Starting phenix.real_space_refine on Sat May 10 16:21:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ka8_37006/05_2025/8ka8_37006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ka8_37006/05_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_37006/05_2025/8ka8_37006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ka8_37006/05_2025/8ka8_37006.map" model { file = "/net/cci-nas-00/data/ceres_data/8ka8_37006/05_2025/8ka8_37006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ka8_37006/05_2025/8ka8_37006.cif" } resolution = 2.96 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.40, per 1000 atoms: 0.83 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: 1.54 Conformation dependent library (CDL) restraints added in 866.0 milliseconds 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: 0.75 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: 1.63 Time building geometry restraints manager: 1.84 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: 22.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.320 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.014 0.001 TRP A 163 HIS 0.002 0.001 HIS A 378 PHE 0.024 0.001 PHE A 327 TYR 0.026 0.001 TYR A 521 ARG 0.002 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 4) link_NAG-ASN : angle 2.29405 ( 12) link_BETA1-4 : bond 0.00528 ( 2) link_BETA1-4 : angle 5.17234 ( 6) hydrogen bonds : bond 0.14480 ( 268) hydrogen bonds : angle 5.61478 ( 774) metal coordination : bond 0.19961 ( 2) SS BOND : bond 0.00557 ( 7) SS BOND : angle 1.91930 ( 14) covalent geometry : bond 0.00302 ( 6655) covalent geometry : angle 0.64268 ( 9041) *********************** 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 : 0.683 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: 1.1191 time to fit residues: 223.5087 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 : 0.747 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.4980 chunk 59 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 70 optimal weight: 0.4980 overall best weight: 0.2876 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.117421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106692 restraints weight = 9666.406| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.14 r_work: 0.3267 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6670 Z= 0.163 Angle : 0.655 8.663 9073 Z= 0.330 Chirality : 0.044 0.182 959 Planarity : 0.005 0.063 1169 Dihedral : 5.798 53.290 992 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.08 % Allowed : 12.37 % Favored : 83.55 % 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: -0.39 (0.30), residues: 786 helix: 1.08 (0.28), residues: 368 sheet: 2.04 (0.91), residues: 37 loop : -1.96 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 436 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.002 PHE A 327 TYR 0.016 0.002 TYR A 521 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00781 ( 4) link_NAG-ASN : angle 3.12968 ( 12) link_BETA1-4 : bond 0.00515 ( 2) link_BETA1-4 : angle 4.48707 ( 6) hydrogen bonds : bond 0.05405 ( 268) hydrogen bonds : angle 4.34593 ( 774) metal coordination : bond 0.00189 ( 2) SS BOND : bond 0.00600 ( 7) SS BOND : angle 1.48947 ( 14) covalent geometry : bond 0.00378 ( 6655) covalent geometry : angle 0.63272 ( 9041) *********************** 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: 28 poor density : 152 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7755 (p0) cc_final: 0.7538 (p0) REVERT: A 208 GLU cc_start: 0.7937 (tp30) cc_final: 0.7651 (tt0) REVERT: A 215 TYR cc_start: 0.7904 (m-10) cc_final: 0.7547 (m-10) REVERT: A 231 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7943 (ttpp) REVERT: A 341 LYS cc_start: 0.8209 (pmmt) cc_final: 0.7988 (ptpp) REVERT: A 347 THR cc_start: 0.8540 (t) cc_final: 0.8168 (p) REVERT: A 401 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7673 (m-70) REVERT: A 406 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: A 470 LYS cc_start: 0.8217 (mppt) cc_final: 0.7975 (mppt) REVERT: A 518 ARG cc_start: 0.8464 (ttp-170) cc_final: 0.8233 (ptt90) REVERT: A 522 GLN cc_start: 0.7961 (tt0) cc_final: 0.7734 (tt0) REVERT: A 557 MET cc_start: 0.7911 (tmm) cc_final: 0.7658 (tmm) REVERT: A 564 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7994 (mm-30) REVERT: E 459 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8172 (p) outliers start: 28 outliers final: 12 residues processed: 163 average time/residue: 1.1204 time to fit residues: 192.1230 Evaluate side-chains 159 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 183 TYR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 394 ASN 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 13 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 21 optimal weight: 0.0370 chunk 73 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 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 