Starting phenix.real_space_refine on Sun Apr 27 21:50:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ka8_37006/04_2025/8ka8_37006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ka8_37006/04_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_37006/04_2025/8ka8_37006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ka8_37006/04_2025/8ka8_37006.map" model { file = "/net/cci-nas-00/data/ceres_data/8ka8_37006/04_2025/8ka8_37006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ka8_37006/04_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-5669/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: 6.27, per 1000 atoms: 0.97 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: 1.46 Conformation dependent library (CDL) restraints added in 981.4 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: 0.69 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: 1.58 Time building geometry restraints manager: 1.76 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: 7.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.620 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.510 ------------------------------------------------------------------------------- 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 : 0.640 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: 1.1399 time to fit residues: 227.9512 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 : 0.709 ------------------------------------------------------------------------------- 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 = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106685 restraints weight = 9666.397| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.14 r_work: 0.3266 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- 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 4.48708 ( 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 1.48948 ( 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 : 0.697 Fit side-chains revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7930 (tppt) cc_final: 0.7730 (tppp) REVERT: A 198 ASP cc_start: 0.7754 (p0) cc_final: 0.7536 (p0) REVERT: A 208 GLU cc_start: 0.7937 (tp30) cc_final: 0.7651 (tt0) REVERT: A 215 TYR cc_start: 0.7901 (m-10) cc_final: 0.7544 (m-10) REVERT: A 231 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7945 (ttpp) REVERT: A 341 LYS cc_start: 0.8209 (pmmt) cc_final: 0.7987 (ptpp) REVERT: A 347 THR cc_start: 0.8539 (t) cc_final: 0.8168 (p) REVERT: A 401 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7674 (m-70) REVERT: A 406 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: A 470 LYS cc_start: 0.8222 (mppt) cc_final: 0.7980 (mppt) REVERT: A 518 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.8235 (ptt90) REVERT: A 522 GLN cc_start: 0.7962 (tt0) cc_final: 0.7735 (tt0) REVERT: A 557 MET cc_start: 0.7910 (tmm) cc_final: 0.7658 (tmm) REVERT: A 564 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7991 (mm-30) REVERT: E 459 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8174 (p) outliers start: 28 outliers final: 12 residues processed: 163 average time/residue: 1.1664 time to fit residues: 199.7311 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 : 0.653 ------------------------------------------------------------------------------- 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: 0.3980 chunk 41 optimal weight: 0.6980 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: 0.2980 chunk 73 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.115902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105300 restraints weight = 9682.486| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.14 r_work: 0.3257 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2281 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= 0.158 Angle : 0.629 10.454 9073 Z= 0.317 Chirality : 0.043 0.176 959 Planarity : 0.005 0.059 1169 Dihedral : 5.313 53.539 992 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.39 % Allowed : 16.01 % 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 (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: -0.29 (0.30), residues: 786 helix: 1.19 (0.29), residues: 371 sheet: 1.87 (0.87), residues: 37 loop : -1.93 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.002 PHE A 327 TYR 0.014 0.001 TYR A 183 ARG 0.003 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 4) link_NAG-ASN : angle 2.26236 ( 12) link_BETA1-4 : bond 0.00590 ( 2) link_BETA1-4 : angle 4.52551 ( 6) hydrogen bonds : bond 0.05401 ( 268) hydrogen bonds : angle 4.25069 ( 774) metal coordination : bond 0.00068 ( 2) SS BOND : bond 0.00529 ( 7) SS BOND : angle 1.53974 ( 14) covalent geometry : bond 0.00370 ( 6655) covalent geometry : angle 0.61104 ( 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 173 