Starting phenix.real_space_refine on Tue Jun 17 10:45:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tsz_26105/06_2025/7tsz_26105.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tsz_26105/06_2025/7tsz_26105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tsz_26105/06_2025/7tsz_26105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tsz_26105/06_2025/7tsz_26105.map" model { file = "/net/cci-nas-00/data/ceres_data/7tsz_26105/06_2025/7tsz_26105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tsz_26105/06_2025/7tsz_26105.cif" } resolution = 4.5 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= 0.006 sd= 0.051 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 S 31 5.16 5 C 6345 2.51 5 N 1712 2.21 5 O 1964 1.98 5 H 9670 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19722 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9195 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 572} Chain breaks: 7 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 4930 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 11, 'TRANS': 320} Chain breaks: 6 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 676 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "E" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1371 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "P" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 160 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Time building chain proxies: 10.08, per 1000 atoms: 0.51 Number of scatterers: 19722 At special positions: 0 Unit cell: (112.751, 125.637, 139.597, 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) S 31 16.00 O 1964 8.00 N 1712 7.00 C 6345 6.00 H 9670 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.70 Conformation dependent library (CDL) restraints added in 1.6 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 24.9% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.898A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.758A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.696A pdb=" N GLY A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.917A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.909A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 550 removed outlier: 4.999A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 4.190A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'D' and resid 32 through 46 removed outlier: 4.148A pdb=" N ALA D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.776A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.590A pdb=" N ARG D 188 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.678A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.758A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 274 removed outlier: 5.667A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.087A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.660A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.638A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.749A pdb=" N TRP A 776 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 785 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.395A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 51 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.497A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.062A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.626A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.777A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 292 Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.045A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.764A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1287 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: 7.94 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9670 1.03 - 1.22: 1 1.22 - 1.42: 4459 1.42 - 1.62: 5749 1.62 - 1.81: 58 Bond restraints: 19937 Sorted by residual: bond pdb=" CG ARG A 366 " pdb=" CD ARG A 366 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.39e+00 bond pdb=" CG LEU A 377 " pdb=" CD1 LEU A 377 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.24e+00 bond pdb=" N ARG A 388 " pdb=" CA ARG A 388 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.21e-02 6.83e+03 2.05e+00 bond pdb=" CB TRP A 745 " pdb=" CG TRP A 745 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 ... (remaining 19932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 34781 1.79 - 3.58: 