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 = 0.3525 r_free = 0.3525 target = 0.115365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104799 restraints weight = 9669.901| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.13 r_work: 0.3248 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2355 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= 0.168 Angle : 0.641 10.448 9073 Z= 0.323 Chirality : 0.043 0.176 959 Planarity : 0.005 0.059 1169 Dihedral : 5.321 53.721 992 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.24 % Allowed : 16.45 % 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 (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: -0.31 (0.30), residues: 786 helix: 1.17 (0.28), residues: 371 sheet: 1.86 (0.87), residues: 37 loop : -1.94 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.013 0.002 PHE A 327 TYR 0.016 0.002 TYR A 183 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 2.35700 ( 12) link_BETA1-4 : bond 0.00531 ( 2) link_BETA1-4 : angle 4.58108 ( 6) hydrogen bonds : bond 0.05577 ( 268) hydrogen bonds : angle 4.26787 ( 774) metal coordination : bond 0.00097 ( 2) SS BOND : bond 0.00549 ( 7) SS BOND : angle 1.61320 ( 14) covalent geometry : bond 0.00396 ( 6655) covalent geometry : angle 0.62190 ( 9041) *********************** 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 171 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7496 (mp0) cc_final: 0.7152 (mp0) REVERT: A 197 GLU cc_start: 0.7716 (mp0) cc_final: 0.7399 (mp0) REVERT: A 198 ASP cc_start: 0.7694 (p0) cc_final: 0.7470 (p0) REVERT: A 208 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 215 TYR cc_start: 0.8026 (m-10) cc_final: 0.7691 (m-10) REVERT: A 231 LYS cc_start: 0.8200 (ttmm) cc_final: 0.8000 (ttpp) REVERT: A 282 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8253 (p) REVERT: A 341 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8012 (ptpp) REVERT: A 347 THR cc_start: 0.8583 (t) cc_final: 0.8226 (p) REVERT: A 401 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7895 (m-70) REVERT: A 406 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: A 465 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8469 (ttpt) REVERT: A 518 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.8276 (ptt90) REVERT: A 522 GLN cc_start: 0.7930 (tt0) cc_final: 0.7705 (tt0) REVERT: E 378 LYS cc_start: 0.8538 (ptpt) cc_final: 0.8320 (ptpp) REVERT: E 459 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8246 (p) outliers start: 36 outliers final: 18 residues processed: 152 average time/residue: 1.1305 time to fit residues: 180.9452 Evaluate side-chains 154 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 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 360 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.0070 chunk 61 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 64 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.115245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104310 restraints weight = 9789.826| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.11 r_work: 0.3245 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6670 Z= 0.144 Angle : 0.614 9.524 9073 Z= 0.308 Chirality : 0.042 0.171 959 Planarity : 0.004 0.057 1169 Dihedral : 4.895 53.331 992 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.80 % Allowed : 16.89 % 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 (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: -0.22 (0.31), residues: 786 helix: 1.23 (0.29), residues: 372 sheet: 1.62 (0.84), residues: 37 loop : -1.85 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.013 0.001 PHE A 327 TYR 0.014 0.001 TYR A 183 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 4) link_NAG-ASN : angle 1.91790 ( 12) link_BETA1-4 : bond 0.00613 ( 2) link_BETA1-4 : angle 4.52753 ( 6) hydrogen bonds : bond 0.05069 ( 268) hydrogen bonds : angle 4.15156 ( 774) metal coordination : bond 0.00174 ( 2) SS BOND : bond 0.00703 ( 7) SS BOND : angle 1.51698 ( 14) covalent geometry : bond 0.00337 ( 6655) covalent geometry : angle 0.59679 ( 9041) *********************** 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: 33 poor density : 138 time to evaluate : 0.664 Fit side-chains REVERT: A 35 GLU cc_start: 0.7569 (mp0) cc_final: 0.7158 (mp0) REVERT: A 179 LEU cc_start: 0.8481 (mp) cc_final: 0.8228 (mt) REVERT: A 197 GLU cc_start: 0.7838 (mp0) cc_final: 0.7478 (mp0) REVERT: A 198 ASP cc_start: 0.7707 (p0) cc_final: 0.7368 (p0) REVERT: A 208 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: A 215 TYR cc_start: 0.8146 (m-10) cc_final: 0.7848 (m-10) REVERT: A 271 TRP cc_start: 0.8963 (m-90) cc_final: 0.8716 (m-90) REVERT: A 282 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 341 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8100 (ptpp) REVERT: A 347 THR cc_start: 0.8612 (t) cc_final: 0.8266 (p) REVERT: A 