Starting phenix.real_space_refine on Fri Jul 19 05:07:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/07_2024/8ka8_37006_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/07_2024/8ka8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/07_2024/8ka8_37006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/07_2024/8ka8_37006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/07_2024/8ka8_37006_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/07_2024/8ka8_37006_neut.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 Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.77, per 1000 atoms: 1.20 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 - 3.50 Amino acid : False - 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: 2.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.68 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: 1.78 Time building geometry restraints manager: 3.07 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: 98.46 - 105.58: 134 105.58 - 112.71: 3316 112.71 - 119.83: 2344 119.83 - 126.96: 3143 126.96 - 134.09: 104 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 2.520 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 2.440 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.216 2.440 ... (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 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: 13.740 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 27.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 0.769 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: 1.1047 time to fit residues: 220.7692 Evaluate side-chains 150 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.4980 chunk 59 optimal weight: 0.0040 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 31 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 overall best weight: 0.1106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 493 HIS A 522 GLN A 531 GLN E 354 ASN E 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6655 Z= 0.159 Angle : 0.577 7.664 9041 Z= 0.293 Chirality : 0.041 0.190 959 Planarity : 0.004 0.059 1169 Dihedral : 5.917 52.834 992 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.78 % Allowed : 13.39 % Favored : 82.82 % 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: 1.20 (0.29), residues: 367 sheet: 2.07 (0.92), residues: 37 loop : -1.93 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 PHE 0.011 0.001 PHE A 327 TYR 0.017 0.001 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 178 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7659 (tppt) cc_final: 0.7425 (tppp) REVERT: A 208 GLU cc_start: 0.7315 (tp30) cc_final: 0.7041 (tt0) REVERT: A 231 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7536 (ttpp) REVERT: A 341 LYS cc_start: 0.7884 (pmmt) cc_final: 0.7627 (ptpp) REVERT: A 347 THR cc_start: 0.8387 (t) cc_final: 0.8076 (p) REVERT: A 368 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6833 (m110) REVERT: A 401 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7420 (m-70) REVERT: A 406 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: A 465 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7910 (ttpp) REVERT: A 557 MET cc_start: 0.7754 (tmm) cc_final: 0.7524 (tmm) REVERT: E 467 ASP cc_start: 0.7056 (p0) cc_final: 0.6728 (p0) REVERT: E 500 THR cc_start: 0.8422 (m) cc_final: 0.8185 (t) outliers start: 26 outliers final: 9 residues processed: 161 average time/residue: 1.0800 time to fit residues: 183.3477 Evaluate side-chains 156 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 210 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 368 ASN 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 602 SER Chi-restraints excluded: chain E residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.0040 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 56 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 60 GLN A 96 GLN A 522 GLN E 354 ASN ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2174 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= 0.261 Angle : 0.623 10.756 9041 Z= 0.317 Chirality : 0.044 0.193 959 Planarity : 0.005 0.058 1169 Dihedral : 5.416 53.973 992 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.51 % Allowed : 17.61 % 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: -0.21 (0.31), residues: 786 helix: 1.27 (0.29), residues: 371 sheet: 1.91 (0.88), residues: 37 loop : -1.90 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 163 HIS 0.011 0.002 HIS A 374 PHE 0.013 0.002 PHE E 377 TYR 0.026 0.002 TYR A 521 ARG 0.003 0.000 ARG A 357 *********************** 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 168 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7875 (tppt) cc_final: 0.7597 (tppp) REVERT: A 121 ASN cc_start: 0.8418 (m-40) cc_final: 0.8205 (m-40) REVERT: A 131 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8345 (mtpp) REVERT: A 208 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: A 231 LYS cc_start: 0.7822 (ttmm) cc_final: 0.7571 (ttpp) REVERT: A 341 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7880 (ptpp) REVERT: A 347 THR cc_start: 0.8417 (t) cc_final: 0.8062 (p) REVERT: A 401 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7592 (m-70) REVERT: A 406 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: A 465 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7887 (ttpp) REVERT: A 600 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7471 (ttmm) REVERT: E 459 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8109 (p) REVERT: E 467 ASP cc_start: 0.6953 (p0) cc_final: 0.6675 (p0) outliers start: 31 outliers final: 16 residues processed: 150 average time/residue: 1.1544 time to fit residues: 182.0280 Evaluate side-chains 153 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 445 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 522 GLN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6655 Z= 0.384 Angle : 0.694 10.509 9041 Z= 0.356 Chirality : 0.046 0.206 959 Planarity : 0.005 0.057 1169 Dihedral : 5.350 55.716 992 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 5.68 % Allowed : 16.30 % 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: -0.39 (0.30), residues: 786 helix: 1.21 (0.29), residues: 363 sheet: 1.31 (0.86), residues: 38 loop : -1.98 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 163 HIS 0.008 0.002 HIS A 241 PHE 0.017 0.002 PHE A 327 TYR 0.024 0.002 TYR A 183 ARG 0.008 0.001 ARG E 454 *********************** 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 174 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7127 (mp0) cc_final: 0.6759 (mp0) REVERT: A 78 LYS cc_start: 0.7995 (tppt) cc_final: 0.7740 (ttmm) REVERT: A 121 ASN cc_start: 0.8541 (m-40) cc_final: 0.8330 (m-40) REVERT: A 131 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8313 (mtpp) REVERT: A 179 LEU cc_start: 0.8433 (mp) cc_final: 0.8194 (mt) REVERT: A 324 THR cc_start: 0.8296 (m) cc_final: 0.8009 (p) REVERT: A 341 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7869 (ptpp) REVERT: A 347 THR cc_start: 0.8424 (t) cc_final: 0.8102 (p) REVERT: A 401 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.8138 (m-70) REVERT: A 406 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: A 465 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7920 (ttpp) REVERT: A 467 ASP cc_start: 0.7601 (m-30) cc_final: 0.7393 (m-30) REVERT: A 493 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8623 (m170) REVERT: A 559 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7430 (ttm110) REVERT: A 600 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7482 (ttmm) REVERT: E 459 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8215 (p) outliers start: 39 outliers final: 20 residues processed: 155 average time/residue: 1.0326 time to fit residues: 169.2393 Evaluate side-chains 155 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 257 SER Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 341 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 493 HIS Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.2980 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 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 34 GLN A 552 GLN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3011 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= 0.246 Angle : 0.625 9.660 9041 Z= 0.320 Chirality : 0.043 0.170 959 Planarity : 0.005 0.081 1169 Dihedral : 5.197 54.843 992 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.08 % Allowed : 18.20 % 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: -0.32 (0.30), residues: 786 helix: 1.28 (0.29), residues: 362 sheet: 1.10 (0.86), residues: 38 loop : -1.92 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.014 0.001 PHE A 327 TYR 0.022 0.002 TYR A 613 ARG 0.003 0.000 ARG E 454 *********************** 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 154 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7055 (mp-120) REVERT: A 35 GLU cc_start: 0.7126 (mp0) cc_final: 0.6799 (mp0) REVERT: A 78 LYS cc_start: 0.7986 (tppt) cc_final: 0.7667 (ttmm) REVERT: A 121 ASN cc_start: 0.8503 (m-40) cc_final: 0.8268 (m-40) REVERT: A 131 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8274 (mtpp) REVERT: A 179 LEU cc_start: 0.8401 (mp) cc_final: 0.8174 (mt) REVERT: A 324 THR cc_start: 0.8272 (m) cc_final: 0.8007 (p) REVERT: A 341 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7817 (ptpp) REVERT: A 347 THR cc_start: 0.8435 (t) cc_final: 0.8110 (p) REVERT: A 376 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7995 (mtt) REVERT: A 401 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.7984 (m-70) REVERT: A 465 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7807 (ttpp) REVERT: A 559 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7398 (ttm110) REVERT: E 378 LYS cc_start: 0.8240 (ptpt) cc_final: 0.8022 (ptpp) REVERT: E 459 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8234 (p) REVERT: E 506 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8238 (mt0) outliers start: 28 outliers final: 13 residues processed: 139 average time/residue: 1.2047 time to fit residues: 176.2811 Evaluate side-chains 142 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 341 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 479 GLU 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 Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.0870 chunk 18 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 552 GLN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6655 Z= 0.220 Angle : 0.600 9.059 9041 Z= 0.306 Chirality : 0.042 0.169 959 Planarity : 0.005 0.069 1169 Dihedral : 5.030 54.230 992 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.09 % Allowed : 18.05 % Favored : 76.86 % 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: 1.32 (0.29), residues: 362 sheet: 0.94 (0.86), residues: 38 loop : -1.91 (0.29), residues: 386 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 0.011 0.001 PHE A 327 TYR 0.023 0.001 TYR A 613 ARG 0.002 0.000 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 