bond 0.00099 ( 2) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 4.57186 ( 6) link_NAG-ASN : bond 0.00290 ( 4) link_NAG-ASN : angle 2.23994 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7500 (mp0) cc_final: 0.7191 (mp0) REVERT: A 78 LYS cc_start: 0.8046 (tppt) cc_final: 0.7745 (tppp) REVERT: A 197 GLU cc_start: 0.7673 (mp0) cc_final: 0.7366 (mp0) REVERT: A 198 ASP cc_start: 0.7705 (p0) cc_final: 0.7465 (p0) REVERT: A 208 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: A 215 TYR cc_start: 0.8012 (m-10) cc_final: 0.7673 (m-10) REVERT: A 282 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8239 (p) REVERT: A 341 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8035 (ptpp) REVERT: A 347 THR cc_start: 0.8588 (t) cc_final: 0.8212 (p) REVERT: A 401 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.7826 (m-70) REVERT: A 406 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: A 465 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8498 (ttpt) REVERT: A 470 LYS cc_start: 0.8234 (mppt) cc_final: 0.8031 (mppt) REVERT: A 518 ARG cc_start: 0.8468 (ttp-170) cc_final: 0.8257 (ptt90) REVERT: A 522 GLN cc_start: 0.7924 (tt0) cc_final: 0.7697 (tt0) REVERT: E 378 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8317 (ptpp) REVERT: E 459 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8239 (p) outliers start: 33 outliers final: 15 residues processed: 152 average time/residue: 0.5906 time to fit residues: 94.2604 Evaluate side-chains 153 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 459 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 578 ASN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102959 restraints weight = 9605.020| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.15 r_work: 0.3226 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6670 Z= 0.173 Angle : 0.642 9.649 9073 Z= 0.324 Chirality : 0.043 0.174 959 Planarity : 0.005 0.057 1169 Dihedral : 4.986 53.990 992 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.09 % Allowed : 16.89 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.31), residues: 786 helix: 1.22 (0.29), residues: 372 sheet: 1.58 (0.85), residues: 37 loop : -1.89 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 454 TYR 0.016 0.001 TYR A 183 PHE 0.014 0.002 PHE A 327 TRP 0.017 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6655) covalent geometry : angle 0.62393 ( 9041) SS BOND : bond 0.00289 ( 7) SS BOND : angle 1.59364 ( 14) hydrogen bonds : bond 0.05593 ( 268) hydrogen bonds : angle 4.21534 ( 774) metal coordination : bond 0.00167 ( 2) link_BETA1-4 : bond 0.00494 ( 2) link_BETA1-4 : angle 4.65979 ( 6) link_NAG-ASN : bond 0.00262 ( 4) link_NAG-ASN : angle 2.11242 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.277 Fit side-chains REVERT: A 35 GLU cc_start: 0.7567 (mp0) cc_final: 0.7181 (mp0) REVERT: A 78 LYS cc_start: 0.8084 (tppt) cc_final: 0.7806 (ttmm) REVERT: A 179 LEU cc_start: 0.8595 (mp) cc_final: 0.8339 (mt) REVERT: A 197 GLU cc_start: 0.7820 (mp0) cc_final: 0.7471 (mp0) REVERT: A 198 ASP cc_start: 0.7672 (p0) cc_final: 0.7336 (p0) REVERT: A 208 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: A 215 TYR cc_start: 0.8175 (m-10) cc_final: 0.7881 (m-10) REVERT: A 271 TRP cc_start: 0.8967 (m-90) cc_final: 0.8741 (m-90) REVERT: A 282 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8270 (p) REVERT: A 324 THR cc_start: 0.8419 (m) cc_final: 0.8135 (p) REVERT: A 341 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8023 (ptpp) REVERT: A 347 THR cc_start: 0.8584 (t) cc_final: 0.8239 (p) REVERT: A 401 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.8048 (m-70) REVERT: A 406 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: A 465 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8434 (ttpt) REVERT: A 522 GLN cc_start: 0.7931 (tt0) cc_final: 0.7710 (tt0) REVERT: E 378 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8344 (ptpp) REVERT: E 459 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8316 (p) outliers start: 35 outliers final: 14 residues processed: 153 average time/residue: 0.5819 time to fit residues: 93.6158 Evaluate side-chains 153 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 459 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.4980 chunk 62 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 0.0030 chunk 75 