401 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7958 (m-70) REVERT: A 406 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: A 465 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8487 (ttpt) REVERT: E 378 LYS cc_start: 0.8551 (ptpt) cc_final: 0.8325 (ptpp) REVERT: E 459 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8310 (p) outliers start: 33 outliers final: 16 residues processed: 153 average time/residue: 1.1098 time to fit residues: 178.8456 Evaluate side-chains 151 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 282 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 360 MET 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 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 43 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 42 optimal weight: 0.2980 chunk 76 optimal weight: 0.0770 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.2496 ------------------------------------------------------------------------------- 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 A 522 GLN E 370 ASN E 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103693 restraints weight = 9655.935| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.16 r_work: 0.3215 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6670 Z= 0.143 Angle : 0.608 9.060 9073 Z= 0.307 Chirality : 0.042 0.168 959 Planarity : 0.004 0.058 1169 Dihedral : 4.774 52.839 992 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.24 % Allowed : 16.74 % 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 (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: -0.16 (0.31), residues: 786 helix: 1.30 (0.29), residues: 372 sheet: 1.25 (0.85), residues: 37 loop : -1.79 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.018 0.001 PHE A 314 TYR 0.025 0.002 TYR A 521 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 4) link_NAG-ASN : angle 1.81264 ( 12) link_BETA1-4 : bond 0.00528 ( 2) link_BETA1-4 : angle 4.47050 ( 6) hydrogen bonds : bond 0.05068 ( 268) hydrogen bonds : angle 4.09633 ( 774) metal coordination : bond 0.00152 ( 2) SS BOND : bond 0.00570 ( 7) SS BOND : angle 1.54403 ( 14) covalent geometry : bond 0.00333 ( 6655) covalent geometry : angle 0.59163 ( 9041) *********************** 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 168 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.653 Fit side-chains REVERT: A 35 GLU cc_start: 0.7573 (mp0) cc_final: 0.7153 (mp0) REVERT: A 131 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8441 (mtpp) REVERT: A 179 LEU cc_start: 0.8493 (mp) cc_final: 0.8252 (mt) REVERT: A 197 GLU cc_start: 0.7827 (mp0) cc_final: 0.7495 (mp0) REVERT: A 198 ASP cc_start: 0.7719 (p0) cc_final: 0.7381 (p0) REVERT: A 208 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: A 215 TYR cc_start: 0.8216 (m-10) cc_final: 0.7962 (m-10) REVERT: A 271 TRP cc_start: 0.8962 (m-90) cc_final: 0.8714 (m-90) REVERT: A 282 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 347 THR cc_start: 0.8605 (t) cc_final: 0.8249 (p) REVERT: A 401 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7944 (m-70) REVERT: A 406 GLU cc_start: 0.8019 (tt0) cc_final: 0.7718 (tt0) REVERT: A 465 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8458 (ttpt) REVERT: E 378 LYS cc_start: 0.8596 (ptpt) cc_final: 0.8362 (ptpp) REVERT: E 459 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8365 (p) REVERT: E 500 THR cc_start: 0.8584 (m) cc_final: 0.8336 (t) outliers start: 36 outliers final: 16 residues processed: 151 average time/residue: 1.0765 time to fit residues: 171.2931 Evaluate side-chains 148 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 142 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 282 THR Chi-restraints excluded: chain A residue 292 ASP 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 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 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 57 optimal weight: 0.0770 chunk 5 optimal weight: 0.1980 chunk 70 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.1276 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.116109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104744 restraints weight = 9620.301| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.16 r_work: 0.3232 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6670 Z= 0.115 Angle : 0.593 9.874 9073 Z= 0.297 Chirality : 0.041 0.162 959 Planarity : 0.004 0.058 1169 Dihedral : 4.647 51.780 992 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.51 % Allowed : 18.05 % 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 (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: -0.10 (0.31), residues: 786 helix: 1.37 (0.29), residues: 371 sheet: 1.03 (0.86), residues: 37 loop : -1.75 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.020 0.001 PHE A 314 TYR 0.032 0.001 TYR A 521 ARG 0.002 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 