161 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7129 (mp0) cc_final: 0.6769 (mp0) REVERT: A 78 LYS cc_start: 0.7971 (tppt) cc_final: 0.7646 (ttmm) REVERT: A 121 ASN cc_start: 0.8488 (m-40) cc_final: 0.8269 (m-40) REVERT: A 131 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8300 (mtpp) REVERT: A 179 LEU cc_start: 0.8389 (mp) cc_final: 0.8162 (mt) REVERT: A 323 MET cc_start: 0.8494 (mmt) cc_final: 0.8266 (mmm) REVERT: A 324 THR cc_start: 0.8274 (m) cc_final: 0.8032 (p) REVERT: A 341 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7809 (ptpp) REVERT: A 347 THR cc_start: 0.8444 (t) cc_final: 0.8118 (p) REVERT: A 376 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7946 (mtt) REVERT: A 401 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7897 (m-70) REVERT: A 465 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7824 (ttpp) REVERT: E 378 LYS cc_start: 0.8227 (ptpt) cc_final: 0.8024 (ptpp) REVERT: E 506 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8179 (mt0) outliers start: 35 outliers final: 16 residues processed: 144 average time/residue: 1.0403 time to fit residues: 158.6652 Evaluate side-chains 142 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 231 LYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 341 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 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 503 VAL Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 30 optimal weight: 0.2980 chunk 44 optimal weight: 0.1980 chunk 22 optimal weight: 0.4980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3104 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= 0.224 Angle : 0.606 10.793 9041 Z= 0.308 Chirality : 0.042 0.169 959 Planarity : 0.005 0.059 1169 Dihedral : 4.885 53.838 992 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.35 % Allowed : 18.49 % Favored : 78.17 % 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 (0.30), residues: 786 helix: 1.36 (0.29), residues: 368 sheet: 0.92 (0.91), residues: 36 loop : -1.96 (0.29), residues: 382 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 0.014 0.001 PHE A 28 TYR 0.024 0.001 TYR A 613 ARG 0.003 0.000 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 147 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7127 (mp0) cc_final: 0.6734 (mp0) REVERT: A 78 LYS cc_start: 0.7953 (tppt) cc_final: 0.7628 (ttmm) REVERT: A 121 ASN cc_start: 0.8449 (m-40) cc_final: 0.8237 (m-40) REVERT: A 131 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8286 (mtpp) REVERT: A 179 LEU cc_start: 0.8408 (mp) cc_final: 0.8171 (mt) REVERT: A 324 THR cc_start: 0.8322 (m) cc_final: 0.8087 (p) REVERT: A 347 THR cc_start: 0.8453 (t) cc_final: 0.8121 (p) REVERT: A 376 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7977 (mtt) REVERT: A 401 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7892 (m-70) REVERT: A 465 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7825 (ttpp) REVERT: E 378 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7989 (ptpp) REVERT: E 506 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8155 (mt0) outliers start: 23 outliers final: 13 residues processed: 139 average time/residue: 1.0762 time to fit residues: 158.0624 Evaluate side-chains 138 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 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 119 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 231 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 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 503 VAL Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 68 optimal weight: 0.0070 chunk 72 optimal weight: 0.0030 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 60 GLN A 368 ASN E 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3261 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= 0.246 Angle : 0.618 10.132 9041 Z= 0.315 Chirality : 0.043 0.170 959 Planarity : 0.005 0.060 1169 Dihedral : 4.842 54.026 992 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.64 % Allowed : 18.92 % 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: -0.29 (0.30), residues: 786 helix: 1.35 (0.29), residues: 368 sheet: 0.77 (0.90), residues: 36 loop : -1.95 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 28 TYR 0.024 0.002 TYR A 613 ARG 0.003 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 150 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7142 (mp0) cc_final: 0.6739 (mp0) REVERT: A 78 LYS cc_start: 0.7964 (tppt) cc_final: 0.7645 (ttmm) REVERT: A 117 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7807 (m-40) REVERT: A 121 ASN cc_start: 0.8467 (m-40) cc_final: 0.8255 (m-40) REVERT: A 131 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8282 (mtpp) REVERT: A 142 LEU cc_start: 0.8169 (mm) cc_final: 0.7944 (mt) REVERT: A 179 LEU cc_start: 0.8400 (mp) cc_final: 0.8165 (mt) REVERT: A 292 ASP cc_start: 0.7760 (t70) cc_final: 0.7537 (t0) REVERT: A 324 THR cc_start: 0.8274 (m) cc_final: 0.8056 (p) REVERT: A 347 THR cc_start: 0.8442 (t) cc_final: 0.8117 (p) REVERT: A 376 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7988 (mtt) REVERT: A 401 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7904 (m-70) REVERT: A 465 LYS cc_start: 0.8284 (ttpt) cc_final: 0.7895 (ttpp) REVERT: E 378 LYS cc_start: 0.8227 (ptpt) cc_final: 0.7993 (ptpp) outliers start: 25 outliers final: 15 residues processed: 140 average time/residue: 1.1031 time to fit residues: 162.8118 Evaluate side-chains 141 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 117 