Starting phenix.real_space_refine on Thu Sep 18 20:18:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tsz_26105/09_2025/7tsz_26105.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tsz_26105/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tsz_26105/09_2025/7tsz_26105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tsz_26105/09_2025/7tsz_26105.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tsz_26105/09_2025/7tsz_26105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tsz_26105/09_2025/7tsz_26105.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.77, per 1000 atoms: 0.19 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: 1.77 Conformation dependent library (CDL) restraints added in 714.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 5.09 Time building geometry restraints manager: 2.51 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: 1.010 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: 0.110 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.190 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG B 281 TYR 0.015 0.002 TYR D 184 PHE 0.013 0.002 PHE A 570 TRP 0.015 0.003 TRP E 73 HIS 0.009 0.003 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00535 (10267) covalent geometry : angle 0.88637 (13944) SS BOND : bond 0.00407 ( 2) SS BOND : angle 1.32199 ( 4) hydrogen bonds : bond 0.14909 ( 473) hydrogen bonds : angle 7.78933 ( 1287) *********************** 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 : 0.514 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: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8425 (mm) cc_final: 0.7997 (tp) REVERT: A 304 MET cc_start: 0.8980 (mtm) cc_final: 0.8407 (ttm) REVERT: A 307 ASP cc_start: 0.8940 (m-30) cc_final: 0.8635 (m-30) REVERT: A 372 MET cc_start: 0.8224 (mtp) cc_final: 0.7910 (mtm) REVERT: A 441 GLN cc_start: 0.9052 (tt0) cc_final: 0.8823 (tp40) REVERT: A 449 TRP cc_start: 0.8513 (t60) cc_final: 0.7990 (t60) REVERT: A 450 LEU cc_start: 0.9366 (mt) cc_final: 0.8804 (tt) REVERT: A 461 THR cc_start: 0.7913 (t) cc_final: 0.7040 (t) REVERT: A 586 PHE cc_start: 0.6726 (m-80) cc_final: 0.6509 (m-10) REVERT: B 112 SER cc_start: 0.8165 (p) cc_final: 0.7684 (p) REVERT: B 150 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7248 (mt-10) REVERT: B 369 THR cc_start: 0.7827 (p) cc_final: 0.7619 (p) REVERT: D 116 ASN cc_start: 0.9394 (m-40) cc_final: 0.8707 (m110) REVERT: D 172 ASP cc_start: 0.8765 (m-30) cc_final: 0.8438 (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: 0.8001 (t80) REVERT: E 92 THR cc_start: 0.8936 (m) cc_final: 0.8680 (p) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2644 time to fit residues: 120.4969 Evaluate side-chains 225 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.0010 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.123733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089389 restraints weight = 79657.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094246 restraints weight = 36067.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095521 restraints weight = 21568.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096010 restraints weight = 17002.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096651 restraints weight = 17114.889| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10269 Z= 0.121 Angle : 0.558 4.945 13948 Z= 0.313 Chirality : 0.043 0.152 1518 Planarity : 0.004 0.057 1829 Dihedral : 5.028 81.414 1399 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.22), residues: 1248 helix: 1.04 (0.31), residues: 265 sheet: 0.49 (0.24), residues: 385 loop : 0.18 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 212 TYR 0.021 0.001 TYR D 184 PHE 0.011 0.001 PHE D 147 TRP 0.013 0.001 TRP A 739 HIS 0.016 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00242 (10267) covalent geometry : angle 0.55809 (13944) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.68837 ( 4) hydrogen bonds : bond 0.04960 ( 473) hydrogen bonds : angle 6.30247 ( 1287) *********************** 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 275 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.659 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: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8365 (mm) cc_final: 0.7885 (tp) REVERT: A 305 GLU cc_start: 0.8883 (tt0) cc_final: 0.8657 (tt0) REVERT: A 307 ASP cc_start: 0.8950 (m-30) cc_final: 0.8563 (m-30) REVERT: A 470 GLU cc_start: 0.8330 (tt0) cc_final: 0.8113 (tt0) REVERT: A 547 ARG cc_start: 0.8512 (ptt90) cc_final: 0.8209 (ptm160) REVERT: A 586 PHE cc_start: 0.6841 (m-80) cc_final: 0.6100 (m-80) REVERT: B 287 ASN cc_start: 0.9278 (m-40) cc_final: 0.8876 (t0) REVERT: D 49 ARG cc_start: 0.9200 (tpt90) cc_final: 0.8964 (tpm170) REVERT: D 50 GLN cc_start: 0.9309 (tm-30) cc_final: 0.9019 (tm-30) REVERT: D 172 ASP cc_start: 0.9025 (m-30) cc_final: 0.8674 (t0) REVERT: D 183 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8013 (mm-30) REVERT: D 204 ASP cc_start: 0.7632 (m-30) cc_final: 0.7415 (m-30) REVERT: E 28 TYR cc_start: 0.8193 (t80) cc_final: 0.7888 (t80) REVERT: E 105 ASP cc_start: 0.7558 (p0) cc_final: 0.7171 (p0) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2487 time to fit residues: 94.1066 Evaluate side-chains 212 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088226 restraints weight = 86273.