Starting phenix.real_space_refine on Sat Aug 3 01:52:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/08_2024/8ka8_37006.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/08_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_37006/08_2024/8ka8_37006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/08_2024/8ka8_37006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/08_2024/8ka8_37006.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ka8_37006/08_2024/8ka8_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 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-5409/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: 6.68, per 1000 atoms: 1.03 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 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: 0.72 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: 1.56 Time building geometry restraints manager: 2.81 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 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: 9.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.180 Process input model: 25.800 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:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.620 ------------------------------------------------------------------------------- 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 : 0.676 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: 1.1125 time to fit residues: 222.2245 Evaluate side-chains 150 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7784 (tppt) cc_final: 0.7570 (tppp) REVERT: A 208 GLU cc_start: 0.7333 (tp30) cc_final: 0.7094 (tt0) REVERT: A 231 LYS cc_start: 0.7809 (ttmm) cc_final: 0.7591 (ttpp) REVERT: A 341 LYS cc_start: 0.8057 (pmmt) cc_final: 0.7823 (ptpp) REVERT: A 347 THR cc_start: 0.8370 (t) cc_final: 0.8029 (p) REVERT: A 401 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7485 (m-70) REVERT: A 406 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: A 470 LYS cc_start: 0.8037 (mppt) cc_final: 0.7791 (mppt) REVERT: A 518 ARG cc_start: 0.8156 (ttp-170) cc_final: 0.7918 (ptt90) REVERT: A 557 MET cc_start: 0.7815 (tmm) cc_final: 0.7526 (tmm) REVERT: E 459 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8035 (p) outliers start: 28 outliers final: 12 residues processed: 163 average time/residue: 1.1779 time to fit residues: 201.8840 Evaluate side-chains 158 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 0.0470 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2463 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= 0.275 Angle : 0.635 10.674 9041 Z= 0.326 Chirality : 0.044 0.179 959 Planarity : 0.005 0.058 1169 Dihedral : 5.330 53.978 992 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.24 % Allowed : 15.87 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.29), residues: 372 sheet: 1.82 (0.87), residues: 37 loop : -1.96 (0.29), residues: 377 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 0.017 0.002 TYR A 183 ARG 0.004 0.001 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 170 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7103 (mp0) cc_final: 0.6776 (mp0) REVERT: A 78 LYS cc_start: 0.7896 (tppt) cc_final: 0.7581 (tppp) REVERT: A 179 LEU cc_start: 0.8389 (mp) cc_final: 0.8147 (mt) REVERT: A 197 GLU cc_start: 0.6841 (mp0) cc_final: 0.6633 (mp0) REVERT: A 208 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: A 282 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 341 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7891 (ptpp) REVERT: A 347 THR cc_start: 0.8433 (t) cc_final: 0.8089 (p) REVERT: A 401 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7730 (m-70) REVERT: A 406 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: A 465 LYS cc_start: 0.8307 (ttpt) cc_final: 0.7933 (ttpt) REVERT: A 479 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: A 518 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7977 (ptt90) REVERT: E 459 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8132 (p) outliers start: 36 outliers final: 17 residues processed: 152 average time/residue: 1.1349 time to fit residues: 181.7500 Evaluate side-chains 151 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 459 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN E 334 ASN E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2880 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= 0.357 Angle : 0.669 10.459 9041 Z= 0.345 Chirality : 0.045 0.190 959 Planarity : 0.005 0.061 1169 Dihedral : 5.195 54.919 992 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.53 % Allowed : 16.01 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.30), residues: 786 helix: 1.14 (0.29), residues: 371 sheet: 1.18 (0.86), residues: 38 loop : -2.00 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.017 0.002 PHE A 327 TYR 0.021 0.002 TYR A 183 ARG 0.006 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 171 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 0.721 Fit side-chains REVERT: A 35 GLU cc_start: 0.7149 (mp0) cc_final: 0.6754 (mp0) REVERT: A 78 LYS cc_start: 0.7960 (tppt) cc_final: 0.7691 (ttmm) REVERT: A 179 LEU cc_start: 0.8439 (mp) cc_final: 0.8198 (mt) REVERT: A 197 GLU cc_start: 0.6889 (mp0) cc_final: 0.6616 (mp0) REVERT: A 198 ASP cc_start: 0.7043 (p0) cc_final: 0.6840 (p0) REVERT: A 271 TRP cc_start: 0.8877 (m-90) cc_final: 0.8641 (m-90) REVERT: A 282 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8190 (p) REVERT: A 341 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7970 (ptpp) REVERT: A 347 THR cc_start: 0.8449 (t) cc_final: 0.8110 (p) REVERT: A 401 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7951 (m-70) REVERT: A 406 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: A 465 