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU 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 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 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 63 optimal weight: 0.2980 chunk 66 optimal weight: 0.3980 chunk 69 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 60 GLN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6655 Z= 0.278 Angle : 0.635 9.859 9041 Z= 0.324 Chirality : 0.043 0.172 959 Planarity : 0.005 0.060 1169 Dihedral : 4.885 54.366 992 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.49 % Allowed : 18.63 % 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: -0.29 (0.30), residues: 786 helix: 1.32 (0.29), residues: 369 sheet: 0.68 (0.89), residues: 36 loop : -1.92 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 473 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 28 TYR 0.028 0.002 TYR A 613 ARG 0.003 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 fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 0.698 Fit side-chains REVERT: A 35 GLU cc_start: 0.7154 (mp0) cc_final: 0.6758 (mp0) REVERT: A 78 LYS cc_start: 0.7964 (tppt) cc_final: 0.7654 (ttmm) REVERT: A 117 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7828 (m-40) REVERT: A 121 ASN cc_start: 0.8498 (m-40) cc_final: 0.8292 (m-40) REVERT: A 131 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8298 (mtpp) REVERT: A 142 LEU cc_start: 0.8164 (mm) cc_final: 0.7930 (mt) REVERT: A 179 LEU cc_start: 0.8382 (mp) cc_final: 0.8140 (mt) REVERT: A 324 THR cc_start: 0.8328 (m) cc_final: 0.8100 (p) REVERT: A 347 THR cc_start: 0.8438 (t) cc_final: 0.8115 (p) REVERT: A 401 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7977 (m-70) REVERT: A 463 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8230 (p) REVERT: A 465 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7807 (ttpp) REVERT: A 467 ASP cc_start: 0.7646 (m-30) cc_final: 0.7017 (m-30) REVERT: A 479 GLU cc_start: 0.7219 (pp20) cc_final: 0.6969 (tm-30) REVERT: A 559 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7502 (ttm110) REVERT: E 378 LYS cc_start: 0.8246 (ptpt) cc_final: 0.8019 (ptpp) outliers start: 24 outliers final: 18 residues processed: 143 average time/residue: 1.1608 time to fit residues: 175.3651 Evaluate side-chains 145 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 117 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU 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 463 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 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 chunk 57 optimal weight: 0.0670 chunk 9 optimal weight: 0.2980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6655 Z= 0.215 Angle : 0.613 8.898 9041 Z= 0.312 Chirality : 0.042 0.169 959 Planarity : 0.005 0.101 1169 Dihedral : 4.787 53.278 992 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.62 % Allowed : 20.38 % 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: -0.23 (0.31), residues: 786 helix: 1.38 (0.29), residues: 368 sheet: 0.63 (0.88), residues: 36 loop : -1.89 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 473 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 28 TYR 0.029 0.001 TYR A 50 ARG 0.003 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 143 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.760 Fit side-chains REVERT: A 35 GLU cc_start: 0.7149 (mp0) cc_final: 0.6793 (mp0) REVERT: A 78 LYS cc_start: 0.7946 (tppt) cc_final: 0.7657 (ttmm) REVERT: A 131 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8286 (mtpp) REVERT: A 142 LEU cc_start: 0.8158 (mm) cc_final: 0.7934 (mt) REVERT: A 179 LEU cc_start: 0.8366 (mp) cc_final: 0.8126 (mt) REVERT: A 324 THR cc_start: 0.8274 (m) cc_final: 0.8056 (p) REVERT: A 347 THR cc_start: 0.8434 (t) cc_final: 0.8109 (p) REVERT: A 376 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7973 (mtt) REVERT: A 401 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7927 (m-70) REVERT: A 465 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7902 (ttpp) REVERT: A 467 ASP cc_start: 0.7618 (m-30) cc_final: 0.7051 (m-30) REVERT: A 479 GLU cc_start: 0.7196 (pp20) cc_final: 0.6941 (tm-30) REVERT: E 500 THR cc_start: 0.8613 (m) cc_final: 0.8338 (t) REVERT: E 519 HIS cc_start: 0.6316 (t-90) cc_final: 0.6064 (t-90) outliers start: 18 outliers final: 13 residues processed: 136 average time/residue: 1.1822 time to fit residues: 170.0760 Evaluate side-chains 137 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 360 MET 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 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 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.0050 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 60 GLN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100776 restraints weight = 9746.078| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.20 r_work: 0.3192 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6655 Z= 0.269 Angle : 0.627 9.242 9041 Z= 0.321 Chirality : 0.043 0.172 959 Planarity : 0.005 0.098 1169 Dihedral : 4.819 53.829 992 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.62 % Allowed : 20.96 % 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: -0.28 (0.30), residues: 786 helix: 1.35 (0.29), residues: 368 sheet: 0.45 (0.85), residues: 38 loop : -1.92 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 28 TYR 0.028 0.002 TYR A 50 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: 3746.06 seconds wall clock time: 67 minutes 38.82 seconds (4058.82 seconds total)