Starting phenix.real_space_refine on Sat Aug 3 13:04:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/08_2024/8u1n_41818.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/08_2024/8u1n_41818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/08_2024/8u1n_41818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/08_2024/8u1n_41818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/08_2024/8u1n_41818.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/08_2024/8u1n_41818.cif" } resolution = 3.9 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= 0.002 sd= 0.015 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5158 2.51 5 N 1366 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 443": "OD1" <-> "OD2" 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: 8164 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4050 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain breaks: 1 Chain: "B" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4050 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.10, per 1000 atoms: 0.62 Number of scatterers: 8164 At special positions: 0 Unit cell: (115.83, 120.978, 103.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1604 8.00 N 1366 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 37.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 4.051A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 61 removed outlier: 3.624A pdb=" N LEU A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.647A pdb=" N LEU A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 66 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.654A pdb=" N ALA A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 4.031A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 397 through 421 removed outlier: 3.681A pdb=" N GLU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 443 removed outlier: 6.972A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.834A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.696A pdb=" N ALA A 494 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.591A pdb=" N LYS A 504 " --> pdb=" O ARG A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.699A pdb=" N LEU B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 61 removed outlier: 3.819A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.763A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.829A pdb=" N SER B 135 " --> pdb=" O GLY B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 296 through 309 removed outlier: 4.240A pdb=" N TYR B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 396 through 418 Processing helix chain 'B' and resid 421 through 443 removed outlier: 6.937A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'B' and resid 468 through 474 removed outlier: 3.615A pdb=" N VAL B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.725A pdb=" N VAL B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.952A pdb=" N ARG B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.588A pdb=" N VAL B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.592A pdb=" N PHE A 15 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 165 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 168 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 159 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 143 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 7.040A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 removed outlier: 7.233A pdb=" N ILE A 73 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 88 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 168 " --> pdb=" O MET A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 322 removed outlier: 6.641A pdb=" N VAL A 334 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 317 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N HIS A 319 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA A 330 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 321 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE A 328 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 485 removed outlier: 7.439A pdb=" N TYR A 483 " --> pdb=" O VAL A 510 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 322 removed outlier: 3.575A pdb=" N LEU B 332 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 320 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET B 362 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 356 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AB1, first strand: chain 'B' and resid 482 through 483 removed outlier: 6.015A pdb=" N ILE B 482 " --> pdb=" O VAL B 533 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 798 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: 2.14 Time building geometry restraints manager: 3.53 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: 