917 3.58 - 5.37: 89 5.37 - 7.16: 9 7.16 - 8.94: 2 Bond angle restraints: 35798 Sorted by residual: angle pdb=" N GLY A 378 " pdb=" CA GLY A 378 " pdb=" C GLY A 378 " ideal model delta sigma weight residual 113.18 104.24 8.94 2.37e+00 1.78e-01 1.42e+01 angle pdb=" C ARG A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 120.68 114.45 6.23 1.70e+00 3.46e-01 1.34e+01 angle pdb=" N GLN D 70 " pdb=" CA GLN D 70 " pdb=" C GLN D 70 " ideal model delta sigma weight residual 112.45 107.40 5.05 1.39e+00 5.18e-01 1.32e+01 angle pdb=" CA TYR D 184 " pdb=" CB TYR D 184 " pdb=" CG TYR D 184 " ideal model delta sigma weight residual 113.90 107.59 6.31 1.80e+00 3.09e-01 1.23e+01 angle pdb=" N ASP A 222 " pdb=" CA ASP A 222 " pdb=" C ASP A 222 " ideal model delta sigma weight residual 112.90 108.49 4.41 1.31e+00 5.83e-01 1.13e+01 ... (remaining 35793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8967 17.82 - 35.65: 307 35.65 - 53.47: 136 53.47 - 71.29: 53 71.29 - 89.11: 17 Dihedral angle restraints: 9480 sinusoidal: 5090 harmonic: 4390 Sorted by residual: dihedral pdb=" CA ASP A 332 " pdb=" C ASP A 332 " pdb=" N LYS A 333 " pdb=" CA LYS A 333 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA A 679 " pdb=" C ALA A 679 " pdb=" N SER A 680 " pdb=" CA SER A 680 " ideal model delta harmonic sigma weight residual 180.00 163.92 16.08 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB GLU B 107 " pdb=" CG GLU B 107 " pdb=" CD GLU B 107 " pdb=" OE1 GLU B 107 " ideal model delta sinusoidal sigma weight residual 0.00 85.38 -85.38 1 3.00e+01 1.11e-03 9.81e+00 ... (remaining 9477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1028 0.041 - 0.082: 315 0.082 - 0.123: 150 0.123 - 0.164: 23 0.164 - 0.205: 2 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA TYR A 522 " pdb=" N TYR A 522 " pdb=" C TYR A 522 " pdb=" CB TYR A 522 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ARG A 366 " pdb=" N ARG A 366 " pdb=" C ARG A 366 " pdb=" CB ARG A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CA VAL A 629 " pdb=" N VAL A 629 " pdb=" C VAL A 629 " pdb=" CB VAL A 629 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 1515 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 389 " 0.024 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C LEU A 389 " -0.083 2.00e-02 2.50e+03 pdb=" O LEU A 389 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN A 390 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 386 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C LYS A 386 " -0.075 2.00e-02 2.50e+03 pdb=" O LYS A 386 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU A 387 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 325 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C MET A 325 " -0.063 2.00e-02 2.50e+03 pdb=" O MET A 325 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO A 326 " 0.021 2.00e-02 2.50e+03 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 406 2.07 - 2.70: 32904 2.70 - 3.34: 54958 3.34 - 3.97: 70752 3.97 - 4.60: 109433 Nonbonded interactions: 268453 Sorted by model distance: nonbonded pdb=" OD2 ASP A 410 " pdb=" H THR E 61 " model vdw 1.438 2.450 nonbonded pdb=" OH TYR D 77 " pdb=" H ARG C 83 " model vdw 1.461 2.450 nonbonded pdb=" H VAL D 192 " pdb=" OE1 GLN E 34 " model vdw 1.468 2.450 nonbonded pdb=" O GLY A 424 " pdb=" H PHE P1300 " model vdw 1.492 2.450 nonbonded pdb=" H ILE A 352 " pdb=" OE2 GLU A 373 " model vdw 1.510 2.450 ... (remaining 268448 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 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: 0.610 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: 0.380 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 46.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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: 51.