Starting phenix.real_space_refine on Tue Feb 11 20:00:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ka8_37006/02_2025/8ka8_37006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ka8_37006/02_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_37006/02_2025/8ka8_37006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ka8_37006/02_2025/8ka8_37006.map" model { file = "/net/cci-nas-00/data/ceres_data/8ka8_37006/02_2025/8ka8_37006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ka8_37006/02_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-5592/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: 6.60, per 1000 atoms: 1.02 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: 1.71 Conformation dependent library (CDL) restraints added in 865.0 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: 0.60 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: 1.64 Time building geometry restraints manager: 1.95 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: 13.180 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.060 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- 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 : 0.003 0.041 6655 Z= 0.191 Angle : 0.643 10.108 9041 Z= 0.341 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 *********************** 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 : 0.733 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: 1.1689 time to fit residues: 233.1836 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 : 0.765 ------------------------------------------------------------------------------- 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 6655 Z= 0.244 Angle : 0.633 8.247 9041 Z= 0.325 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 *********************** 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 : 0.676 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: 1.1544 time to fit residues: 197.9145 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 : 0.743 ------------------------------------------------------------------------------- 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: 0.4980 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.115803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105228 restraints weight = 9705.718| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.13 r_work: 0.3253 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6655 Z= 0.246 Angle : 0.614 10.271 9041 Z= 0.314 Chirality : 0.043 0.175 959 Planarity : 0.005 0.059 1169 Dihedral : 5.312 53.536 992 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.24 % Allowed : 16.30 % 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: -0.30 (0.30), residues: 786 helix: 1.18 (0.28), residues: 371 sheet: 1.88 (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 0.015 0.001 TYR A 183 ARG 0.003 0.000 ARG E 454 *********************** 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 172 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7491 (mp0) cc_final: 0.7202 (mp0) REVERT: A 197 GLU cc_start: 0.7707 (mp0) cc_final: 0.7414 (mp0) REVERT: A 198 ASP cc_start: 0.7707 (p0) cc_final: 0.7476 (p0) REVERT: A 208 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: A 215 TYR cc_start: 0.8015 (m-10) cc_final: 0.7683 (m-10) REVERT: A 231 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7986 (ttpp) REVERT: A 282 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8243 (p) REVERT: A 341 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7991 (ptpp) REVERT: A 347 THR cc_start: 0.8572 (t) cc_final: 0.8198 (p) REVERT: A 401 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.7830 (m-70) REVERT: A 406 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: A 465 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8489 (ttpt) REVERT: A 518 ARG cc_start: 0.8471 (ttp-170) cc_final: 0.8271 (ptt90) REVERT: A 522 GLN cc_start: 0.7933 (tt0) cc_final: 0.7700 (tt0) REVERT: E 378 LYS cc_start: 0.8537 (ptpt) cc_final: 0.8322 (ptpp) REVERT: E 459 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8237 (p) outliers start: 36 outliers final: 17 residues processed: 153 average time/residue: 1.2164 time to fit residues: 195.6848 Evaluate side-chains 156 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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: 0.0040 chunk 61 optimal weight: 0.9980 chunk 62 optimal weight: 0.0040 chunk 24 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.0470 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.2302 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.115858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104887 restraints weight = 9792.840| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.20 r_work: 0.3239 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6655 Z= 0.205 Angle : 0.588 9.560 9041 Z= 0.299 Chirality : 0.042 0.170 959 Planarity : 0.004 0.058 1169 Dihedral : 4.880 53.025 992 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.51 % Allowed : 17.47 % 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: -0.19 (0.31), residues: 786 helix: 1.25 (0.29), residues: 371 sheet: 1.71 (0.85), residues: 37 loop : -1.83 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.013 0.001 TYR A 183 ARG 0.003 0.000 ARG E 466 *********************** 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 168 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7550 (mp0) cc_final: 0.7135 (mp0) REVERT: A 131 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8510 (mtpp) REVERT: A 179 LEU cc_start: 0.8480 (mp) cc_final: 0.8222 (mt) REVERT: A 197 GLU cc_start: 0.7783 (mp0) cc_final: 0.7426 (mp0) REVERT: A 198 ASP cc_start: 0.7711 (p0) cc_final: 0.7433 (p0) REVERT: A 208 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: A 210 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7393 (pp20) REVERT: A 215 TYR cc_start: 0.8102 (m-10) cc_final: 0.7827 (m-10) REVERT: A 271 TRP cc_start: 0.8960 (m-90) cc_final: 0.8691 (m-90) REVERT: A 282 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8263 (p) REVERT: A 341 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8077 (ptpp) REVERT: A 347 THR cc_start: 0.8603 (t) cc_final: 0.8260 (p) REVERT: A 401 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7859 (m-70) REVERT: A 406 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: A 465 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8511 (ttpt) REVERT: A 522 GLN cc_start: 0.7903 (tt0) cc_final: 0.7688 (tt0) REVERT: E 378 LYS cc_start: 0.8528 (ptpt) cc_final: 0.8307 (ptpp) REVERT: E 459 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8322 (p) outliers start: 31 outliers final: 14 residues processed: 152 average time/residue: 1.1594 time to fit residues: 185.2414 Evaluate side-chains 152 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 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 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 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: 0.0970 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 42 optimal weight: 0.0980 chunk 76 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.0370 chunk 12 optimal weight: 0.4980 overall best weight: 0.1656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 417 HIS E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105965 restraints weight = 9658.671| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.18 r_work: 0.3266 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6655 Z= 0.177 Angle : 0.569 8.735 9041 Z= 0.289 Chirality : 0.041 0.164 959 Planarity : 0.004 0.058 1169 Dihedral : 4.673 51.757 992 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.09 % Allowed : 17.18 % Favored : 77.73 % 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: 1.30 (0.29), residues: 371 sheet: 1.35 (0.84), residues: 37 loop : -1.77 (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 0.016 0.001 PHE A 314 TYR 0.026 0.001 TYR A 521 ARG 0.003 0.000 ARG A 518 *********************** 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 165 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.892 Fit side-chains REVERT: A 35 GLU cc_start: 0.7535 (mp0) cc_final: 0.7117 (mp0) REVERT: A 131 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8437 (mtpp) REVERT: A 179 LEU cc_start: 0.8453 (mp) cc_final: 0.8201 (mt) REVERT: A 197 GLU cc_start: 0.7768 (mp0) cc_final: 0.7422 (mp0) REVERT: A 198 ASP cc_start: 0.7719 (p0) cc_final: 0.7411 (p0) REVERT: A 208 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: A 215 TYR cc_start: 0.8169 (m-10) cc_final: 0.7878 (m-10) REVERT: A 271 TRP cc_start: 0.8950 (m-90) cc_final: 0.8656 (m-90) REVERT: A 282 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 341 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7936 (ptpp) REVERT: A 347 THR cc_start: 0.8597 (t) cc_final: 0.8252 (p) REVERT: A 401 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7791 (m-70) REVERT: A 406 GLU cc_start: 0.8001 (tt0) cc_final: 0.7736 (tt0) REVERT: A 465 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8435 (ttpt) REVERT: E 459 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8311 (p) REVERT: E 500 THR cc_start: 0.8556 (m) cc_final: 0.8316 (t) outliers start: 35 outliers final: 16 residues processed: 146 average time/residue: 1.1429 time to fit residues: 175.6648 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 : 0.897 ------------------------------------------------------------------------------- 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 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 401 HIS 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 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: 0.9980 chunk 6 optimal weight: 0.9990 chunk 68 optimal weight: 0.0170 chunk 50 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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 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 = 0.3513 r_free = 0.3513 target = 0.114767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103490 restraints weight = 9548.582| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.22 r_work: 0.3218 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6655 Z= 0.249 Angle : 0.605 10.143 9041 Z= 0.308 Chirality : 0.043 0.170 959 Planarity : 0.004 0.058 1169 Dihedral : 4.685 52.809 992 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.09 % Allowed : 17.03 % 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: -0.13 (0.31), residues: 786 helix: 1.32 (0.29), residues: 372 sheet: 1.32 (0.85), residues: 37 loop : -1.77 (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 241 PHE 0.022 0.002 PHE A 314 TYR 0.035 0.002 TYR A 521 ARG 0.004 0.001 ARG E 454 *********************** 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 166 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.689 Fit side-chains REVERT: A 35 GLU cc_start: 0.7564 (mp0) cc_final: 0.7118 (mp0) REVERT: A 131 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8442 (mtpp) REVERT: A 179 LEU cc_start: 0.8510 (mp) cc_final: 0.8267 (mt) REVERT: A 197 GLU cc_start: 0.7789 (mp0) cc_final: 0.7437 (mp0) REVERT: A 198 ASP cc_start: 0.7733 (p0) cc_final: 0.7383 (p0) REVERT: A 208 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: A 210 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7456 (pp20) REVERT: A 215 TYR cc_start: 0.8237 (m-10) cc_final: 0.8021 (m-10) REVERT: A 271 TRP cc_start: 0.8960 (m-90) cc_final: 0.8678 (m-90) REVERT: A 282 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 341 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8001 (ptpp) REVERT: A 347 THR cc_start: 0.8588 (t) cc_final: 0.8238 (p) REVERT: A 401 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7947 (m-70) REVERT: A 406 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 465 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8496 (ttpt) REVERT: A 473 TRP cc_start: 0.7355 (t-100) cc_final: 0.7043 (t-100) REVERT: E 459 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8362 (p) outliers start: 35 outliers final: 18 residues processed: 146 average time/residue: 1.1649 time to fit residues: 179.0148 Evaluate side-chains 154 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 333 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 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 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: 0.7980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.0670 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.111808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100861 restraints weight = 9448.500| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.13 r_work: 0.3187 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6655 Z= 0.361 Angle : 0.671 10.385 9041 Z= 0.346 Chirality : 0.046 0.182 959 Planarity : 0.005 0.059 1169 Dihedral : 4.946 54.531 992 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.24 % Allowed : 17.32 % 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: -0.31 (0.30), residues: 786 helix: 1.29 (0.29), residues: 369 sheet: 0.77 (0.87), residues: 36 loop : -1.92 (0.29), residues: 381 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 0.024 0.002 PHE A 314 TYR 0.029 0.002 TYR A 521 ARG 0.006 0.001 ARG E 454 *********************** 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 165 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.722 Fit side-chains REVERT: A 35 GLU cc_start: 0.7601 (mp0) cc_final: 0.7175 (mp0) REVERT: A 179 LEU cc_start: 0.8588 (mp) cc_final: 0.8331 (mt) REVERT: A 208 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: A 210 GLU cc_start: 0.7661 (pm20) cc_final: 0.7395 (pp20) REVERT: A 271 TRP cc_start: 0.8973 (m-90) cc_final: 0.8700 (m-90) REVERT: A 282 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8305 (p) REVERT: A 292 ASP cc_start: 0.7960 (t70) cc_final: 0.7715 (t0) REVERT: A 341 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8098 (ptpp) REVERT: A 347 THR cc_start: 0.8593 (t) cc_final: 0.8252 (p) REVERT: A 401 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.8208 (m-70) REVERT: A 406 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: A 465 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8518 (ttpt) REVERT: A 479 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: A 559 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7964 (ttm110) REVERT: A 581 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8304 (t) REVERT: E 378 LYS cc_start: 0.8585 (ptpt) cc_final: 0.8365 (ptpp) REVERT: E 440 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8223 (p0) REVERT: E 459 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8379 (p) outliers start: 36 outliers final: 18 residues processed: 147 average time/residue: 1.1421 time to fit residues: 176.8902 Evaluate side-chains 152 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 142 LEU 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 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 341 LYS Chi-restraints excluded: chain A residue 376 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 552 GLN ** 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 = 0.3493 r_free = 0.3493 target = 0.112654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102246 restraints weight = 9737.272| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.12 r_work: 0.3212 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6655 Z= 0.241 Angle : 0.627 9.727 9041 Z= 0.321 Chirality : 0.043 0.171 959 Planarity : 0.004 0.060 1169 Dihedral : 4.826 53.416 992 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.22 % Allowed : 18.20 % Favored : 77.58 % 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: -0.24 (0.31), residues: 786 helix: 1.35 (0.29), residues: 369 sheet: 0.67 (0.88), residues: 36 loop : -1.86 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.023 0.001 PHE A 314 TYR 0.026 0.002 TYR A 613 ARG 0.004 0.000 ARG E 454 *********************** 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: 29 poor density : 125 time to evaluate : 0.681 Fit side-chains REVERT: A 35 GLU cc_start: 0.7652 (mp0) cc_final: 0.7175 (mp0) REVERT: A 179 LEU cc_start: 0.8570 (mp) cc_final: 0.8316 (mt) REVERT: A 198 ASP cc_start: 0.7667 (p0) cc_final: 0.7302 (p0) REVERT: A 208 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: A 210 GLU cc_start: 0.7606 (pm20) cc_final: 0.7365 (pp20) REVERT: A 271 TRP cc_start: 0.8978 (m-90) cc_final: 0.8643 (m-90) REVERT: A 282 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8255 (p) REVERT: A 292 ASP cc_start: 0.7879 (t70) cc_final: 0.7623 (t0) REVERT: A 341 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8039 (ptpp) REVERT: A 347 THR cc_start: 0.8596 (t) cc_final: 0.8251 (p) REVERT: A 401 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.8040 (m-70) REVERT: A 406 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: A 463 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8308 (t) REVERT: A 465 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8486 (ttpt) REVERT: A 479 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: A 581 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8249 (t) REVERT: E 378 LYS cc_start: 0.8559 (ptpt) cc_final: 0.8321 (ptpp) REVERT: E 440 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8229 (p0) REVERT: E 459 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8351 (p) outliers start: 29 outliers final: 10 residues processed: 143 average time/residue: 1.2129 time to fit residues: 184.1944 Evaluate side-chains 142 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 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 341 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 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 440 ASN 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: 0.2980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 