4) link_NAG-ASN : angle 1.57056 ( 12) link_BETA1-4 : bond 0.00602 ( 2) link_BETA1-4 : angle 4.31009 ( 6) hydrogen bonds : bond 0.04482 ( 268) hydrogen bonds : angle 4.04303 ( 774) metal coordination : bond 0.00102 ( 2) SS BOND : bond 0.00432 ( 7) SS BOND : angle 1.54002 ( 14) covalent geometry : bond 0.00259 ( 6655) covalent geometry : angle 0.57803 ( 9041) *********************** 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 161 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.080 Fit side-chains REVERT: A 35 GLU cc_start: 0.7585 (mp0) cc_final: 0.7183 (mp0) REVERT: A 131 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8376 (mtmm) REVERT: A 179 LEU cc_start: 0.8492 (mp) cc_final: 0.8246 (mt) REVERT: A 198 ASP cc_start: 0.7744 (p0) cc_final: 0.7405 (p0) REVERT: A 208 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: A 215 TYR cc_start: 0.8242 (m-10) cc_final: 0.8009 (m-10) REVERT: A 271 TRP cc_start: 0.8964 (m-90) cc_final: 0.8689 (m-90) REVERT: A 282 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8270 (p) REVERT: A 292 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7426 (t0) REVERT: A 347 THR cc_start: 0.8589 (t) cc_final: 0.8248 (p) REVERT: A 401 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7904 (m-70) REVERT: A 465 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8505 (ttpt) REVERT: E 459 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8348 (p) REVERT: E 500 THR cc_start: 0.8606 (m) cc_final: 0.8339 (t) outliers start: 31 outliers final: 14 residues processed: 145 average time/residue: 1.1384 time to fit residues: 174.0259 Evaluate side-chains 149 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 142 LEU 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 229 THR 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 391 LEU Chi-restraints excluded: chain A residue 401 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.0060 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.114471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103926 restraints weight = 9614.947| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.10 r_work: 0.3218 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6670 Z= 0.158 Angle : 0.626 9.641 9073 Z= 0.315 Chirality : 0.043 0.170 959 Planarity : 0.004 0.058 1169 Dihedral : 4.667 52.646 992 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.08 % Allowed : 18.49 % 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 (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: -0.17 (0.31), residues: 786 helix: 1.33 (0.29), residues: 372 sheet: 0.82 (0.87), residues: 37 loop : -1.79 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.023 0.002 PHE A 314 TYR 0.027 0.002 TYR A 521 ARG 0.004 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 4) link_NAG-ASN : angle 1.72775 ( 12) link_BETA1-4 : bond 0.00579 ( 2) link_BETA1-4 : angle 4.33535 ( 6) hydrogen bonds : bond 0.05090 ( 268) hydrogen bonds : angle 4.08977 ( 774) metal coordination : bond 0.00188 ( 2) SS BOND : bond 0.00661 ( 7) SS BOND : angle 2.37114 ( 14) covalent geometry : bond 0.00376 ( 6655) covalent geometry : angle 0.60657 ( 9041) *********************** 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 157 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.713 Fit side-chains REVERT: A 35 GLU cc_start: 0.7596 (mp0) cc_final: 0.7146 (mp0) REVERT: A 179 LEU cc_start: 0.8505 (mp) cc_final: 0.8254 (mt) REVERT: A 198 ASP cc_start: 0.7696 (p0) cc_final: 0.7347 (p0) REVERT: A 208 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: A 210 GLU cc_start: 0.7631 (pm20) cc_final: 0.7426 (pp20) REVERT: A 215 TYR cc_start: 0.8299 (m-10) cc_final: 0.8097 (m-10) REVERT: A 271 TRP cc_start: 0.8956 (m-90) cc_final: 0.8696 (m-90) REVERT: A 282 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8287 (p) REVERT: A 292 ASP cc_start: 0.7828 (t70) cc_final: 0.7573 (t0) REVERT: A 347 THR cc_start: 0.8606 (t) cc_final: 0.8262 (p) REVERT: A 401 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.8004 (m-70) REVERT: A 465 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8496 (ttpt) REVERT: A 473 TRP cc_start: 0.7298 (t-100) cc_final: 0.7094 (t-100) REVERT: E 369 TYR cc_start: 0.8100 (t80) cc_final: 0.7804 (t80) REVERT: E 459 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8352 (p) outliers start: 28 outliers final: 17 residues processed: 144 average time/residue: 1.1146 time to fit residues: 169.0438 Evaluate side-chains 146 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 172 VAL 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 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 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 459 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 58 optimal weight: 0.0000 chunk 1 optimal weight: 0.0980 chunk 67 optimal weight: 0.4980 chunk 3 