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 0.055 10269 Z= 0.277 Angle : 0.887 8.944 13948 Z= 0.540 Chirality : 0.048 0.205 1518 Planarity : 0.005 0.048 1829 Dihedral : 11.128 89.114 3684 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1248 helix: 0.09 (0.29), residues: 247 sheet: 0.84 (0.24), residues: 389 loop : 0.58 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 73 HIS 0.009 0.003 HIS D 139 PHE 0.013 0.002 PHE A 570 TYR 0.015 0.002 TYR D 184 ARG 0.011 0.001 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.14909 ( 473) hydrogen bonds : angle 7.78933 ( 1287) SS BOND : bond 0.00407 ( 2) SS BOND : angle 1.32199 ( 4) covalent geometry : bond 0.00535 (10267) covalent geometry : angle 0.88637 (13944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8425 (mm) cc_final: 0.7996 (tp) REVERT: A 303 LYS cc_start: 0.9390 (tttm) cc_final: 0.8941 (ttpp) REVERT: A 304 MET cc_start: 0.8980 (mtm) cc_final: 0.8404 (ttm) REVERT: A 307 ASP cc_start: 0.8940 (m-30) cc_final: 0.8634 (m-30) REVERT: A 372 MET cc_start: 0.8224 (mtp) cc_final: 0.7911 (mtm) REVERT: A 441 GLN cc_start: 0.9052 (tt0) cc_final: 0.8822 (tp40) REVERT: A 449 TRP cc_start: 0.8513 (t60) cc_final: 0.7989 (t60) REVERT: A 450 LEU cc_start: 0.9366 (mt) cc_final: 0.8810 (tt) REVERT: A 461 THR cc_start: 0.7913 (t) cc_final: 0.7044 (t) REVERT: A 540 GLN cc_start: 0.8476 (tp40) cc_final: 0.8058 (tp40) REVERT: B 112 SER cc_start: 0.8165 (p) cc_final: 0.7682 (p) REVERT: B 150 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 369 THR cc_start: 0.7827 (p) cc_final: 0.7622 (p) REVERT: D 116 ASN cc_start: 0.9394 (m-40) cc_final: 0.8749 (m110) REVERT: D 172 ASP cc_start: 0.8765 (m-30) cc_final: 0.8422 (t0) REVERT: D 183 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8226 (pt0) REVERT: E 28 TYR cc_start: 0.8302 (t80) cc_final: 0.7999 (t80) REVERT: E 92 THR cc_start: 0.8936 (m) cc_final: 0.8678 (p) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.5320 time to fit residues: 242.3696 Evaluate side-chains 222 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 230 GLN E 36 ASN E 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.119499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080079 restraints weight = 89244.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084628 restraints weight = 41773.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087494 restraints weight = 27024.668| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10269 Z= 0.334 Angle : 0.723 8.363 13948 Z= 0.413 Chirality : 0.044 0.154 1518 Planarity : 0.006 0.078 1829 Dihedral : 5.605 82.131 1399 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1248 helix: 0.89 (0.31), residues: 251 sheet: -0.02 (0.24), residues: 385 loop : -0.20 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 73 HIS 0.017 0.002 HIS B 324 PHE 0.022 0.002 PHE D 147 TYR 0.024 0.002 TYR A 578 ARG 0.006 0.001 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.05571 ( 473) hydrogen bonds : angle 6.82566 ( 1287) SS BOND : bond 0.00341 ( 2) SS BOND : angle 0.61072 ( 4) covalent geometry : bond 0.00676 (10267) covalent geometry : angle 0.72316 (13944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.6707 (tt0) cc_final: 0.6441 (tt0) REVERT: A 284 ILE cc_start: 0.8409 (mm) cc_final: 0.7959 (tp) REVERT: A 303 LYS cc_start: 0.9371 (tttm) cc_final: 0.9116 (tttt) REVERT: A 307 ASP cc_start: 0.8925 (m-30) cc_final: 0.8607 (m-30) REVERT: A 367 ARG cc_start: 0.9221 (mtm180) cc_final: 0.8953 (mtm-85) REVERT: A 383 ASP cc_start: 0.8694 (m-30) cc_final: 0.8431 (m-30) REVERT: A 419 LYS cc_start: 0.9096 (tttt) cc_final: 0.8791 (tppt) REVERT: A 420 GLU cc_start: 0.8620 (pm20) cc_final: 0.8084 (pm20) REVERT: A 423 THR cc_start: 0.9377 (p) cc_final: 0.9166 (p) REVERT: A 449 TRP cc_start: 0.8327 (t60) cc_final: 0.8056 (t60) REVERT: A 450 LEU cc_start: 0.9437 (mt) cc_final: 0.8993 (tt) REVERT: A 521 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8243 (mt-10) REVERT: A 531 TYR cc_start: 0.8804 (p90) cc_final: 0.8566 (p90) REVERT: A 586 PHE cc_start: 0.6686 (m-80) cc_final: 0.5644 (m-10) REVERT: A 775 GLN cc_start: 0.9156 (tt0) cc_final: 0.8760 (tt0) REVERT: B 287 ASN cc_start: 0.9262 (m-40) cc_final: 0.8861 (t0) REVERT: B 388 TYR cc_start: 0.6073 (m-80) cc_final: 0.5654 (m-80) REVERT: D 50 GLN cc_start: 0.9411 (tm-30) cc_final: 0.9157 (tm-30) REVERT: D 102 HIS cc_start: 0.8740 (t70) cc_final: 0.8070 (t70) REVERT: D 111 MET cc_start: 0.9161 (mmm) cc_final: 0.8752 (mtt) REVERT: D 116 ASN cc_start: 0.9332 (m-40) cc_final: 0.8306 (m110) REVERT: D 131 ASP cc_start: 0.8332 (t0) cc_final: 0.8082 (t0) REVERT: D 135 ARG cc_start: 0.7933 (mpt180) cc_final: 0.7677 (mtt90) REVERT: D 172 ASP cc_start: 0.9102 (m-30) cc_final: 0.8683 (t0) REVERT: E 42 ASP cc_start: 0.8512 (m-30) cc_final: 0.8273 (m-30) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.5223 time to fit residues: 181.4936 Evaluate side-chains 188 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 75 optimal weight: 0.9990 chunk 23 optimal weight: 40.0000 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.0010 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN E 36 ASN E 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.121944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086553 restraints weight = 85452.