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 417 HIS E 370 ASN E 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102975 restraints weight = 9789.516| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.19 r_work: 0.3215 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6670 Z= 0.152 Angle : 0.619 9.232 9073 Z= 0.312 Chirality : 0.042 0.170 959 Planarity : 0.004 0.059 1169 Dihedral : 4.874 53.202 992 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 6.55 % Allowed : 15.57 % Favored : 77.87 % 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 aren not related in a simple way. whole: -0.26 (0.31), residues: 786 helix: 1.23 (0.29), residues: 375 sheet: 1.20 (0.85), residues: 37 loop : -1.89 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 454 TYR 0.019 0.001 TYR A 207 PHE 0.013 0.001 PHE A 327 TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6655) covalent geometry : angle 0.60213 ( 9041) SS BOND : bond 0.00553 ( 7) SS BOND : angle 1.56297 ( 14) hydrogen bonds : bond 0.05245 ( 268) hydrogen bonds : angle 4.16253 ( 774) metal coordination : bond 0.00221 ( 2) link_BETA1-4 : bond 0.00587 ( 2) link_BETA1-4 : angle 4.50990 ( 6) link_NAG-ASN : bond 0.00210 ( 4) link_NAG-ASN : angle 1.86626 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.248 Fit side-chains REVERT: A 35 GLU cc_start: 0.7592 (mp0) cc_final: 0.7162 (mp0) REVERT: A 78 LYS cc_start: 0.8092 (tppt) cc_final: 0.7803 (ttmm) REVERT: A 179 LEU cc_start: 0.8589 (mp) cc_final: 0.8339 (mt) REVERT: A 197 GLU cc_start: 0.7827 (mp0) cc_final: 0.7501 (mp0) REVERT: A 198 ASP cc_start: 0.7718 (p0) cc_final: 0.7386 (p0) REVERT: A 208 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: A 215 TYR cc_start: 0.8238 (m-10) cc_final: 0.8001 (m-10) REVERT: A 271 TRP cc_start: 0.8961 (m-90) cc_final: 0.8690 (m-90) REVERT: A 282 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 324 THR cc_start: 0.8459 (m) cc_final: 0.8204 (p) REVERT: A 341 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8068 (ptpp) REVERT: A 347 THR cc_start: 0.8594 (t) cc_final: 0.8252 (p) REVERT: A 401 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.8013 (m-70) REVERT: A 406 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: A 465 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8423 (ttpt) REVERT: A 473 TRP cc_start: 0.7329 (t-100) cc_final: 0.7086 (t-100) REVERT: A 581 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8208 (t) REVERT: E 378 LYS cc_start: 0.8588 (ptpt) cc_final: 0.8353 (ptpp) REVERT: E 459 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8359 (p) REVERT: E 500 THR cc_start: 0.8587 (m) cc_final: 0.8345 (t) outliers start: 45 outliers final: 22 residues processed: 156 average time/residue: 0.5315 time to fit residues: 87.5212 Evaluate side-chains 155 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 29 optimal weight: 0.3980 chunk 60 optimal weight: 0.2980 chunk 48 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 137 ASN A 522 GLN E 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103135 restraints weight = 9718.524| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.11 r_work: 0.3211 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6670 Z= 0.169 Angle : 0.644 10.350 9073 Z= 0.324 Chirality : 0.043 0.171 959 Planarity : 0.005 0.060 1169 Dihedral : 4.858 53.619 992 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.95 % Allowed : 16.74 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.31), residues: 786 helix: 1.25 (0.29), residues: 375 sheet: 1.26 (0.85), residues: 37 loop : -1.90 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 454 TYR 0.026 0.002 TYR A 521 PHE 0.013 0.002 PHE A 327 TRP 0.017 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 6655) covalent geometry : angle 0.62381 ( 9041) SS BOND : bond 0.00700 ( 7) SS BOND : angle 2.41322 ( 14) hydrogen bonds : bond 0.05451 ( 268) hydrogen bonds : angle 4.15022 ( 774) metal coordination : bond 0.00215 ( 2) link_BETA1-4 : bond 0.00553 ( 2) link_BETA1-4 : angle 4.50875 ( 6) link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 1.89901 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.259 Fit side-chains REVERT: A 35 GLU cc_start: 0.7598 (mp0) cc_final: 0.7166 (mp0) REVERT: A 78 LYS cc_start: 0.8129 (tppt) cc_final: 0.7838 (ttmm) REVERT: A 136 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7760 (mmmm) REVERT: A 179 LEU cc_start: 