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7483 (mp0) cc_final: 0.7191 (mp0) REVERT: A 78 LYS cc_start: 0.8039 (tppt) cc_final: 0.7731 (tppp) REVERT: A 197 GLU cc_start: 0.7699 (mp0) cc_final: 0.7401 (mp0) REVERT: A 198 ASP cc_start: 0.7714 (p0) cc_final: 0.7493 (p0) REVERT: A 208 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: A 215 TYR cc_start: 0.8000 (m-10) cc_final: 0.7632 (m-10) REVERT: A 231 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7981 (ttpp) REVERT: A 282 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8238 (p) REVERT: A 341 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7984 (ptpp) REVERT: A 347 THR cc_start: 0.8567 (t) cc_final: 0.8192 (p) REVERT: A 401 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7825 (m-70) REVERT: A 406 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: A 522 GLN cc_start: 0.7927 (tt0) cc_final: 0.7696 (tt0) REVERT: E 378 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8317 (ptpp) REVERT: E 459 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8231 (p) outliers start: 37 outliers final: 17 residues processed: 153 average time/residue: 1.2275 time to fit residues: 197.3424 Evaluate side-chains 157 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 61 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 64 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.113118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102334 restraints weight = 9751.569| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.16 r_work: 0.3209 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6670 Z= 0.192 Angle : 0.661 10.030 9073 Z= 0.335 Chirality : 0.044 0.175 959 Planarity : 0.005 0.057 1169 Dihedral : 5.059 54.363 992 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.53 % Allowed : 16.01 % Favored : 78.46 % 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: -0.29 (0.30), residues: 786 helix: 1.25 (0.29), residues: 366 sheet: 1.37 (0.86), residues: 38 loop : -1.91 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.002 PHE A 327 TYR 0.018 0.002 TYR A 183 ARG 0.005 0.001 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 4) link_NAG-ASN : angle 2.25206 ( 12) link_BETA1-4 : bond 0.00747 ( 2) link_BETA1-4 : angle 4.67369 ( 6) hydrogen bonds : bond 0.05932 ( 268) hydrogen bonds : angle 4.24343 ( 774) metal coordination : bond 0.00241 ( 2) SS BOND : bond 0.00442 ( 7) SS BOND : angle 1.91416 ( 14) covalent geometry : bond 0.00457 ( 6655) covalent geometry : angle 0.64183 ( 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 175 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.825 Fit side-chains REVERT: A 35 GLU cc_start: 0.7562 (mp0) cc_final: 0.7175 (mp0) REVERT: A 78 LYS cc_start: 0.8132 (tppt) cc_final: 0.7863 (ttmm) REVERT: A 131 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8494 (mtpp) REVERT: A 179 LEU cc_start: 0.8594 (mp) cc_final: 0.8335 (mt) REVERT: A 197 GLU cc_start: 0.7840 (mp0) cc_final: 0.7504 (mp0) REVERT: A 208 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: A 215 TYR cc_start: 0.8187 (m-10) cc_final: 0.7859 (m-10) REVERT: A 271 TRP cc_start: 0.8977 (m-90) cc_final: 0.8709 (m-90) REVERT: A 282 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 341 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8112 (ptpp) REVERT: A 347 THR cc_start: 0.8566 (t) cc_final: 0.8224 (p) REVERT: A 401 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8061 (m-70) REVERT: A 406 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 465 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8552 (ttpt) REVERT: A 473 TRP cc_start: 0.7494 (t-100) cc_final: 0.7203 (t-100) REVERT: A 522 GLN cc_start: 0.7931 (tt0) cc_final: 0.7729 (tt0) REVERT: E 378 LYS cc_start: 0.8575 (ptpt) cc_final: 0.8344 (ptpp) REVERT: E 459 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8333 (p) REVERT: E 506 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8311 (mt0) outliers start: 38 outliers final: 19 residues processed: 153 average time/residue: 1.1914 time to fit residues: 191.8980 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 : 0.708 ------------------------------------------------------------------------------- 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 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 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 394 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.0980 chunk 45 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 42 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.0770 chunk 40 optimal weight: 0.0670 chunk 36 optimal weight: 0.0970 chunk 12 optimal weight: 0.0270 overall best weight: 0.0732 ------------------------------------------------------------------------------- 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 552 GLN E 