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.2784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102582 restraints weight = 9790.352| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.15 r_work: 0.3228 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6670 Z= 0.151 Angle : 0.625 9.515 9073 Z= 0.315 Chirality : 0.042 0.170 959 Planarity : 0.004 0.058 1169 Dihedral : 4.676 52.749 992 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.49 % Allowed : 19.51 % Favored : 77.00 % 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: -0.17 (0.31), residues: 786 helix: 1.34 (0.29), residues: 375 sheet: 1.01 (0.88), residues: 35 loop : -1.83 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.024 0.001 PHE A 314 TYR 0.024 0.002 TYR A 613 ARG 0.004 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 4) link_NAG-ASN : angle 1.73616 ( 12) link_BETA1-4 : bond 0.00577 ( 2) link_BETA1-4 : angle 4.29168 ( 6) hydrogen bonds : bond 0.05130 ( 268) hydrogen bonds : angle 4.08677 ( 774) metal coordination : bond 0.00169 ( 2) SS BOND : bond 0.00629 ( 7) SS BOND : angle 1.90229 ( 14) covalent geometry : bond 0.00359 ( 6655) covalent geometry : angle 0.60833 ( 9041) *********************** 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 154 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.660 Fit side-chains REVERT: A 35 GLU cc_start: 0.7624 (mp0) cc_final: 0.7212 (mp0) REVERT: A 179 LEU cc_start: 0.8569 (mp) cc_final: 0.8311 (mt) REVERT: A 208 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 210 GLU cc_start: 0.7602 (pm20) cc_final: 0.7363 (pp20) REVERT: A 271 TRP cc_start: 0.8964 (m-90) cc_final: 0.8664 (m-90) REVERT: A 282 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8257 (p) REVERT: A 292 ASP cc_start: 0.7850 (t70) cc_final: 0.7610 (t0) REVERT: A 347 THR cc_start: 0.8584 (t) cc_final: 0.8241 (p) REVERT: A 351 LEU cc_start: 0.8636 (mm) cc_final: 0.8422 (mp) REVERT: A 401 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8062 (m-70) REVERT: A 465 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8509 (ttpt) REVERT: A 581 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8275 (t) REVERT: E 440 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8155 (p0) REVERT: E 459 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8364 (p) outliers start: 24 outliers final: 11 residues processed: 146 average time/residue: 1.0336 time to fit residues: 159.2820 Evaluate side-chains 143 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 183 TYR Chi-restraints excluded: chain A residue 208 GLU 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 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 440 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 26 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 42 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 0.0270 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.2636 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102242 restraints weight = 9963.591| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.18 r_work: 0.3224 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3244 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= 0.148 Angle : 0.621 9.291 9073 Z= 0.312 Chirality : 0.042 0.169 959 Planarity : 0.004 0.059 1169 Dihedral : 4.666 52.667 992 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.49 % Allowed : 19.51 % Favored : 77.00 % 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: -0.16 (0.31), residues: 786 helix: 1.32 (0.29), residues: 376 sheet: 1.03 (0.89), residues: 35 loop : -1.81 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.024 0.001 PHE A 314 TYR 0.025 0.002 TYR A 613 ARG 0.004 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 4) link_NAG-ASN : angle 1.70374 ( 12) link_BETA1-4 : bond 0.00570 ( 2) link_BETA1-4 : angle 4.23758 ( 6) hydrogen bonds : bond 0.05058 ( 268) hydrogen bonds : angle 4.09942 ( 774) metal coordination : bond 0.00158 ( 2) SS BOND : bond 0.00684 ( 7) SS BOND : angle 1.90632 ( 14) covalent geometry : bond 0.00352 ( 6655) covalent geometry : angle 0.60509 ( 9041) *********************** 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 149 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.717 Fit side-chains REVERT: A 35 GLU cc_start: 0.7604 (mp0) cc_final: 0.7190 (mp0) REVERT: A 179 LEU cc_start: 0.8561 (mp) cc_final: 0.8305 (mt) REVERT: A 208 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: A 210 GLU cc_start: 0.7579 (pm20) cc_final: 0.7356 (pp20) REVERT: A 271 TRP cc_start: 0.8958 (m-90) cc_final: 0.8595 (m-90) REVERT: A 282 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8256 (p) REVERT: A 347 THR cc_start: 0.8575 (t) cc_final: 0.8224 (p) REVERT: A 401 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.8057 (m-70) REVERT: A 463 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8327 (t) REVERT: A 465 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8514 (ttpt) REVERT: A 581 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8268 (t) REVERT: E 440 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8167 (p0) REVERT: E 459 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8368 (p) outliers start: 24 outliers final: 11 residues processed: 141 average time/residue: 1.0689 time to fit residues: 158.9999 Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 208 GLU Chi-restraints excluded: chain A residue 231 LYS 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 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 440 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 0.0670 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.0670 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102133 restraints weight = 9960.842| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.18 r_work: 0.3211 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6670 Z= 0.150 Angle : 0.630 9.071 9073 Z= 0.318 Chirality : 0.042 0.169 959 Planarity : 0.004 0.059 1169 Dihedral : 4.640 52.555 992 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.06 % Allowed : 19.80 % Favored : 77.15 % 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: -0.15 (0.31), residues: 786 helix: 1.35 (0.29), residues: 375 sheet: 1.01 (0.89), residues: 35 loop : -1.81 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.027 0.001 PHE A 314 TYR 0.036 0.002 TYR A 521 ARG 0.004 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 4) link_NAG-ASN : angle 1.68247 ( 12) link_BETA1-4 : bond 0.00574 ( 2) link_BETA1-4 : angle 4.19074 ( 6) hydrogen bonds : bond 0.05113 ( 268) hydrogen bonds : angle 4.10729 ( 774) metal coordination : bond 0.00180 ( 2) SS BOND : bond 0.00679 ( 7) SS BOND : angle 1.83645 ( 14) covalent geometry : bond 0.00359 ( 6655) covalent geometry : angle 0.61488 ( 9041) ********************** 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 149 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.309 Fit side-chains REVERT: A 35 GLU cc_start: 0.7611 (mp0) cc_final: 0.7180 (mp0) REVERT: A 89 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7290 (mp-120) REVERT: A 179 LEU cc_start: 0.8544 (mp) cc_final: 0.8281 (mt) REVERT: A 208 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: A 210 GLU cc_start: 0.7592 (pm20) cc_final: 0.7364 (pp20) REVERT: A 271 TRP cc_start: 0.8976 (m-90) cc_final: 0.8607 (m-90) REVERT: A 282 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 347 THR cc_start: 0.8587 (t) cc_final: 0.8231 (p) REVERT: A 401 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.8039 (m-70) REVERT: A 463 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8336 (t) REVERT: A 465 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8523 (ttpt) REVERT: A 581 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8255 (t) REVERT: E 440 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8168 (p0) REVERT: E 459 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8348 (p) outliers start: 21 outliers final: 12 residues processed: 143 average time/residue: 1.0714 time to fit residues: 163.2663 Evaluate side-chains 143 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 125 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 231 LYS 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 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 440 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 0.0040 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 586 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 = 0.3465 r_free = 0.3465 target = 0.110721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100186 restraints weight = 9946.939| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.17 r_work: 0.3187 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6670 Z= 0.204 Angle : 0.682 9.117 9073 Z= 0.347 Chirality : 0.045 0.181 959 Planarity : 0.005 0.059 1169 Dihedral : 4.832 53.815 992 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.49 % Allowed : 19.36 % Favored : 77.15 % 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: -0.25 (0.31), residues: 786 helix: 1.32 (0.29), residues: 371 sheet: 0.77 (0.90), residues: 36 loop : -1.87 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 473 HIS 0.006 0.001 HIS A 241 PHE 0.027 0.002 PHE A 314 TYR 0.038 0.002 TYR A 521 ARG 0.006 0.001 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 4) link_NAG-ASN : angle 2.07420 ( 12) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 4.28042 ( 6) hydrogen bonds : bond 0.06158 ( 268) hydrogen bonds : angle 4.23178 ( 774) metal coordination : bond 0.00276 ( 2) SS BOND : bond 0.00763 ( 7) SS BOND : angle 2.21715 ( 14) covalent geometry : bond 0.00489 ( 6655) covalent geometry : angle 0.66459 ( 9041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5653.48 seconds wall clock time: 99 minutes 33.73 seconds (5973.73 seconds total)