0.8603 (mp) cc_final: 0.8347 (mt) REVERT: A 198 ASP cc_start: 0.7683 (p0) cc_final: 0.7340 (p0) REVERT: A 208 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: A 215 TYR cc_start: 0.8302 (m-10) cc_final: 0.8052 (m-10) REVERT: A 271 TRP cc_start: 0.8964 (m-90) cc_final: 0.8705 (m-90) REVERT: A 282 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 292 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7507 (t0) REVERT: A 324 THR cc_start: 0.8452 (m) cc_final: 0.8208 (p) REVERT: A 341 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8065 (ptpp) REVERT: A 347 THR cc_start: 0.8606 (t) cc_final: 0.8259 (p) REVERT: A 401 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.8030 (m-70) REVERT: A 406 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: A 465 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8401 (ttpt) REVERT: A 473 TRP cc_start: 0.7329 (t-100) cc_final: 0.7120 (t-100) REVERT: A 581 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8229 (t) REVERT: E 378 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8341 (ptpp) REVERT: E 440 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8134 (p0) REVERT: E 459 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8353 (p) outliers start: 34 outliers final: 18 residues processed: 146 average time/residue: 0.5810 time to fit residues: 89.3596 Evaluate side-chains 152 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.1696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104566 restraints weight = 9570.084| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.10 r_work: 0.3226 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6670 Z= 0.121 Angle : 0.595 9.733 9073 Z= 0.298 Chirality : 0.041 0.165 959 Planarity : 0.004 0.060 1169 Dihedral : 4.705 52.226 992 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.20 % Allowed : 18.20 % Favored : 78.60 % 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 aren not related in a simple way. whole: -0.19 (0.31), residues: 786 helix: 1.32 (0.29), residues: 374 sheet: 1.09 (0.85), residues: 37 loop : -1.85 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 454 TYR 0.019 0.001 TYR A 521 PHE 0.010 0.001 PHE A 28 TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6655) covalent geometry : angle 0.57887 ( 9041) SS BOND : bond 0.00606 ( 7) SS BOND : angle 1.75112 ( 14) hydrogen bonds : bond 0.04658 ( 268) hydrogen bonds : angle 4.06649 ( 774) metal coordination : bond 0.00115 ( 2) link_BETA1-4 : bond 0.00649 ( 2) link_BETA1-4 : angle 4.31489 ( 6) link_NAG-ASN : bond 0.00179 ( 4) link_NAG-ASN : angle 1.58922 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.254 Fit side-chains REVERT: A 35 GLU cc_start: 0.7597 (mp0) cc_final: 0.7158 (mp0) REVERT: A 78 LYS cc_start: 0.8110 (tppt) cc_final: 0.7805 (ttmm) REVERT: A 179 LEU cc_start: 0.8583 (mp) cc_final: 0.8332 (mt) REVERT: A 198 ASP cc_start: 0.7678 (p0) cc_final: 0.7342 (p0) REVERT: A 208 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: A 271 TRP cc_start: 0.8961 (m-90) cc_final: 0.8688 (m-90) REVERT: A 282 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8270 (p) REVERT: A 292 ASP cc_start: 0.7870 (t70) cc_final: 0.7614 (t0) REVERT: A 324 THR cc_start: 0.8466 (m) cc_final: 0.8220 (p) REVERT: A 341 LYS cc_start: 0.8220 (pmmt) cc_final: 0.7983 (ptpp) REVERT: A 347 THR cc_start: 0.8602 (t) cc_final: 0.8259 (p) REVERT: A 401 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.7974 (m-70) REVERT: A 406 GLU cc_start: 0.7987 (tt0) cc_final: 0.7710 (tt0) REVERT: A 465 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8405 (ttpt) REVERT: A 581 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8179 (t) REVERT: E 459 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8361 (p) outliers start: 22 outliers final: 11 residues processed: 141 average time/residue: 0.5589 time to fit residues: 83.0052 Evaluate side-chains 143 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 459 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 76 optimal weight: 0.0040 chunk 18 optimal weight: 0.0870 chunk 26 optimal weight: 0.2980 chunk 66 optimal weight: 0.3980 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 137 ASN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103642 restraints weight = 9706.717| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.10 r_work: 0.3231 