Starting phenix.real_space_refine on Sat Aug 3 01:03:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlr_37629/08_2024/8wlr_37629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlr_37629/08_2024/8wlr_37629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlr_37629/08_2024/8wlr_37629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlr_37629/08_2024/8wlr_37629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlr_37629/08_2024/8wlr_37629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlr_37629/08_2024/8wlr_37629.cif" } resolution = 3.12 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= 0.001 sd= 0.043 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 37 5.16 5 C 4107 2.51 5 N 1063 2.21 5 O 1223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 216": "OD1" <-> "OD2" Residue "B TYR 369": "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: 6431 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4873 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.25, per 1000 atoms: 0.82 Number of scatterers: 6431 At special positions: 0 Unit cell: (85, 84.15, 118.15, 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 37 16.00 O 1223 8.00 N 1063 7.00 C 4107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 2.55 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 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 56.3% alpha, 5.9% 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 21 through 53 removed outlier: 3.623A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 82 removed outlier: 3.788A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.945A pdb=" N GLN A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.851A pdb=" N ALA A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.225A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.728A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 250 removed outlier: 4.001A pdb=" N THR A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.197A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) 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 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.544A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.908A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.720A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.604A pdb=" N ARG A 393 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.009A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.651A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.909A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.699A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.873A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.865A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 removed outlier: 3.510A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.609A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.642A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.705A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.987A 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 352 removed outlier: 6.183A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 281 hydrogen bonds defined for protein. 792 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: 1.60 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2065 1.34 - 1.46: 1587 1.46 - 1.58: 2898 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6608 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" CA ASP A 216 " pdb=" CB ASP A 216 " ideal model delta sigma weight residual 1.535 1.557 -0.023 1.93e-02 2.68e+03 1.36e+00 bond pdb=" CB ASP A 216 " pdb=" CG ASP A 216 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" C ASP A 36 " pdb=" O ASP A 36 " ideal model delta sigma weight residual 1.237 1.249 -0.013 1.19e-02 7.06e+03 1.17e+00 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 6603 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.89: 204 106.89 - 113.71: 3499 113.71 - 120.54: 2836 120.54 - 127.36: 2345 127.36 - 134.19: 89 Bond angle restraints: 8973 Sorted by residual: angle pdb=" C ALA A 384 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " ideal model delta sigma weight residual 122.65 117.89 4.76 1.66e+00 3.63e-01 8.22e+00 angle pdb=" N ASN B 343 " pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 108.49 104.37 4.12 1.65e+00 3.67e-01 6.23e+00 angle pdb=" CA TYR A 385 " pdb=" CB TYR A 385 " pdb=" CG TYR A 385 " ideal model delta sigma weight residual 113.90 118.38 -4.48 1.80e+00 3.09e-01 6.19e+00 angle pdb=" CA ASP A 216 " pdb=" CB ASP A 216 " pdb=" CG ASP A 216 " ideal model delta sigma weight residual 112.60 114.82 -2.22 1.00e+00 1.00e+00 4.92e+00 angle pdb=" CB MET A 249 " pdb=" CG MET A 249 " pdb=" SD MET A 249 " ideal model delta sigma weight residual 112.70 119.22 -6.52 3.00e+00 1.11e-01 4.73e+00 ... (remaining 8968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 3369 16.89 - 33.79: 408 33.79 - 50.68: 112 50.68 - 67.57: 26 67.57 - 84.46: 7 Dihedral angle restraints: 3922 sinusoidal: 1598 harmonic: 2324 Sorted by residual: dihedral pdb=" CG ARG A 340 " pdb=" CD ARG A 340 " pdb=" NE ARG A 340 " pdb=" CZ ARG A 340 " ideal model delta sinusoidal sigma weight residual -180.00 -136.27 -43.73 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA PHE B 342 " pdb=" C PHE B 342 " pdb=" N ASN B 343 " pdb=" CA ASN B 343 " ideal model delta harmonic sigma weight residual -180.00 -164.41 -15.59 0 5.00e+00 4.00e-02 9.72e+00 dihedral pdb=" CA ASP A 368 " pdb=" CB ASP A 368 " pdb=" CG ASP A 368 " pdb=" OD1 ASP A 368 " ideal model delta sinusoidal sigma weight residual -30.00 -83.30 53.30 1 2.00e+01 2.50e-03 9.66e+00 ... (remaining 3919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 735 0.049 - 0.097: 170 0.097 - 0.146: 33 0.146 - 0.195: 0 0.195 - 0.243: 1 Chirality restraints: 939 Sorted by residual: chirality pdb=" CA ASN B 343 " pdb=" N ASN B 343 " pdb=" C ASN B 343 " pdb=" CB ASN B 343 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C5 NAG B1301 " pdb=" C4 NAG B1301 " pdb=" C6 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 936 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 146 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO B 521 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 522 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C GLN A 522 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN A 522 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 523 " 0.010 2.00e-02 2.50e+03 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1629 2.79 - 3.32: 5642 3.32 - 3.85: 10164 3.85 - 4.37: 12323 4.37 - 4.90: 21611 Nonbonded interactions: 51369 Sorted by model distance: nonbonded pdb=" OE1 GLU A 435 " pdb=" OH TYR A 540 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASN B 343 " pdb=" N2 NAG B1301 " model vdw 2.299 3.120 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.315 3.040 nonbonded pdb=" N PRO A 425 " pdb=" CG PRO A 425 " model vdw 2.315 2.816 ... (remaining 51364 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 10.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.140 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 0.033 6608 Z= 0.196 Angle : 0.533 6.750 8973 Z= 0.289 Chirality : 0.042 0.243 939 Planarity : 0.004 0.055 1159 Dihedral : 16.120 84.462 2416 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.14 % Allowed : 19.36 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 788 helix: 0.57 (0.27), residues: 363 sheet: 1.24 (0.79), residues: 49 loop : -0.42 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.011 0.001 PHE A 369 TYR 0.023 0.001 TYR A 385 ARG 0.002 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.742 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2298 time to fit residues: 24.9258 Evaluate side-chains 76 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.0470 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 77 GLN A 97 GLN A 102 GLN A 122 ASN A 137 ASN A 374 HIS A 493 HIS A 531 GLN B 414 GLN B 450 ASN B 501 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6608 Z= 0.164 Angle : 0.484 5.959 8973 Z= 0.259 Chirality : 0.041 0.129 939 Planarity : 0.004 0.059 1159 Dihedral : 4.113 24.345 890 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.01 % Allowed : 17.20 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.44 (0.30), residues: 788 helix: 0.79 (0.28), residues: 372 sheet: 1.17 (0.75), residues: 51 loop : -0.25 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.011 0.001 PHE A 327 TYR 0.015 0.001 TYR B 369 ARG 0.001 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.850 Fit side-chains REVERT: B 498 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7030 (mp10) outliers start: 7 outliers final: 2 residues processed: 84 average time/residue: 0.1991 time to fit residues: 22.3016 Evaluate side-chains 76 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6608 Z= 0.151 Angle : 0.456 5.196 8973 Z= 0.241 Chirality : 0.040 0.125 939 Planarity : 0.004 0.060 1159 Dihedral : 3.865 18.131 890 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.30 % Allowed : 16.76 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.63 (0.30), residues: 788 helix: 0.97 (0.28), residues: 373 sheet: 1.11 (0.75), residues: 51 loop : -0.16 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.009 0.001 PHE A 327 TYR 0.013 0.001 TYR A 385 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.742 Fit side-chains REVERT: A 536 GLU cc_start: 0.7997 (pm20) cc_final: 0.7752 (mp0) REVERT: B 498 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.6932 (mp10) outliers start: 9 outliers final: 4 residues processed: 89 average time/residue: 0.1976 time to fit residues: 23.2231 Evaluate side-chains 84 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 90 GLN B 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6608 Z= 0.191 Angle : 0.485 7.690 8973 Z= 0.253 Chirality : 0.041 0.126 939 Planarity : 0.004 0.058 1159 Dihedral : 3.912 16.437 890 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.30 % Allowed : 17.05 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.70 (0.30), residues: 788 helix: 1.04 (0.28), residues: 373 sheet: 1.11 (0.76), residues: 51 loop : -0.14 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.012 0.001 PHE A 327 TYR 0.018 0.001 TYR B 369 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.779 Fit side-chains REVERT: A 305 LYS cc_start: 0.8101 (tttm) cc_final: 0.7614 (mptt) REVERT: A 536 GLU cc_start: 0.8012 (pm20) cc_final: 0.7781 (mp0) REVERT: B 498 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7061 (mp10) outliers start: 9 outliers final: 5 residues processed: 89 average time/residue: 0.2246 time to fit residues: 25.8716 Evaluate side-chains 85 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6608 Z= 0.139 Angle : 0.464 6.955 8973 Z= 0.242 Chirality : 0.040 0.127 939 Planarity : 0.004 0.058 1159 Dihedral : 3.764 15.531 890 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.59 % Allowed : 17.77 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.80 (0.30), residues: 788 helix: 1.13 (0.28), residues: 374 sheet: 1.20 (0.76), residues: 51 loop : -0.10 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.007 0.001 PHE A 327 TYR 0.014 0.001 TYR A 385 ARG 0.001 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.748 Fit side-chains REVERT: A 305 LYS cc_start: 0.8116 (tttm) cc_final: 0.7683 (mptt) REVERT: B 498 