2661 1.34 - 1.46: 1767 1.46 - 1.58: 3826 1.58 - 1.70: 4 1.70 - 1.82: 48 Bond restraints: 8306 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.93e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.222 0.221 1.00e-02 1.00e+04 4.90e+02 bond pdb=" C1' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.416 1.359 0.057 1.30e-02 5.92e+03 1.94e+01 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.377 0.046 1.10e-02 8.26e+03 1.73e+01 ... (remaining 8301 not shown) Histogram of bond angle deviations from ideal: 80.15 - 95.26: 6 95.26 - 110.36: 1768 110.36 - 125.47: 9324 125.47 - 140.57: 82 140.57 - 155.68: 2 Bond angle restraints: 11182 Sorted by residual: angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.68 -34.41 1.00e+00 1.00e+00 1.18e+03 angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 154.53 -33.26 1.00e+00 1.00e+00 1.11e+03 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 82.86 32.33 1.76e+00 3.23e-01 3.37e+02 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 84.99 30.20 1.76e+00 3.23e-01 2.95e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 138.61 -29.78 2.33e+00 1.85e-01 1.64e+02 ... (remaining 11177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4300 17.84 - 35.67: 613 35.67 - 53.51: 153 53.51 - 71.34: 34 71.34 - 89.18: 16 Dihedral angle restraints: 5116 sinusoidal: 2194 harmonic: 2922 Sorted by residual: dihedral pdb=" CA TYR B 511 " pdb=" C TYR B 511 " pdb=" N MET B 512 " pdb=" CA MET B 512 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA TYR A 507 " pdb=" C TYR A 507 " pdb=" N GLU A 508 " pdb=" CA GLU A 508 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA GLU B 514 " pdb=" C GLU B 514 " pdb=" N PRO B 515 " pdb=" CA PRO B 515 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1161 0.096 - 0.192: 55 0.192 - 0.288: 4 0.288 - 0.384: 0 0.384 - 0.480: 2 Chirality restraints: 1222 Sorted by residual: chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.95 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1219 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 514 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO B 515 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 515 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 515 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 285 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO B 286 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 76 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 77 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " -0.024 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 86 2.49 - 3.09: 5771 3.09 - 3.69: 12970 3.69 - 4.30: 17680 4.30 - 4.90: 27978 Nonbonded interactions: 64485 Sorted by model distance: nonbonded pdb=" O2G ATP A 801 " pdb="MG MG A 802 " model vdw 1.883 2.170 nonbonded pdb=" O5' ATP B 801 " pdb="MG MG B 802 " model vdw 1.893 2.170 nonbonded pdb=" O2A ATP B 801 " pdb="MG MG B 802 " model vdw 1.914 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.915 2.170 nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.962 2.170 ... (remaining 64480 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 'A' selection = chain 'B' } 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 group one per residue 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.810 Find NCS groups from input model: 0.230 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.222 8306 Z= 0.330 Angle : 1.169 34.407 11182 Z= 0.710 Chirality : 0.048 0.480 1222 Planarity : 0.004 0.087 1426 Dihedral : 17.981 89.180 3232 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 26.00 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.26), residues: 986 helix: -0.15 (0.29), residues: 317 sheet: 0.20 (0.44), residues: 158 loop : -1.53 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 311 HIS 0.004 0.001 HIS A 481 PHE 0.010 0.001 PHE B 165 TYR 0.023 0.001 TYR B 519 ARG 0.004 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 LEU cc_start: 0.8395 (mt) cc_final: 0.8118 (mt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1694 time to fit residues: 14.3490 Evaluate side-chains 45 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 40.0000 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 479 GLN A 492 GLN B 149 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8306 Z= 0.255 Angle : 0.635 7.756 11182 Z= 0.333 Chirality : 0.043 0.147 1222 Planarity : 0.004 0.056 1426 Dihedral : 10.409 88.869 1150 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.24 % Allowed : 22.99 % Favored : 72.77 % 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: -1.16 (0.27), residues: 986 helix: -0.05 (0.28), residues: 318 sheet: 0.07 (0.42), residues: 176 loop : -1.58 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.006 0.001 HIS A 481 PHE 0.010 