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105490 restraints weight = 9693.103| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.17 r_work: 0.3264 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6670 Z= 0.110 Angle : 0.584 8.924 9073 Z= 0.293 Chirality : 0.040 0.161 959 Planarity : 0.004 0.057 1169 Dihedral : 4.795 51.654 992 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.08 % Allowed : 18.05 % 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 (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: 1.30 (0.29), residues: 371 sheet: 1.38 (0.85), residues: 37 loop : -1.78 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 PHE 0.010 0.001 PHE A 32 TYR 0.015 0.001 TYR A 207 ARG 0.002 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 4) link_NAG-ASN : angle 1.63406 ( 12) link_BETA1-4 : bond 0.00671 ( 2) link_BETA1-4 : angle 4.40850 ( 6) hydrogen bonds : bond 0.04396 ( 268) hydrogen bonds : angle 4.09879 ( 774) metal coordination : bond 0.00082 ( 2) SS BOND : bond 0.00523 ( 7) SS BOND : angle 1.31343 ( 14) covalent geometry : bond 0.00237 ( 6655) covalent geometry : angle 0.56869 ( 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 160 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.651 Fit side-chains REVERT: A 35 GLU cc_start: 0.7575 (mp0) cc_final: 0.7186 (mp0) REVERT: A 78 LYS cc_start: 0.8030 (tppt) cc_final: 0.7713 (tppp) REVERT: A 131 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8477 (mtpp) REVERT: A 179 LEU cc_start: 0.8445 (mp) cc_final: 0.8198 (mt) REVERT: A 197 GLU cc_start: 0.7819 (mp0) cc_final: 0.7491 (mp0) REVERT: A 198 ASP cc_start: 0.7733 (p0) cc_final: 0.7411 (p0) REVERT: A 208 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: A 215 TYR cc_start: 0.8166 (m-10) cc_final: 0.7878 (m-10) REVERT: A 271 TRP cc_start: 0.8956 (m-90) cc_final: 0.8711 (m-90) REVERT: A 282 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8254 (p) REVERT: A 292 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7341 (t0) REVERT: A 341 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7937 (ptpp) REVERT: A 347 THR cc_start: 0.8582 (t) cc_final: 0.8242 (p) REVERT: A 401 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.7875 (m-70) REVERT: A 406 GLU cc_start: 0.8006 (tt0) cc_final: 0.7690 (tt0) REVERT: A 465 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8448 (ttpt) REVERT: A 522 GLN cc_start: 0.7809 (tt0) cc_final: 0.7607 (tt0) REVERT: E 369 TYR cc_start: 0.8083 (t80) cc_final: 0.7784 (t80) REVERT: E 378 LYS cc_start: 0.8539 (ptpt) cc_final: 0.8307 (ptpp) REVERT: E 459 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8319 (p) REVERT: E 500 THR cc_start: 0.8574 (m) cc_final: 0.8329 (t) outliers start: 28 outliers final: 13 residues processed: 147 average time/residue: 1.1354 time to fit residues: 175.5102 Evaluate side-chains 148 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL 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: 0.4980 chunk 68 optimal weight: 0.0980 chunk 50 optimal weight: 0.4980 chunk 61 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 5 optimal weight: 0.2980 chunk 70 optimal weight: 0.0270 chunk 62 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 overall best weight: 0.1636 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.115887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104959 restraints weight = 9754.933| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.20 r_work: 0.3256 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6670 Z= 0.119 Angle : 0.591 10.027 9073 Z= 0.295 Chirality : 0.041 0.163 959 Planarity : 0.004 0.058 1169 Dihedral : 4.611 51.533 992 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.37 % Allowed : 17.61 % 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: -0.13 (0.31), residues: 786 helix: 1.36 (0.29), residues: 371 sheet: 1.17 (0.85), residues: 37 loop : -1.80 (0.30), 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 0.019 0.001 PHE A 314 TYR 0.024 0.001 TYR A 521 ARG 0.003 0.000 ARG E 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 4) link_NAG-ASN : angle 1.61428 ( 12) link_BETA1-4 : bond 0.00634 ( 2) link_BETA1-4 : angle 4.30316 ( 6) hydrogen bonds : bond 0.04519 ( 268) hydrogen bonds : angle 4.02945 ( 774) metal coordination : bond 0.00134 ( 2) SS BOND : bond 0.00715 ( 7) SS BOND : angle 1.57435 ( 14) covalent geometry : bond 0.00275 ( 6655) covalent geometry : angle 0.57557 ( 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 160 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.753 Fit side-chains REVERT: A 35 GLU cc_start: 0.7571 (mp0) cc_final: 0.7157 (mp0) REVERT: A 78 LYS cc_start: 0.8048 (tppt) cc_final: 0.7708 (tppp) REVERT: A 131 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8462 (mtpp) REVERT: A 179 LEU cc_start: 0.8477 (mp) cc_final: 0.8228 (mt) REVERT: A 198 ASP cc_start: 0.7737 (p0) cc_final: 0.7394 (p0) REVERT: A 208 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: A 215 TYR cc_start: 0.8214 (m-10) cc_final: 0.7949 (m-10) REVERT: A 271 TRP cc_start: 0.8963 (m-90) cc_final: 0.8686 (m-90) REVERT: A 282 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 341 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7937 (ptpp) REVERT: A 347 THR cc_start: 0.8595 (t) cc_final: 0.8248 (p) REVERT: A 401 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.7887 (m-70) REVERT: A 406 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: A 465 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8471 (ttpt) REVERT: A 581 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8166 (t) REVERT: E 369 TYR cc_start: 0.8085 (t80) cc_final: 0.7787 (t80) REVERT: E 459 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8326 (p) REVERT: E 500 THR cc_start: 0.8589 (m) cc_final: 0.8316 (t) outliers start: 30 outliers final: 10 residues processed: 146 average time/residue: 1.1145 time to fit residues: 171.3306 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 : 0.728 ------------------------------------------------------------------------------- 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 249 MET 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 401 HIS Chi-restraints excluded: chain A residue 406 GLU 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 459 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 39 optimal weight: 0.1980 chunk 47 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101206 restraints weight = 9460.562| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.11 r_work: 0.3194 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6670 Z= 0.227 Angle : 0.691 10.405 9073 Z= 0.352 Chirality : 0.045 0.188 959 Planarity : 0.005 0.058 1169 Dihedral : 4.913 54.657 992 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.37 % Allowed : 17.61 % 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: -0.31 (0.31), residues: 786 helix: 1.29 (0.29), residues: 369 sheet: 0.67 (0.88), residues: 38 loop : -1.93 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.023 0.002 PHE A 314 TYR 0.024 0.002 TYR A 613 ARG 0.005 0.001 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 2.19104 ( 12) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 4.55077 ( 6) hydrogen bonds : bond 0.06303 ( 268) hydrogen bonds : angle 4.20181 ( 774) metal coordination : bond 0.00292 ( 2) SS BOND : bond 0.00913 ( 7) SS BOND : angle 2.72975 ( 14) covalent geometry : bond 0.00547 ( 6655) covalent geometry : angle 0.66876 ( 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 160 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.665 Fit side-chains REVERT: A 35 GLU cc_start: 0.7635 (mp0) cc_final: 0.7202 (mp0) REVERT: A 78 LYS cc_start: 0.8172 (tppt) cc_final: 0.7885 (ttmm) REVERT: A 179 LEU cc_start: 0.8569 (mp) cc_final: 0.8311 (mt) REVERT: A 208 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: A 271 TRP cc_start: 0.8969 (m-90) cc_final: 0.8635 (m-90) REVERT: A 282 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8299 (p) REVERT: A 341 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8117 (ptpp) REVERT: A 347 THR cc_start: 0.8595 (t) cc_final: 0.8233 (p) REVERT: A 401 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.8187 (m-70) REVERT: A 406 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: A 465 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8493 (ttpt) REVERT: A 479 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: A 559 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7936 (ttm110) REVERT: A 581 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8292 (t) REVERT: E 378 LYS cc_start: 0.8603 (ptpt) cc_final: 0.8372 (ptpp) REVERT: E 459 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8367 (p) outliers start: 30 outliers final: 13 residues processed: 146 average time/residue: 1.1277 time to fit residues: 173.5004 Evaluate side-chains 150 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 172 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 229 THR 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 351 LEU 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 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 459 SER Chi-restraints excluded: chain E residue 503 VAL 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: 0.3980 chunk 28 optimal weight: 0.0670 chunk 46 optimal weight: 0.0980 chunk 58 optimal weight: 0.0970 chunk 1 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 17 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103998 restraints weight = 9822.088| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.16 r_work: 0.3243 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3174 