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6670 Z= 0.133 Angle : 0.608 9.506 9073 Z= 0.306 Chirality : 0.041 0.166 959 Planarity : 0.004 0.059 1169 Dihedral : 4.616 52.247 992 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.78 % Allowed : 17.32 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.31), residues: 786 helix: 1.37 (0.29), residues: 375 sheet: 0.81 (0.85), residues: 37 loop : -1.89 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 454 TYR 0.031 0.001 TYR A 521 PHE 0.019 0.001 PHE A 314 TRP 0.017 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6655) covalent geometry : angle 0.59279 ( 9041) SS BOND : bond 0.00590 ( 7) SS BOND : angle 1.64990 ( 14) hydrogen bonds : bond 0.04839 ( 268) hydrogen bonds : angle 4.07518 ( 774) metal coordination : bond 0.00132 ( 2) link_BETA1-4 : bond 0.00571 ( 2) link_BETA1-4 : angle 4.27024 ( 6) link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 1.61664 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.256 Fit side-chains REVERT: A 35 GLU cc_start: 0.7605 (mp0) cc_final: 0.7196 (mp0) REVERT: A 78 LYS cc_start: 0.8105 (tppt) cc_final: 0.7805 (ttmm) REVERT: A 179 LEU cc_start: 0.8554 (mp) cc_final: 0.8294 (mt) REVERT: A 198 ASP cc_start: 0.7692 (p0) cc_final: 0.7354 (p0) REVERT: A 208 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: A 271 TRP cc_start: 0.8963 (m-90) cc_final: 0.8688 (m-90) REVERT: A 282 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 292 ASP cc_start: 0.7907 (t70) cc_final: 0.7660 (t0) REVERT: A 324 THR cc_start: 0.8453 (m) cc_final: 0.8214 (p) REVERT: A 347 THR cc_start: 0.8607 (t) cc_final: 0.8257 (p) REVERT: A 401 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.7963 (m-70) REVERT: A 406 GLU cc_start: 0.7998 (tt0) cc_final: 0.7716 (tt0) REVERT: A 465 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8407 (ttpt) REVERT: A 479 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: A 581 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8218 (t) REVERT: E 459 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8354 (p) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 0.5462 time to fit residues: 82.2468 Evaluate side-chains 146 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 459 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 48 optimal weight: 0.0370 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 0.0980 chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 0.0040 chunk 40 optimal weight: 0.0370 chunk 0 optimal weight: 1.9990 overall best weight: 0.0948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN E 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104777 restraints weight = 9901.302| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.18 r_work: 0.3226 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6670 Z= 0.112 Angle : 0.594 8.974 9073 Z= 0.298 Chirality : 0.041 0.161 959 Planarity : 0.004 0.059 1169 Dihedral : 4.514 51.048 992 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.06 % Allowed : 19.07 % Favored : 77.87 % 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 aren not related in a simple way. whole: -0.12 (0.31), residues: 786 helix: 1.41 (0.29), residues: 376 sheet: 1.02 (0.90), residues: 35 loop : -1.85 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.026 0.001 TYR A 521 PHE 0.022 0.001 PHE A 314 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6655) covalent geometry : angle 0.58008 ( 9041) SS BOND : bond 0.00607 ( 7) SS BOND : angle 1.53590 ( 14) hydrogen bonds : bond 0.04211 ( 268) hydrogen bonds : angle 4.02504 ( 774) metal coordination : bond 0.00062 ( 2) link_BETA1-4 : bond 0.00669 ( 2) link_BETA1-4 : angle 4.13295 ( 6) link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 1.39246 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.291 Fit side-chains REVERT: A 35 GLU cc_start: 0.7588 (mp0) cc_final: 0.7199 (mp0) REVERT: A 78 LYS cc_start: 0.8083 (tppt) cc_final: 0.7768 (ttmm) REVERT: A 179 LEU cc_start: 0.8555 (mp) cc_final: 0.8302 (mt) REVERT: A 208 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 210 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7325 (pp20) REVERT: A 271 TRP cc_start: 0.8950 (m-90) cc_final: 0.8661 (m-90) REVERT: A 324 THR cc_start: 0.8464 (m) cc_final: 0.8219 (p) REVERT: A 347 THR cc_start: 0.8604 (t) cc_final: 0.8259 (p) REVERT: A 401 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7861 (m-70) REVERT: A 465 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8436 (ttpt) REVERT: A 467 ASP cc_start: 0.8271 (m-30) cc_final: 0.7696 (m-30) REVERT: E 459 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8369 (p) REVERT: E 500 THR cc_start: 0.8664 (m) cc_final: 0.8351 (t) outliers start: 21 outliers final: 10 residues processed: 145 average time/residue: 0.5665 time to fit residues: 86.4559 Evaluate side-chains 141 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 459 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 49 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 0.0970 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 137 ASN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101675 restraints weight = 9783.385| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.13 r_work: 0.3208 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6670 Z= 0.176 Angle : 0.653 9.580 9073 Z= 0.331 Chirality : 0.043 0.170 959 Planarity : 0.005 0.059 1169 Dihedral : 4.617 52.590 992 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.18 % Allowed : 20.38 % Favored : 77.44 % 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 aren not related in a simple way. whole: -0.16 (0.31), residues: 786 helix: 1.47 (0.29), residues: 370 sheet: 0.49 (0.88), residues: 38 loop : -1.90 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 454 TYR 0.043 0.002 TYR A 521 PHE 0.027 0.002 PHE A 314 TRP 0.019 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6655) covalent geometry : angle 0.63805 ( 9041) SS BOND : bond 0.00701 ( 7) SS BOND : angle 1.85715 ( 14) hydrogen bonds : bond 0.05328 ( 268) hydrogen bonds : angle 4.11608 ( 774) metal coordination : bond 0.00239 ( 2) link_BETA1-4 : bond 0.00514 ( 2) link_BETA1-4 : angle 4.21898 ( 6) link_NAG-ASN : bond 0.00279 ( 4) link_NAG-ASN : angle 1.73452 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.260 Fit side-chains REVERT: A 35 GLU cc_start: 0.7609 (mp0) cc_final: 0.7188 (mp0) REVERT: A 78 LYS cc_start: 0.8128 (tppt) cc_final: 0.7843 (ttmm) REVERT: A 179 LEU cc_start: 0.8551 (mp) cc_final: 0.8284 (mt) REVERT: A 208 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: A 210 GLU cc_start: 0.7614 (pm20) cc_final: 0.7335 (pp20) REVERT: A 271 TRP cc_start: 0.8976 (m-90) cc_final: 0.8621 (m-90) REVERT: A 323 MET cc_start: 0.8928 (mmt) cc_final: 0.8659 (mmm) REVERT: A 324 THR cc_start: 0.8459 (m) cc_final: 0.8205 (p) REVERT: A 347 THR cc_start: 0.8593 (t) cc_final: 0.8232 (p) REVERT: A 401 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8034 (m-70) REVERT: A 465 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8451 (ttpt) REVERT: E 459 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8315 (p) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.5413 time to fit residues: 77.1072 Evaluate side-chains 135 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 459 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.2980 chunk 49 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 15 optimal weight: 0.0970 chunk 30 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102742 restraints weight = 9880.458| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.16 r_work: 0.3222 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6670 Z= 0.135 Angle : 0.625 9.024 9073 Z= 0.315 Chirality : 0.042 0.169 959 Planarity : 0.004 0.059 1169 Dihedral : 4.583 52.051 992 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.04 % Allowed : 20.52 % Favored : 77.44 % 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 aren not related in a simple way. whole: -0.15 (0.31), residues: 786 helix: 1.36 (0.29), residues: 377 sheet: 0.96 (0.90), residues: 35 loop : -1.84 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 454 TYR 0.037 0.002 TYR A 521 PHE 0.026 0.001 PHE A 314 TRP 0.034 0.002 TRP A 473 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6655) covalent geometry : angle 0.61167 ( 9041) SS BOND : bond 0.00653 ( 7) SS BOND : angle 1.63133 ( 14) hydrogen bonds : bond 0.04776 ( 268) hydrogen bonds : angle 4.09963 ( 774) metal coordination : bond 0.00142 ( 2) link_BETA1-4 : bond 0.00674 ( 2) link_BETA1-4 : angle 4.10938 ( 6) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 1.54508 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2835.18 seconds wall clock time: 49 minutes 10.22 seconds (2950.22 seconds total)