0.001 PHE B 84 TYR 0.019 0.002 TYR A 527 ARG 0.004 0.001 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 48 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 267 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.6959 (pptt) REVERT: A 508 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5837 (mt-10) REVERT: B 84 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6129 (t80) REVERT: B 152 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8553 (t70) REVERT: B 512 MET cc_start: 0.5644 (tmm) cc_final: 0.5108 (tmm) outliers start: 38 outliers final: 15 residues processed: 83 average time/residue: 0.1560 time to fit residues: 20.0956 Evaluate side-chains 66 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.123 8306 Z= 0.602 Angle : 0.894 11.108 11182 Z= 0.461 Chirality : 0.049 0.161 1222 Planarity : 0.006 0.056 1426 Dihedral : 10.485 80.743 1150 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 6.70 % Allowed : 24.55 % Favored : 68.75 % 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: -2.00 (0.25), residues: 986 helix: -0.84 (0.26), residues: 315 sheet: -0.63 (0.41), residues: 179 loop : -1.91 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 157 HIS 0.008 0.002 HIS A 481 PHE 0.019 0.003 PHE B 360 TYR 0.020 0.003 TYR A 428 ARG 0.007 0.001 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 38 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: A 46 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7079 (t0) REVERT: A 125 MET cc_start: 0.8696 (mmm) cc_final: 0.8364 (mmm) REVERT: A 514 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.6112 (pm20) REVERT: A 527 TYR cc_start: 0.8196 (t80) cc_final: 0.7766 (t80) REVERT: B 84 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6443 (t80) REVERT: B 93 MET cc_start: 0.8110 (mmt) cc_final: 0.7784 (mmt) REVERT: B 152 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8199 (t0) REVERT: B 300 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.5113 (m-10) REVERT: B 342 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.5385 (tp) REVERT: B 398 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6530 (pttm) REVERT: B 512 MET cc_start: 0.6097 (tmm) cc_final: 0.5837 (tmm) outliers start: 60 outliers final: 35 residues processed: 95 average time/residue: 0.1645 time to fit residues: 23.3377 Evaluate side-chains 79 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 36 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 78 optimal weight: 0.0030 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8306 Z= 0.188 Angle : 0.613 7.492 11182 Z= 0.321 Chirality : 0.042 0.152 1222 Planarity : 0.004 0.052 1426 Dihedral : 9.561 84.231 1150 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.79 % Allowed : 26.23 % Favored : 69.98 % 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: -1.58 (0.26), residues: 986 helix: -0.23 (0.28), residues: 314 sheet: -0.26 (0.43), residues: 174 loop : -1.91 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 157 HIS 0.005 0.001 HIS A 441 PHE 0.010 0.001 PHE A 432 TYR 0.014 0.001 TYR A 428 ARG 0.003 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 47 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: A 93 MET cc_start: 0.7468 (mmt) cc_final: 0.7118 (mmp) REVERT: A 117 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8402 (mp) REVERT: A 125 MET cc_start: 0.8714 (mmm) cc_final: 0.8205 (mmm) REVERT: A 267 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.6661 (pptt) REVERT: A 527 TYR cc_start: 0.8061 (t80) cc_final: 0.7673 (t80) REVERT: B 152 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8587 (t70) REVERT: B 156 MET cc_start: 0.6416 (mmp) cc_final: 0.6182 (mmp) REVERT: B 300 TYR cc_start: 0.5241 (OUTLIER) cc_final: 0.4713 (m-10) REVERT: B 512 MET cc_start: 0.5947 (tmm) cc_final: 0.5500 (tmm) outliers start: 34 outliers final: 18 residues processed: 77 average time/residue: 0.1652 time to fit residues: 19.1012 Evaluate side-chains 66 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 43 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8306 Z= 0.283 Angle : 0.648 8.186 11182 Z= 0.336 Chirality : 0.042 0.143 1222 Planarity : 0.004 0.049 1426 Dihedral : 9.644 75.682 1150 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.36 % Allowed : 26.79 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.26), residues: 986 helix: -0.13 (0.28), residues: 314 sheet: -0.22 (0.43), residues: 174 loop : -1.99 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 311 HIS 0.005 0.001 HIS A 441 PHE 0.012 0.002 PHE B 360 TYR 0.014 0.002 TYR A 428 ARG 0.003 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 42 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7965 (mmt) cc_final: 0.7243 (mmt) REVERT: A 117 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 267 