42 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.111591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101054 restraints weight = 9994.009| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.18 r_work: 0.3195 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6655 Z= 0.263 Angle : 0.629 9.763 9041 Z= 0.323 Chirality : 0.043 0.170 959 Planarity : 0.005 0.060 1169 Dihedral : 4.814 53.839 992 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.93 % Allowed : 19.07 % 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: -0.27 (0.31), residues: 786 helix: 1.33 (0.29), residues: 369 sheet: 0.71 (0.90), residues: 36 loop : -1.91 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.024 0.002 PHE A 314 TYR 0.026 0.002 TYR A 613 ARG 0.004 0.000 ARG E 454 *********************** 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 152 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.665 Fit side-chains REVERT: A 35 GLU cc_start: 0.7645 (mp0) cc_final: 0.7216 (mp0) REVERT: A 179 LEU cc_start: 0.8547 (mp) cc_final: 0.8285 (mt) REVERT: A 208 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: A 210 GLU cc_start: 0.7618 (pm20) cc_final: 0.7370 (pp20) REVERT: A 271 TRP cc_start: 0.8978 (m-90) cc_final: 0.8648 (m-90) REVERT: A 282 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8256 (p) REVERT: A 292 ASP cc_start: 0.7935 (t70) cc_final: 0.7685 (t0) REVERT: A 347 THR cc_start: 0.8582 (t) cc_final: 0.8225 (p) REVERT: A 376 MET cc_start: 0.8652 (ttm) cc_final: 0.8328 (mtt) REVERT: A 401 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.8062 (m-70) REVERT: A 406 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 463 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8278 (p) REVERT: A 465 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8526 (ttpt) REVERT: A 479 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: A 581 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8269 (t) REVERT: E 440 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8242 (p0) REVERT: E 459 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8374 (p) outliers start: 27 outliers final: 11 residues processed: 141 average time/residue: 1.1475 time to fit residues: 170.8099 Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 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 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: 0.0370 chunk 57 optimal weight: 0.0670 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.2794 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101420 restraints weight = 9930.466| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.16 r_work: 0.3205 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6655 Z= 0.242 Angle : 0.617 9.440 9041 Z= 0.316 Chirality : 0.043 0.170 959 Planarity : 0.004 0.060 1169 Dihedral : 4.757 53.466 992 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.35 % Allowed : 19.65 % 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: -0.24 (0.31), residues: 786 helix: 1.36 (0.29), residues: 369 sheet: 0.66 (0.90), residues: 36 loop : -1.88 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.026 0.001 PHE A 314 TYR 0.023 0.002 TYR A 613 ARG 0.004 0.000 ARG E 454 ********************** 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 148 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.721 Fit side-chains REVERT: A 35 GLU cc_start: 0.7616 (mp0) cc_final: 0.7203 (mp0) REVERT: A 131 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8471 (mtpp) REVERT: A 179 LEU cc_start: 0.8547 (mp) cc_final: 0.8291 (mt) REVERT: A 208 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: A 210 GLU cc_start: 0.7572 (pm20) cc_final: 0.7337 (pp20) REVERT: A 271 TRP cc_start: 0.8972 (m-90) cc_final: 0.8651 (m-90) REVERT: A 282 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8255 (p) REVERT: A 347 THR cc_start: 0.8586 (t) cc_final: 0.8241 (p) REVERT: A 376 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8346 (mtt) REVERT: A 401 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8102 (m-70) REVERT: A 406 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: A 463 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8272 (p) REVERT: A 465 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8490 (ttpt) REVERT: A 479 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: A 581 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8251 (t) REVERT: E 440 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8250 (p0) REVERT: E 459 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8354 (p) REVERT: E 519 HIS cc_start: 0.7058 (t-90) cc_final: 0.6728 (t-90) outliers start: 23 outliers final: 10 residues processed: 139 average time/residue: 1.1366 time to fit residues: 166.7652 Evaluate side-chains 144 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 143 LEU 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 376 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 463 VAL Chi-restraints excluded: chain A residue 479 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 367 VAL Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.111621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100684 restraints weight = 9953.382| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.24 r_work: 0.3191 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6655 Z= 0.268 Angle : 0.632 9.420 9041 Z= 0.325 Chirality : 0.044 0.171 959 Planarity : 0.005 0.060 1169 Dihedral : 4.779 53.928 992 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.64 % Allowed : 19.36 % 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: -0.28 (0.31), residues: 786 helix: 1.31 (0.29), residues: 369 sheet: 0.60 (0.89), residues: 36 loop : -1.88 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.027 0.002 PHE A 314 TYR 0.038 0.002 TYR A 521 ARG 0.004 0.000 ARG E 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5537.89 seconds wall clock time: 99 minutes 6.75 seconds (5946.75 seconds total)