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= 0.114 Angle : 0.601 9.609 9073 Z= 0.299 Chirality : 0.041 0.165 959 Planarity : 0.004 0.059 1169 Dihedral : 4.680 51.779 992 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.49 % Allowed : 19.80 % Favored : 76.71 % 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: -0.22 (0.31), residues: 786 helix: 1.27 (0.29), residues: 376 sheet: 0.94 (0.88), residues: 35 loop : -1.82 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 473 HIS 0.003 0.001 HIS A 241 PHE 0.022 0.001 PHE A 314 TYR 0.023 0.001 TYR A 613 ARG 0.002 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 4) link_NAG-ASN : angle 1.49536 ( 12) link_BETA1-4 : bond 0.00817 ( 2) link_BETA1-4 : angle 4.22603 ( 6) hydrogen bonds : bond 0.04403 ( 268) hydrogen bonds : angle 4.06966 ( 774) metal coordination : bond 0.00110 ( 2) SS BOND : bond 0.00577 ( 7) SS BOND : angle 1.75422 ( 14) covalent geometry : bond 0.00259 ( 6655) covalent geometry : angle 0.58538 ( 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 153 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.910 Fit side-chains REVERT: A 35 GLU cc_start: 0.7585 (mp0) cc_final: 0.7182 (mp0) REVERT: A 78 LYS cc_start: 0.8068 (tppt) cc_final: 0.7772 (ttmm) REVERT: A 179 LEU cc_start: 0.8477 (mp) cc_final: 0.8230 (mt) REVERT: A 208 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: A 271 TRP cc_start: 0.8960 (m-90) cc_final: 0.8696 (m-90) REVERT: A 282 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8235 (p) REVERT: A 341 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7971 (ptpp) REVERT: A 347 THR cc_start: 0.8580 (t) cc_final: 0.8215 (p) REVERT: A 401 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7885 (m-70) REVERT: A 406 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: A 465 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8531 (ttpt) REVERT: E 459 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8355 (p) outliers start: 24 outliers final: 7 residues processed: 142 average time/residue: 1.3085 time to fit residues: 197.7120 Evaluate side-chains 136 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER 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 401 HIS Chi-restraints excluded: chain A residue 406 GLU 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 Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 64 optimal weight: 0.0020 chunk 37 optimal weight: 0.0070 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 overall best weight: 0.1606 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103623 restraints weight = 10026.588| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.20 r_work: 0.3236 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3189 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= 0.122 Angle : 0.606 9.230 9073 Z= 0.305 Chirality : 0.041 0.164 959 Planarity : 0.004 0.058 1169 Dihedral : 4.505 51.604 992 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.06 % Allowed : 20.23 % Favored : 76.71 % 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: -0.14 (0.31), residues: 786 helix: 1.35 (0.29), residues: 374 sheet: 0.91 (0.89), residues: 35 loop : -1.79 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 473 HIS 0.003 0.001 HIS A 241 PHE 0.026 0.001 PHE A 314 TYR 0.030 0.001 TYR A 521 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 1.51400 ( 12) link_BETA1-4 : bond 0.00592 ( 2) link_BETA1-4 : angle 4.13862 ( 6) hydrogen bonds : bond 0.04541 ( 268) hydrogen bonds : angle 4.02647 ( 774) metal coordination : bond 0.00103 ( 2) SS BOND : bond 0.00536 ( 7) SS BOND : angle 1.59919 ( 14) covalent geometry : bond 0.00281 ( 6655) covalent geometry : angle 0.59139 ( 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 147 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.617 Fit side-chains REVERT: A 35 GLU cc_start: 0.7592 (mp0) cc_final: 0.7162 (mp0) REVERT: A 78 LYS cc_start: 0.8102 (tppt) cc_final: 0.7799 (ttmm) REVERT: A 179 LEU cc_start: 0.8534 (mp) cc_final: 0.8277 (mt) REVERT: A 208 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 271 TRP cc_start: 0.8960 (m-90) cc_final: 0.8591 (m-90) REVERT: A 282 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8242 (p) REVERT: A 292 ASP cc_start: 0.7941 (t70) cc_final: 0.7697 (t0) REVERT: A 341 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8065 (ptpp) REVERT: A 347 THR cc_start: 0.8581 (t) cc_final: 0.8204 (p) REVERT: A 401 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7952 (m-70) REVERT: A 406 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 463 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8287 (t) REVERT: A 465 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8533 (ttpt) REVERT: E 459 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8340 (p) REVERT: E 500 THR