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.6730 (pptt) REVERT: A 527 TYR cc_start: 0.8101 (t80) cc_final: 0.7778 (t80) REVERT: B 84 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6178 (t80) REVERT: B 152 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8485 (t70) REVERT: B 300 TYR cc_start: 0.5234 (OUTLIER) cc_final: 0.4805 (m-10) REVERT: B 342 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.5359 (tp) REVERT: B 512 MET cc_start: 0.5899 (tmm) cc_final: 0.5697 (tmm) outliers start: 48 outliers final: 30 residues processed: 87 average time/residue: 0.1567 time to fit residues: 21.0635 Evaluate side-chains 78 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 42 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8306 Z= 0.266 Angle : 0.644 8.115 11182 Z= 0.332 Chirality : 0.043 0.142 1222 Planarity : 0.004 0.050 1426 Dihedral : 9.526 77.808 1150 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 6.58 % Allowed : 25.78 % Favored : 67.63 % 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: -1.50 (0.26), residues: 986 helix: -0.01 (0.29), residues: 314 sheet: -0.15 (0.44), residues: 173 loop : -2.00 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 311 HIS 0.005 0.001 HIS A 441 PHE 0.010 0.001 PHE B 360 TYR 0.013 0.001 TYR A 428 ARG 0.003 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 43 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 138 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9309 (tp) REVERT: A 267 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.6776 (pptt) REVERT: A 434 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9167 (mmmt) REVERT: A 527 TYR cc_start: 0.8149 (t80) cc_final: 0.7861 (t80) REVERT: B 84 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6200 (t80) REVERT: B 152 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8367 (t70) REVERT: B 300 TYR cc_start: 0.5106 (OUTLIER) cc_final: 0.4691 (m-10) REVERT: B 342 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.5329 (tp) outliers start: 59 outliers final: 38 residues processed: 97 average time/residue: 0.1845 time to fit residues: 26.4059 Evaluate side-chains 88 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 42 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 523 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.0670 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8306 Z= 0.154 Angle : 0.607 8.908 11182 Z= 0.313 Chirality : 0.042 0.160 1222 Planarity : 0.004 0.049 1426 Dihedral : 9.275 85.273 1150 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.79 % Allowed : 28.57 % Favored : 68.64 % 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: -1.22 (0.27), residues: 986 helix: 0.33 (0.30), residues: 308 sheet: 0.03 (0.44), residues: 174 loop : -1.91 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 157 HIS 0.004 0.001 HIS A 441 PHE 0.023 0.001 PHE B 498 TYR 0.011 0.001 TYR A 428 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 51 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 267 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6656 (pptt) REVERT: A 463 ASP cc_start: 0.9016 (m-30) cc_final: 0.8792 (p0) REVERT: A 527 TYR cc_start: 0.8113 (t80) cc_final: 0.7868 (t80) REVERT: B 98 LEU cc_start: 0.8472 (mt) cc_final: 0.8200 (mt) REVERT: B 152 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8422 (t70) REVERT: B 300 TYR cc_start: 0.4885 (OUTLIER) cc_final: 0.4488 (m-10) REVERT: B 342 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5265 (tp) REVERT: B 512 MET cc_start: 0.5039 (tmm) cc_final: 0.4333 (tmm) outliers start: 25 outliers final: 12 residues processed: 74 average time/residue: 0.1543 time to fit residues: 17.5916 Evaluate side-chains 62 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 523 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 0.0770 chunk 74 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 overall best weight: 2.6744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8306 Z= 0.238 Angle : 0.636 9.912 11182 Z= 0.326 Chirality : 0.042 0.142 1222 Planarity : 0.004 0.049 1426 Dihedral : 9.264 80.016 1150 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.57 % Allowed : 28.35 % Favored : 68.08 % 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: -1.25 (0.27), residues: 986 helix: 0.19 (0.29), residues: 315 sheet: 0.02 (0.44), residues: 171 loop : -1.85 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.004 0.001 HIS A 441 PHE 0.010 0.001 PHE B 165 TYR 0.021 0.001 TYR A 428 ARG 0.003 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8403 (mp) REVERT: A 267 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6659 (pptt) REVERT: A 393 MET cc_start: 0.7592 (mmm) cc_final: 0.7287 (mmm) REVERT: A 463 ASP cc_start: 0.9074 (m-30) cc_final: 0.8833 (p0) REVERT: A 527 TYR cc_start: 0.8226 (t80) cc_final: 0.7871 (t80) REVERT: B 93 MET cc_start: 0.7683 (mmt) cc_final: 0.7056 (mmt) REVERT: B 152 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8507 (t70) REVERT: B 300 TYR cc_start: 0.5075 (OUTLIER) cc_final: 0.4641 (m-10) REVERT: B 342 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5217 (tp) REVERT: B 512 MET cc_start: 0.5074 (tmm) cc_final: 0.4375 (tmm) outliers start: 32 outliers final: 21 residues processed: 72 average time/residue: 0.1508 time to fit residues: 16.8385 Evaluate side-chains 68 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 42 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 380 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8306 Z= 0.162 Angle : 0.601 10.073 11182 Z= 0.307 Chirality : 0.041 0.146 1222 Planarity : 0.004 0.049 1426 Dihedral : 8.957 82.772 1150 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.79 % Allowed : 28.79 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.27), residues: 986 helix: 0.46 (0.30), residues: 307 sheet: 0.26 (0.44), residues: 166 loop : -1.86 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 157 HIS 0.004 0.001 HIS A 441 PHE 0.008 0.001 PHE A 165 TYR 0.017 0.001 TYR A 428 ARG 0.002 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 43 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 267 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6558 (pptt) REVERT: A 393 MET cc_start: 0.7528 (mmm) cc_final: 0.7181 (mmm) REVERT: A 434 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9127 (mmmt) REVERT: A 463 ASP cc_start: 0.9107 (m-30) cc_final: 0.8897 (p0) REVERT: A 527 TYR cc_start: 0.8196 (t80) cc_final: 0.7799 (t80) REVERT: B 93 MET cc_start: 0.7409 (mmt) cc_final: 0.6859 (mmt) REVERT: B 300 TYR cc_start: 0.5053 (OUTLIER) cc_final: 0.4601 (m-10) REVERT: B 342 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5210 (tp) REVERT: B 512 MET cc_start: 0.5008 (tmm) cc_final: 0.4247 (tmm) outliers start: 25 outliers final: 18 residues processed: 67 average time/residue: 0.1575 time to fit residues: 16.4517 Evaluate side-chains 66 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 43 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8306 Z= 0.237 Angle : 0.635 10.073 11182 Z= 0.324 Chirality : 0.042 0.142 1222 Planarity : 0.004 0.048 1426 Dihedral : 9.087 85.007 1150 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.01 % Allowed : 28.68 % Favored : 68.30 % 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: -1.18 (0.27), residues: 986 helix: 0.29 (0.29), residues: 315 sheet: 0.18 (0.44), residues: 167 loop : -1.89 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.004 0.001 HIS B 205 PHE 0.009 0.001 PHE B 84 TYR 0.020 0.001 TYR A 428 ARG 0.003 0.000 ARG B 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 42 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.6981 (mmt) cc_final: 0.6742 (mmp) REVERT: A 117 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 267 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6511 (pptt) REVERT: A 393 MET cc_start: 0.7627 (mmm) cc_final: 0.7329 (mmm) REVERT: A 434 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.9106 (mmmt) REVERT: A 527 TYR cc_start: 0.8272 (t80) cc_final: 0.7843 (t80) REVERT: B 93 MET cc_start: 0.7616 (mmt) cc_final: 0.6987 (mmt) REVERT: B 300 TYR cc_start: 0.5104 (OUTLIER) cc_final: 0.4650 (m-10) REVERT: B 342 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.5283 (tp) REVERT: B 512 MET cc_start: 0.5242 (tmm) cc_final: 0.4451 (tmm) outliers start: 27 outliers final: 20 residues processed: 68 average time/residue: 0.1571 time to fit residues: 16.2950 Evaluate side-chains 67 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 42 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 469 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.066413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046077 restraints weight = 41524.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.048278 restraints weight = 21669.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.049682 restraints weight = 14543.813| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8306 Z= 0.160 Angle : 0.600 10.087 11182 Z= 0.306 Chirality : 0.041 0.146 1222 Planarity : 0.003 0.048 1426 Dihedral : 9.035 83.435 1150 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.79 % Allowed : 28.91 % Favored : 68.30 % 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: -1.08 (0.27), residues: 986 helix: 0.39 (0.29), residues: 315 sheet: 0.27 (0.44), residues: 166 loop : -1.85 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 157 HIS 0.003 0.001 HIS A 441 PHE 0.007 0.001 PHE A 165 TYR 0.014 0.001 TYR A 428 ARG 0.002 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.91 seconds wall clock time: 30 minutes 15.03 seconds (1815.03 seconds total)