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7867 (ttpt) REVERT: A 518 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7982 (ptt90) REVERT: A 559 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7397 (ttm110) REVERT: A 600 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7513 (ttmm) REVERT: E 378 LYS cc_start: 0.8261 (ptpt) cc_final: 0.8045 (ptpp) REVERT: E 459 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8193 (p) REVERT: E 500 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8273 (m) outliers start: 38 outliers final: 18 residues processed: 149 average time/residue: 1.1148 time to fit residues: 175.1865 Evaluate side-chains 152 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 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 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 231 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 500 THR 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: 0.3980 chunk 56 optimal weight: 0.0870 chunk 31 optimal weight: 0.1980 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 0.0670 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 0.4980 overall best weight: 0.1696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 60 GLN A 552 GLN E 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6655 Z= 0.188 Angle : 0.597 9.177 9041 Z= 0.304 Chirality : 0.041 0.166 959 Planarity : 0.004 0.060 1169 Dihedral : 4.985 53.304 992 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.80 % Allowed : 17.61 % 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: -0.32 (0.30), residues: 786 helix: 1.18 (0.29), residues: 375 sheet: 1.23 (0.85), residues: 37 loop : -1.91 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 473 HIS 0.004 0.001 HIS A 241 PHE 0.018 0.001 PHE A 314 TYR 0.014 0.001 TYR A 207 ARG 0.002 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 161 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 0.756 Fit side-chains REVERT: A 35 GLU cc_start: 0.7129 (mp0) cc_final: 0.6734 (mp0) REVERT: A 78 LYS cc_start: 0.7894 (tppt) cc_final: 0.7556 (ttmm) REVERT: A 179 LEU cc_start: 0.8405 (mp) cc_final: 0.8166 (mt) REVERT: A 197 GLU cc_start: 0.6871 (mp0) cc_final: 0.6619 (mp0) REVERT: A 271 TRP cc_start: 0.8857 (m-90) cc_final: 0.8656 (m-90) REVERT: A 282 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8170 (p) REVERT: A 341 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7837 (ptpp) REVERT: A 347 THR cc_start: 0.8448 (t) cc_final: 0.8095 (p) REVERT: A 401 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7807 (m-70) REVERT: A 406 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: A 463 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8137 (t) REVERT: A 465 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8030 (ttpt) REVERT: E 378 LYS cc_start: 0.8240 (ptpt) cc_final: 0.8035 (ptpp) REVERT: E 459 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8188 (p) REVERT: E 500 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8192 (p) outliers start: 33 outliers final: 13 residues processed: 146 average time/residue: 1.2103 time to fit residues: 186.1522 Evaluate side-chains 145 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 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 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 500 THR Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.3242 > 50: distance: 25 - 44: 19.423 distance: 29 - 53: 30.515 distance: 36 - 61: 34.054 distance: 40 - 44: 22.667 distance: 41 - 66: 31.939 distance: 44 - 45: 33.454 distance: 45 - 46: 28.209 distance: 45 - 48: 18.648 distance: 46 - 47: 25.565 distance: 46 - 53: 37.845 distance: 48 - 49: 35.346 distance: 49 - 50: 27.373 distance: 50 - 51: 7.562 distance: 51 - 52: 21.256 distance: 53 - 54: 36.227 distance: 54 - 55: 31.241 distance: 54 - 57: 11.478 distance: 55 - 56: 24.282 distance: 55 - 61: 34.946 distance: 57 - 58: 22.079 distance: 58 - 59: 31.145 distance: 58 - 60: 29.761 distance: 61 - 62: 40.066 distance: 62 - 63: 13.493 distance: 62 - 65: 35.228 distance: 63 - 64: 39.096 distance: 63 - 66: 45.027 distance: 66 - 67: 40.256 distance: 67 - 68: 41.074 distance: 67 - 70: 43.923 distance: 68 - 69: 25.044 distance: 68 - 75: 25.513 distance: 70 - 71: 29.429 distance: 71 - 72: 22.635 distance: 72 - 73: 26.277 distance: 73 - 74: 22.392 distance: 75 - 76: 23.238 distance: 76 - 77: 21.500 distance: 76 - 79: 13.756 distance: 77 - 78: 29.758 distance: 77 - 83: 35.398 distance: 79 - 80: 27.712 distance: 80 - 81: 23.243 distance: 80 - 82: 21.174 distance: 82 - 174: 21.338 distance: 83 - 84: 7.641 distance: 84 - 85: 14.279 distance: 84 - 87: 43.174 distance: 85 - 86: 37.601 distance: 85 - 95: 34.430 distance: 87 - 88: 23.704 distance: 88 - 89: 23.894 distance: 88 - 90: 25.073 distance: 89 - 91: 26.178 distance: 90 - 92: 33.004 distance: 91 - 93: 18.195 distance: 92 - 93: 46.495 distance: 93 - 94: 23.795 distance: 95 - 96: 29.840 distance: 96 - 97: 31.636 distance: 96 - 99: 31.050 distance: 97 - 98: 12.779 distance: 97 - 101: 12.959 distance: 99 - 100: 38.337 distance: 101 - 102: 26.548 distance: 102 - 103: 28.296 distance: 102 - 105: 38.196 distance: 103 - 104: 21.855 distance: 103 - 109: 29.979 distance: 105 - 106: 34.265 distance: 106 - 107: 17.686 distance: 106 - 108: 24.053 distance: 109 - 110: 20.699 distance: 110 - 111: 19.751 distance: 110 - 113: 23.819 distance: 111 - 112: 26.610 distance: 111 - 118: 29.961 distance: 113 - 114: 29.557 distance: 114 - 115: 7.241 distance: 115 - 116: 25.335 distance: 115 - 117: 23.224 distance: 118 - 119: 11.675 distance: 119 - 120: 28.414 distance: 119 - 122: 13.412 distance: 120 - 121: 22.685 distance: 120 - 127: 8.401 distance: 122 - 123: 9.127 distance: 124 - 125: 18.076 distance: 124 - 126: 27.991