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090596 restraints weight = 44030.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091717 restraints weight = 25368.331| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10269 Z= 0.122 Angle : 0.531 6.481 13948 Z= 0.297 Chirality : 0.043 0.159 1518 Planarity : 0.004 0.057 1829 Dihedral : 5.134 76.588 1399 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1248 helix: 1.23 (0.32), residues: 260 sheet: 0.07 (0.25), residues: 369 loop : -0.27 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 739 HIS 0.006 0.001 HIS D 139 PHE 0.014 0.001 PHE D 147 TYR 0.025 0.001 TYR D 184 ARG 0.003 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 473) hydrogen bonds : angle 6.11981 ( 1287) SS BOND : bond 0.00232 ( 2) SS BOND : angle 2.28874 ( 4) covalent geometry : bond 0.00249 (10267) covalent geometry : angle 0.52991 (13944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.6653 (tt0) cc_final: 0.6427 (tt0) REVERT: A 303 LYS cc_start: 0.9327 (tttm) cc_final: 0.9014 (ttpt) REVERT: A 305 GLU cc_start: 0.8859 (tt0) cc_final: 0.8592 (tt0) REVERT: A 307 ASP cc_start: 0.8881 (m-30) cc_final: 0.8561 (m-30) REVERT: A 367 ARG cc_start: 0.9088 (mtm180) cc_final: 0.8812 (mtm-85) REVERT: A 419 LYS cc_start: 0.9020 (tttt) cc_final: 0.8682 (tppt) REVERT: A 420 GLU cc_start: 0.8682 (pm20) cc_final: 0.8073 (pm20) REVERT: A 449 TRP cc_start: 0.8245 (t60) cc_final: 0.7907 (t60) REVERT: A 450 LEU cc_start: 0.9413 (mt) cc_final: 0.8917 (tt) REVERT: B 111 LEU cc_start: 0.8701 (mt) cc_final: 0.8491 (mp) REVERT: B 287 ASN cc_start: 0.9347 (m-40) cc_final: 0.8943 (t0) REVERT: B 388 TYR cc_start: 0.6112 (m-80) cc_final: 0.5765 (m-80) REVERT: D 50 GLN cc_start: 0.9338 (tm-30) cc_final: 0.9090 (tm-30) REVERT: D 102 HIS cc_start: 0.8731 (t70) cc_final: 0.7930 (t70) REVERT: D 131 ASP cc_start: 0.8343 (t0) cc_final: 0.8082 (t70) REVERT: D 136 ASP cc_start: 0.8974 (t0) cc_final: 0.8631 (t0) REVERT: D 172 ASP cc_start: 0.9003 (m-30) cc_final: 0.8601 (t0) REVERT: E 36 ASN cc_start: 0.8169 (m-40) cc_final: 0.7916 (m-40) REVERT: E 42 ASP cc_start: 0.8592 (m-30) cc_final: 0.8369 (m-30) REVERT: E 50 MET cc_start: 0.8894 (mtm) cc_final: 0.8509 (mtm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.4932 time to fit residues: 172.8066 Evaluate side-chains 198 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.119169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080693 restraints weight = 81869.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.085097 restraints weight = 38663.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087953 restraints weight = 25009.094| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10269 Z= 0.186 Angle : 0.538 6.161 13948 Z= 0.302 Chirality : 0.041 0.150 1518 Planarity : 0.004 0.050 1829 Dihedral : 4.898 59.100 1399 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1248 helix: 1.16 (0.31), residues: 261 sheet: -0.16 (0.25), residues: 363 loop : -0.57 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 739 HIS 0.005 0.001 HIS B 324 PHE 0.021 0.001 PHE D 95 TYR 0.022 0.002 TYR D 184 ARG 0.003 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 473) hydrogen bonds : angle 6.01751 ( 1287) SS BOND : bond 0.00160 ( 2) SS BOND : angle 1.57126 ( 4) covalent geometry : bond 0.00386 (10267) covalent geometry : angle 0.53775 (13944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8730 (m-30) cc_final: 0.8325 (m-30) REVERT: A 262 GLU cc_start: 0.6718 (tt0) cc_final: 0.6480 (tt0) REVERT: A 303 LYS cc_start: 0.9327 (tttm) cc_final: 0.8994 (ttpt) REVERT: A 304 MET cc_start: 0.8981 (mtm) cc_final: 0.8377 (ttm) REVERT: A 307 ASP cc_start: 0.8847 (m-30) cc_final: 0.8568 (m-30) REVERT: A 419 LYS cc_start: 0.9000 (tttt) cc_final: 0.8681 (tppt) REVERT: A 420 GLU cc_start: 0.8658 (pm20) cc_final: 0.8068 (pm20) REVERT: A 449 TRP cc_start: 0.8406 (t60) cc_final: 0.8176 (t60) REVERT: A 450 LEU cc_start: 0.9453 (mt) cc_final: 0.9121 (mm) REVERT: A 586 PHE cc_start: 0.7013 (m-80) cc_final: 0.6059 (m-10) REVERT: A 774 LEU cc_start: 0.8859 (tp) cc_final: 0.8651 (tp) REVERT: B 42 PHE cc_start: 0.6508 (t80) cc_final: 0.6165 (t80) REVERT: B 287 ASN cc_start: 0.9349 (m-40) cc_final: 0.8956 (t0) REVERT: B 388 TYR cc_start: 0.6164 (m-80) cc_final: 0.5881 (m-80) REVERT: D 50 GLN cc_start: 0.9330 (tm-30) cc_final: 0.9103 (tm-30) REVERT: D 102 HIS cc_start: 0.8717 (t70) cc_final: 0.7905 (t70) REVERT: D 172 ASP cc_start: 0.9056 (m-30) cc_final: 0.8612 (t0) REVERT: E 36 ASN cc_start: 0.8323 (m110) cc_final: 0.7972 (m-40) REVERT: E 42 ASP cc_start: 0.8504 (m-30) cc_final: 0.8259 (m-30) REVERT: E 50 MET cc_start: 0.8859 (mtm) cc_final: 0.8584 (mtm) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.5198 time to fit residues: 174.1727 Evaluate side-chains 189 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.0370 chunk 53 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 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 = 0.3961 r_free = 0.3961 target = 0.121669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.083259 restraints weight = 82308.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088032 restraints weight = 37797.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.091149 restraints weight = 23963.228| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10269 Z= 0.097 Angle : 0.481 4.770 13948 Z= 0.264 Chirality : 0.042 0.150 1518 Planarity : 0.003 0.041 1829 Dihedral : 4.566 52.074 1399 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1248 helix: 1.41 (0.32), residues: 262 sheet: -0.10 (0.25), residues: 364 loop : -0.45 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 376 HIS 0.005 0.001 HIS B 165 PHE 0.014 0.001 PHE D 147 TYR 0.022 0.001 TYR D 184 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 473) hydrogen bonds : angle 5.64040 ( 1287) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.97668 ( 4) covalent geometry : bond 0.00200 (10267) covalent geometry : angle 0.48052 (13944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8619 (m-30) cc_final: 0.8213 (m-30) REVERT: A 262 GLU cc_start: 0.6694 (tt0) cc_final: 0.6446 (tt0) REVERT: A 303 LYS cc_start: 0.9303 (tttm) cc_final: 0.8998 (tttt) REVERT: A 304 MET cc_start: 0.8924 (mtm) cc_final: 0.8634 (mtp) REVERT: A 305 GLU cc_start: 0.8807 (tt0) cc_final: 0.8572 (tt0) REVERT: A 307 ASP cc_start: 0.8833 (m-30) cc_final: 0.8522 (m-30) REVERT: A 367 ARG cc_start: 0.9211 (mtm180) cc_final: 0.8610 (mtm-85) REVERT: A 449 TRP cc_start: 0.8339 (t60) cc_final: 0.8028 (t60) REVERT: A 450 LEU cc_start: 0.9381 (mt) cc_final: 0.8743 (tt) REVERT: A 533 HIS cc_start: 0.7996 (t-90) cc_final: 0.7753 (t-90) REVERT: A 780 LEU cc_start: 0.9191 (mt) cc_final: 0.8783 (tp) REVERT: B 42 PHE cc_start: 0.6469 (t80) cc_final: 0.6118 (t80) REVERT: B 134 LEU cc_start: 0.9244 (mp) cc_final: 0.8864 (mp) REVERT: B 287 ASN cc_start: 0.9383 (m-40) cc_final: 0.8965 (t0) REVERT: B 388 TYR cc_start: 0.6062 (m-80) cc_final: 0.5767 (m-80) REVERT: D 50 GLN cc_start: 0.9328 (tm-30) cc_final: 0.9090 (tm-30) REVERT: D 131 ASP cc_start: 0.8071 (t0) cc_final: 0.7785 (t70) REVERT: D 172 ASP cc_start: 0.8987 (m-30) cc_final: 0.8510 (t0) REVERT: E 36 ASN cc_start: 0.8439 (m110) cc_final: 0.8094 (m-40) REVERT: E 42 ASP cc_start: 0.8366 (m-30) cc_final: 0.8152 (m-30) REVERT: E 50 MET cc_start: 0.8695 (mtm) cc_final: 0.8453 (mtm) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.4789 time to fit residues: 160.5510 Evaluate side-chains 199 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN D 54 GLN D 230 GLN E 36 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.117138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084904 restraints weight = 85211.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089915 restraints weight = 56207.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.090644 restraints weight = 34937.435| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10269 Z= 0.304 Angle : 0.645 7.548 13948 Z= 0.366 Chirality : 0.043 0.142 1518 Planarity : 0.006 0.092 1829 Dihedral : 5.061 35.656 1399 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1248 helix: 0.80 (0.31), residues: 254 sheet: -0.58 (0.25), residues: 369 loop : -0.92 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 745 HIS 0.006 0.002 HIS D 102 PHE 0.016 0.002 PHE A 791 TYR 0.022 0.002 TYR E 75 ARG 0.026 0.001 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 473) hydrogen bonds : angle 6.19807 ( 1287) SS BOND : bond 0.00199 ( 2) SS BOND : angle 0.99851 ( 4) covalent geometry : bond 