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.6867 (mp10) outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.2258 time to fit residues: 26.3944 Evaluate side-chains 87 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6608 Z= 0.191 Angle : 0.495 6.862 8973 Z= 0.256 Chirality : 0.041 0.128 939 Planarity : 0.004 0.058 1159 Dihedral : 3.840 15.346 890 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 17.92 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.80 (0.30), residues: 788 helix: 1.11 (0.28), residues: 374 sheet: 1.18 (0.75), residues: 51 loop : -0.08 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.017 0.001 TYR B 369 ARG 0.001 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.744 Fit side-chains REVERT: A 67 ARG cc_start: 0.8263 (ttm170) cc_final: 0.8047 (ttm170) REVERT: A 305 LYS cc_start: 0.8136 (tttm) cc_final: 0.7702 (mptt) REVERT: B 498 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7002 (mp10) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.2129 time to fit residues: 24.5309 Evaluate side-chains 84 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0050 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6608 Z= 0.179 Angle : 0.479 6.375 8973 Z= 0.249 Chirality : 0.040 0.127 939 Planarity : 0.004 0.057 1159 Dihedral : 3.822 16.087 890 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.16 % Allowed : 18.21 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.84 (0.30), residues: 788 helix: 1.15 (0.28), residues: 374 sheet: 1.21 (0.75), residues: 51 loop : -0.06 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.003 0.001 HIS A 265 PHE 0.010 0.001 PHE A 327 TYR 0.016 0.001 TYR A 385 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.759 Fit side-chains REVERT: A 67 ARG cc_start: 0.8243 (ttm170) cc_final: 0.8000 (ttm170) REVERT: A 305 LYS cc_start: 0.8094 (tttm) cc_final: 0.7664 (mptt) REVERT: B 498 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7040 (mp10) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.2211 time to fit residues: 24.5672 Evaluate side-chains 85 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6608 Z= 0.174 Angle : 0.485 6.566 8973 Z= 0.250 Chirality : 0.040 0.128 939 Planarity : 0.004 0.058 1159 Dihedral : 3.790 15.757 890 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.59 % Allowed : 17.77 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.84 (0.30), residues: 788 helix: 1.17 (0.28), residues: 375 sheet: 1.21 (0.76), residues: 51 loop : -0.09 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.003 0.001 HIS A 265 PHE 0.010 0.001 PHE A 327 TYR 0.018 0.001 TYR B 369 ARG 0.001 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.689 Fit side-chains REVERT: A 67 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7989 (ttm170) REVERT: A 305 LYS cc_start: 0.8085 (tttm) cc_final: 0.7653 (mptt) REVERT: B 498 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7029 (mp10) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.2215 time to fit residues: 25.3878 Evaluate side-chains 85 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6608 Z= 0.200 Angle : 0.497 6.578 8973 Z= 0.258 Chirality : 0.041 0.135 939 Planarity : 0.004 0.057 1159 Dihedral : 3.852 16.330 890 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.16 % Allowed : 18.64 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.79 (0.30), residues: 788 helix: 1.11 (0.28), residues: 375 sheet: 1.20 (0.75), residues: 51 loop : -0.10 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.017 0.001 TYR A 385 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.752 Fit side-chains REVERT: A 305 LYS cc_start: 0.8097 (tttm) cc_final: 0.7679 (mptt) REVERT: B 498 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7086 (mp10) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.2151 time to fit residues: 24.0581 Evaluate side-chains 87 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6608 Z= 0.186 Angle : 0.492 6.722 8973 Z= 0.255 Chirality : 0.041 0.128 939 Planarity : 0.004 0.057 1159 Dihedral : 3.828 16.492 890 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.30 % Allowed : 18.50 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.81 (0.30), residues: 788 helix: 1.12 (0.28), residues: 375 sheet: 1.21 (0.75), residues: 51 loop : -0.09 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.003 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.020 0.001 TYR B 369 ARG 0.001 0.000 ARG B 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.809 Fit side-chains REVERT: A 297 MET cc_start: 0.8623 (ttm) cc_final: 0.8405 (mtp) REVERT: A 305 LYS cc_start: 0.8064 (tttm) cc_final: 0.7664 (mptt) REVERT: B 498 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: B 518 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8205 (mt) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.2332 time to fit residues: 26.7829 Evaluate side-chains 88 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096054 restraints weight = 9107.217| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.41 r_work: 0.2986 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6608 Z= 0.240 Angle : 0.517 6.619 8973 Z= 0.269 Chirality : 0.042 0.144 939 Planarity : 0.004 0.055 1159 Dihedral : 3.976 16.922 890 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.59 % Allowed : 18.79 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.70 (0.30), residues: 788 helix: 1.04 (0.28), residues: 375 sheet: 1.17 (0.75), residues: 51 loop : -0.15 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.014 0.001 PHE A 327 TYR 0.019 0.001 TYR A 385 ARG 0.001 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.25 seconds wall clock time: 34 minutes 50.44 seconds (2090.44 seconds total)