cc_start: 0.8671 (m) cc_final: 0.8365 (t) REVERT: E 519 HIS cc_start: 0.7236 (t70) cc_final: 0.7016 (t-90) outliers start: 21 outliers final: 5 residues processed: 139 average time/residue: 1.7484 time to fit residues: 256.5192 Evaluate side-chains 134 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU 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 341 LYS 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 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 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.109823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099437 restraints weight = 9946.961| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.14 r_work: 0.3162 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 6670 Z= 0.258 Angle : 0.727 9.852 9073 Z= 0.370 Chirality : 0.047 0.206 959 Planarity : 0.005 0.060 1169 Dihedral : 4.907 55.013 992 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.62 % Allowed : 20.82 % Favored : 76.56 % 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: -0.35 (0.30), residues: 786 helix: 1.23 (0.29), residues: 371 sheet: 0.52 (0.88), residues: 38 loop : -1.92 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.028 0.002 PHE A 314 TYR 0.056 0.002 TYR A 521 ARG 0.007 0.001 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 4) link_NAG-ASN : angle 2.27093 ( 12) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 4.42183 ( 6) hydrogen bonds : bond 0.06635 ( 268) hydrogen bonds : angle 4.26646 ( 774) metal coordination : bond 0.00419 ( 2) SS BOND : bond 0.00759 ( 7) SS BOND : angle 2.52729 ( 14) covalent geometry : bond 0.00628 ( 6655) covalent geometry : angle 0.70730 ( 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 151 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.237 Fit side-chains REVERT: A 35 GLU cc_start: 0.7669 (mp0) cc_final: 0.7256 (mp0) REVERT: A 78 LYS cc_start: 0.8191 (tppt) cc_final: 0.7901 (ttmm) REVERT: A 179 LEU cc_start: 0.8588 (mp) cc_final: 0.8329 (mt) REVERT: A 208 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: A 271 TRP cc_start: 0.8981 (m-90) cc_final: 0.8641 (m-90) REVERT: A 282 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 341 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8091 (ptpp) REVERT: A 347 THR cc_start: 0.8591 (t) cc_final: 0.8221 (p) REVERT: A 401 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.8302 (m-70) REVERT: A 463 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8480 (t) REVERT: A 465 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8492 (ttpt) REVERT: A 559 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.8004 (ttm110) REVERT: A 581 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8310 (t) REVERT: E 459 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8338 (p) outliers start: 18 outliers final: 7 residues processed: 143 average time/residue: 1.7312 time to fit residues: 262.0863 Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 172 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 341 LYS 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 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 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: 0.9980 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 77 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 30 optimal weight: 0.0870 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 300 GLN A 552 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 = 0.3471 r_free = 0.3471 target = 0.111348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100560 restraints weight = 9965.443| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.21 r_work: 0.3190 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3476 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= 0.165 Angle : 0.664 9.417 9073 Z= 0.337 Chirality : 0.043 0.175 959 Planarity : 0.005 0.107 1169 Dihedral : 4.829 53.512 992 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.47 % Allowed : 21.11 % Favored : 76.42 % 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 (0.31), residues: 786 helix: 1.23 (0.29), residues: 372 sheet: 0.67 (0.91), residues: 36 loop : -1.86 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.025 0.002 PHE A 314 TYR 0.045 0.002 TYR A 521 ARG 0.004 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 4) link_NAG-ASN : angle 1.76976 ( 12) link_BETA1-4 : bond 0.00561 ( 2) link_BETA1-4 : angle 4.24279 ( 6) hydrogen bonds : bond 0.05445 ( 268) hydrogen bonds : angle 4.20879 ( 774) metal coordination : bond 0.00198 ( 2) SS BOND : bond 0.00720 ( 7) SS BOND : angle 2.02004 ( 14) covalent geometry : bond 0.00397 ( 6655) covalent geometry : angle 0.64772 ( 9041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6925.99 seconds wall clock time: 123 minutes 23.88 seconds (7403.88 seconds total)