0.00621 (10267) covalent geometry : angle 0.64509 (13944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8712 (m-30) cc_final: 0.8347 (m-30) REVERT: A 262 GLU cc_start: 0.6846 (tt0) cc_final: 0.6583 (tt0) REVERT: A 368 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8609 (mm-30) REVERT: A 735 THR cc_start: 0.9135 (m) cc_final: 0.8891 (p) REVERT: A 774 LEU cc_start: 0.8926 (tp) cc_final: 0.8662 (tp) REVERT: A 780 LEU cc_start: 0.9266 (mt) cc_final: 0.8890 (tp) REVERT: B 42 PHE cc_start: 0.6641 (t80) cc_final: 0.6311 (t80) REVERT: B 287 ASN cc_start: 0.9342 (m-40) cc_final: 0.9037 (t0) REVERT: B 388 TYR cc_start: 0.6458 (m-80) cc_final: 0.6181 (m-80) REVERT: D 114 LEU cc_start: 0.9114 (mt) cc_final: 0.8910 (mt) REVERT: D 116 ASN cc_start: 0.9396 (m-40) cc_final: 0.8679 (m110) REVERT: E 42 ASP cc_start: 0.8605 (m-30) cc_final: 0.8316 (m-30) REVERT: E 50 MET cc_start: 0.8893 (mtm) cc_final: 0.8659 (mtm) REVERT: E 101 LEU cc_start: 0.8666 (tp) cc_final: 0.8340 (tp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.5146 time to fit residues: 151.8818 Evaluate side-chains 181 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 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 = 0.3916 r_free = 0.3916 target = 0.119111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086371 restraints weight = 83200.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087848 restraints weight = 51113.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089314 restraints weight = 39694.921| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10269 Z= 0.123 Angle : 0.501 5.473 13948 Z= 0.276 Chirality : 0.042 0.150 1518 Planarity : 0.004 0.043 1829 Dihedral : 4.564 29.603 1399 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1248 helix: 1.13 (0.32), residues: 262 sheet: -0.57 (0.25), residues: 379 loop : -0.76 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 739 HIS 0.005 0.001 HIS B 165 PHE 0.012 0.001 PHE D 147 TYR 0.023 0.001 TYR D 184 ARG 0.013 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 473) hydrogen bonds : angle 5.70332 ( 1287) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.87753 ( 4) covalent geometry : bond 0.00253 (10267) covalent geometry : angle 0.50058 (13944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8574 (m-30) cc_final: 0.8215 (m-30) REVERT: A 262 GLU cc_start: 0.6788 (tt0) cc_final: 0.6545 (tt0) REVERT: A 368 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8651 (mm-30) REVERT: A 533 HIS cc_start: 0.7907 (t-90) cc_final: 0.7613 (t-90) REVERT: A 735 THR cc_start: 0.9136 (m) cc_final: 0.8783 (p) REVERT: A 774 LEU cc_start: 0.8918 (tp) cc_final: 0.8301 (tp) REVERT: A 775 GLN cc_start: 0.9089 (tt0) cc_final: 0.8622 (mp10) REVERT: A 776 TRP cc_start: 0.6875 (p90) cc_final: 0.6626 (p-90) REVERT: A 780 LEU cc_start: 0.9276 (mt) cc_final: 0.8854 (tp) REVERT: B 42 PHE cc_start: 0.6673 (t80) cc_final: 0.6317 (t80) REVERT: B 287 ASN cc_start: 0.9379 (m-40) cc_final: 0.9034 (t0) REVERT: B 388 TYR cc_start: 0.6347 (m-80) cc_final: 0.6002 (m-80) REVERT: D 50 GLN cc_start: 0.9339 (tm-30) cc_final: 0.9116 (tm-30) REVERT: D 116 ASN cc_start: 0.9293 (m-40) cc_final: 0.8568 (m110) REVERT: D 131 ASP cc_start: 0.8180 (t0) cc_final: 0.7804 (t70) REVERT: D 136 ASP cc_start: 0.9092 (t0) cc_final: 0.8891 (t0) REVERT: D 172 ASP cc_start: 0.8968 (m-30) cc_final: 0.8496 (t0) REVERT: D 219 GLU cc_start: 0.8866 (tt0) cc_final: 0.8573 (tp30) REVERT: E 36 ASN cc_start: 0.8159 (m-40) cc_final: 0.7945 (m-40) REVERT: E 42 ASP cc_start: 0.8484 (m-30) cc_final: 0.8216 (m-30) REVERT: E 50 MET cc_start: 0.8890 (mtm) cc_final: 0.8626 (mtm) REVERT: E 101 LEU cc_start: 0.8620 (tp) cc_final: 0.8346 (tp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.5395 time to fit residues: 177.8223 Evaluate side-chains 193 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 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 = 0.3932 r_free = 0.3932 target = 0.119879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081046 restraints weight = 82878.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085608 restraints weight = 38042.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088570 restraints weight = 24292.928| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10269 Z= 0.123 Angle : 0.486 5.359 13948 Z= 0.268 Chirality : 0.041 0.150 1518 Planarity : 0.004 0.043 1829 Dihedral : 4.393 26.037 1399 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1248 helix: 1.31 (0.32), residues: 263 sheet: -0.56 (0.25), residues: 379 loop : -0.73 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 PHE 0.010 0.001 PHE D 147 TYR 0.022 0.001 TYR D 184 ARG 0.010 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 473) hydrogen bonds : angle 5.56178 ( 1287) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.78983 ( 4) covalent geometry : bond 0.00255 (10267) covalent geometry : angle 0.48602 (13944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8678 (m-30) cc_final: 0.8343 (m-30) REVERT: A 262 GLU cc_start: 0.6639 (tt0) cc_final: 0.6348 (tt0) REVERT: A 368 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8785 (mm-30) REVERT: A 470 GLU cc_start: 0.8171 (tt0) cc_final: 0.7758 (tt0) REVERT: A 533 HIS cc_start: 0.8106 (t-90) cc_final: 0.7878 (t-90) REVERT: A 735 THR cc_start: 0.9172 (m) cc_final: 0.8937 (p) REVERT: A 780 LEU cc_start: 0.9238 (mt) cc_final: 0.8864 (tp) REVERT: B 42 PHE cc_start: 0.6925 (t80) cc_final: 0.6543 (t80) REVERT: B 287 ASN cc_start: 0.9411 (m-40) cc_final: 0.8942 (t0) REVERT: B 388 TYR cc_start: 0.6253 (m-80) cc_final: 0.5899 (m-80) REVERT: D 50 GLN cc_start: 0.9433 (tm-30) cc_final: 0.9195 (tm-30) REVERT: D 116 ASN cc_start: 0.9292 (m-40) cc_final: 0.8549 (m110) REVERT: D 131 ASP cc_start: 0.8120 (t0) cc_final: 0.7755 (t70) REVERT: D 136 ASP cc_start: 0.9151 (t0) cc_final: 0.8949 (t0) REVERT: D 172 ASP cc_start: 0.9118 (m-30) cc_final: 0.8646 (t0) REVERT: E 42 ASP cc_start: 0.8505 (m-30) cc_final: 0.8234 (m-30) REVERT: E 50 MET cc_start: 0.8862 (mtm) cc_final: 0.8653 (mtm) REVERT: E 101 LEU cc_start: 0.8511 (tp) cc_final: 0.8213 (tp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.5091 time to fit residues: 162.5854 Evaluate side-chains 194 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 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 = 0.3941 r_free = 0.3941 target = 0.120465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085670 restraints weight = 82801.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089935 restraints weight = 45152.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090463 restraints weight = 26133.633| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10269 Z= 0.108 Angle : 0.470 4.870 13948 Z= 0.258 Chirality : 0.041 0.148 1518 Planarity : 0.004 0.040 1829 Dihedral : 4.249 24.650 1399 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1248 helix: 1.49 (0.32), residues: 264 sheet: -0.49 (0.25), residues: 378 loop : -0.65 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 PHE 0.010 0.001 PHE D 147 TYR 0.023 0.001 TYR D 159 ARG 0.007 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 473) hydrogen bonds : angle 5.39032 ( 1287) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.78166 ( 4) covalent geometry : bond 0.00224 (10267) covalent geometry : angle 0.46943 (13944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8668 (m-30) cc_final: 0.8329 (m-30) REVERT: A 262 GLU cc_start: 0.6689 (tt0) cc_final: 0.6413 (tt0) REVERT: A 304 MET cc_start: 0.8827 (ttm) cc_final: 0.8507 (ttm) REVERT: A 306 ASP cc_start: 0.9020 (m-30) cc_final: 0.8764 (m-30) REVERT: A 307 ASP cc_start: 0.8835 (m-30) cc_final: 0.8511 (m-30) REVERT: A 367 ARG cc_start: 0.9101 (mtm180) cc_final: 0.8335 (mtm180) REVERT: A 368 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8543 (mm-30) REVERT: A 470 GLU cc_start: 0.8117 (tt0) cc_final: 0.7653 (tt0) REVERT: A 533 HIS cc_start: 0.8049 (t-90) cc_final: 0.7774 (t-90) REVERT: A 735 THR cc_start: 0.9158 (m) cc_final: 0.8811 (p) REVERT: A 774 LEU cc_start: 0.9034 (tp) cc_final: 0.8454 (tp) REVERT: A 775 GLN cc_start: 0.9112 (tt0) cc_final: 0.8672 (mp10) REVERT: A 780 LEU cc_start: 0.9250 (mt) cc_final: 0.8875 (tp) REVERT: B 42 PHE cc_start: 0.6786 (t80) cc_final: 0.6454 (t80) REVERT: B 287 ASN cc_start: 0.9385 (m-40) cc_final: 0.8986 (t0) REVERT: B 388 TYR cc_start: 0.6362 (m-80) cc_final: 0.5992 (m-80) REVERT: D 50 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9128 (tm-30) REVERT: D 116 ASN cc_start: 0.9365 (m-40) cc_final: 0.8670 (m110) REVERT: D 131 ASP cc_start: 0.8173 (t0) cc_final: 0.7789 (t70) REVERT: D 172 ASP cc_start: 0.9019 (m-30) cc_final: 0.8526 (t0) REVERT: D 219 GLU cc_start: 0.8965 (tt0) cc_final: 0.8477 (tp30) REVERT: C 81 ASP cc_start: 0.8401 (m-30) cc_final: 0.8195 (m-30) REVERT: E 42 ASP cc_start: 0.8576 (m-30) cc_final: 0.8316 (m-30) REVERT: E 101 LEU cc_start: 0.8591 (tp) cc_final: 0.8303 (tp) REVERT: P 1293 ASN cc_start: 0.9151 (p0) cc_final: 0.8930 (p0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.4866 time to fit residues: 154.2624 Evaluate side-chains 187 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 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 = 0.3934 r_free = 0.3934 target = 0.120012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081345 restraints weight = 82036.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085910 restraints weight = 37986.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088793 restraints weight = 24333.796| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10269 Z= 0.131 Angle : 0.484 5.215 13948 Z= 0.266 Chirality : 0.041 0.153 1518 Planarity : 0.004 0.046 1829 Dihedral : 4.276 28.693 1399 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1248 helix: 1.39 (0.32), residues: 265 sheet: -0.55 (0.25), residues: 378 loop : -0.73 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 PHE 0.014 0.001 PHE A 648 TYR 0.024 0.001 TYR D 159 ARG 0.007 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 473) hydrogen bonds : angle 5.37156 ( 1287) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.75578 ( 4) covalent geometry : bond 0.00273 (10267) covalent geometry : angle 0.48400 (13944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8682 (m-30) cc_final: 0.8369 (m-30) REVERT: A 262 GLU cc_start: 0.6594 (tt0) cc_final: 0.6282 (tt0) REVERT: A 304 MET cc_start: 0.8690 (ttm) cc_final: 0.8222 (ttm) REVERT: A 307 ASP cc_start: 0.8846 (m-30) cc_final: 0.8539 (m-30) REVERT: A 367 ARG cc_start: 0.9119 (mtm180) cc_final: 0.8310 (mtm180) REVERT: A 368 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8723 (mm-30) REVERT: A 470 GLU cc_start: 0.8174 (tt0) cc_final: 0.7784 (tt0) REVERT: A 533 HIS cc_start: 0.8245 (t-90) cc_final: 0.8011 (t-90) REVERT: A 618 TYR cc_start: 0.7609 (m-80) cc_final: 0.7147 (m-80) REVERT: A 735 THR cc_start: 0.9180 (m) cc_final: 0.8907 (p) REVERT: A 774 LEU cc_start: 0.9029 (tp) cc_final: 0.8807 (tp) REVERT: B 42 PHE cc_start: 0.7089 (t80) cc_final: 0.6699 (t80) REVERT: B 170 GLN cc_start: 0.9111 (mt0) cc_final: 0.8572 (tp-100) REVERT: B 171 LEU cc_start: 0.9469 (tt) cc_final: 0.9038 (tt) REVERT: B 287 ASN cc_start: 0.9436 (m-40) cc_final: 0.8934 (t0) REVERT: B 388 TYR cc_start: 0.6278 (m-80) cc_final: 0.5975 (m-80) REVERT: D 50 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9202 (tm-30) REVERT: D 116 ASN cc_start: 0.9359 (m-40) cc_final: 0.8685 (m110) REVERT: D 159 TYR cc_start: 0.8197 (p90) cc_final: 0.7990 (p90) REVERT: D 172 ASP cc_start: 0.9152 (m-30) cc_final: 0.8680 (t0) REVERT: C 81 ASP cc_start: 0.8530 (m-30) cc_final: 0.8321 (m-30) REVERT: E 36 ASN cc_start: 0.8477 (m-40) cc_final: 0.8059 (m-40) REVERT: E 42 ASP cc_start: 0.8575 (m-30) cc_final: 0.8313 (m-30) REVERT: P 1293 ASN cc_start: 0.9222 (p0) cc_final: 0.8979 (p0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5488 time to fit residues: 167.5983 Evaluate side-chains 189 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 66 optimal weight: 7.9990 chunk 20 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 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 = 0.3940 r_free = 0.3940 target = 0.120390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081730 restraints weight = 82543.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.086225 restraints weight = 38612.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.089105 restraints weight = 24944.395| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10269 Z= 0.107 Angle : 0.457 4.602 13948 Z= 0.251 Chirality : 0.041 0.148 1518 Planarity : 0.004 0.046 1829 Dihedral : 4.166 28.230 1399 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1248 helix: 1.55 (0.32), residues: 265 sheet: -0.54 (0.26), residues: 376 loop : -0.68 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 PHE 0.008 0.001 PHE D 147 TYR 0.021 0.001 TYR D 159 ARG 0.006 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 473) hydrogen bonds : angle 5.22980 ( 1287) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.73628 ( 4) covalent geometry : bond 0.00222 (10267) covalent geometry : angle 0.45666 (13944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6900.07 seconds wall clock time: 118 minutes 16.92 seconds (7096.92 seconds total)