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090435 restraints weight = 45531.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092346 restraints weight = 33682.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.093532 restraints weight = 25178.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094078 restraints weight = 23807.461| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10269 Z= 0.203 Angle : 0.560 5.141 13948 Z= 0.316 Chirality : 0.042 0.147 1518 Planarity : 0.004 0.052 1829 Dihedral : 5.120 86.544 1399 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.22), residues: 1248 helix: 1.29 (0.32), residues: 260 sheet: 0.15 (0.24), residues: 374 loop : -0.08 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 135 TYR 0.018 0.002 TYR D 184 PHE 0.014 0.001 PHE D 95 TRP 0.008 0.001 TRP A 576 HIS 0.006 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00418 (10267) covalent geometry : angle 0.56004 (13944) SS BOND : bond 0.00396 ( 2) SS BOND : angle 1.35155 ( 4) hydrogen bonds : bond 0.04463 ( 473) hydrogen bonds : angle 6.05958 ( 1287) *********************** 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 254 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.548 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: A 306 ASP cc_start: 0.9060 (m-30) cc_final: 0.8837 (m-30) REVERT: A 307 ASP cc_start: 0.8926 (m-30) cc_final: 0.8553 (m-30) REVERT: A 371 GLN cc_start: 0.8251 (tp40) cc_final: 0.7985 (tp40) REVERT: A 420 GLU cc_start: 0.8426 (pm20) cc_final: 0.7992 (pm20) REVERT: A 470 GLU cc_start: 0.8474 (tt0) cc_final: 0.8183 (tt0) REVERT: A 586 PHE cc_start: 0.6999 (m-80) cc_final: 0.6158 (m-80) REVERT: B 174 LEU cc_start: 0.9404 (mp) cc_final: 0.9190 (mp) REVERT: B 287 ASN cc_start: 0.9288 (m-40) cc_final: 0.8924 (t0) REVERT: B 369 THR cc_start: 0.7990 (p) cc_final: 0.7785 (p) REVERT: B 388 TYR cc_start: 0.6131 (m-80) cc_final: 0.5732 (m-80) REVERT: D 50 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9033 (tm-30) REVERT: D 172 ASP cc_start: 0.9012 (m-30) cc_final: 0.8611 (t0) REVERT: D 219 GLU cc_start: 0.8935 (tt0) cc_final: 0.8530 (tp30) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2482 time to fit residues: 86.7232 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 : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.121235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086980 restraints weight = 80862.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091043 restraints weight = 41310.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091654 restraints weight = 23269.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092140 restraints weight = 21627.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092362 restraints weight = 20495.901| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4049 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= 0.125 Angle : 0.490 5.628 13948 Z= 0.273 Chirality : 0.042 0.143 1518 Planarity : 0.004 0.057 1829 Dihedral : 4.965 89.651 1399 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.23), residues: 1248 helix: 1.43 (0.32), residues: 262 sheet: 0.02 (0.25), residues: 373 loop : -0.22 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.021 0.001 TYR A 578 PHE 0.009 0.001 PHE D 147 TRP 0.006 0.001 TRP A 635 HIS 0.005 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00254 (10267) covalent geometry : angle 0.48986 (13944) SS BOND : bond 0.00165 ( 2) SS BOND : angle 1.53686 ( 4) hydrogen bonds : bond 0.03854 ( 473) hydrogen bonds : angle 5.67699 ( 1287) *********************** 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 243 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.431 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: 0.8661 (m-30) cc_final: 0.8227 (m-30) REVERT: A 304 MET cc_start: 0.8943 (mtm) cc_final: 0.8655 (mtp) REVERT: A 305 GLU cc_start: 0.8824 (tt0) cc_final: 0.8593 (tt0) REVERT: A 307 ASP cc_start: 0.8882 (m-30) cc_final: 0.8520 (m-30) REVERT: A 371 GLN cc_start: 0.8269 (tp40) cc_final: 0.7901 (tp-100) REVERT: A 419 LYS cc_start: 0.8495 (tppt) cc_final: 0.8169 (mtmt) REVERT: A 547 ARG cc_start: 0.8384 (ptm160) cc_final: 0.7781 (ptm160) REVERT: A 586 PHE cc_start: 0.6912 (m-80) cc_final: 0.6070 (m-80) REVERT: B 111 LEU cc_start: 0.8726 (mp) cc_final: 0.8355 (mp) REVERT: B 287 ASN cc_start: 0.9317 (m-40) cc_final: 0.8967 (t0) REVERT: B 388 TYR cc_start: 0.6142 (m-80) cc_final: 0.5773 (m-80) REVERT: D 50 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8997 (tm-30) REVERT: D 131 ASP cc_start: 0.8176 (t0) cc_final: 0.7972 (t0) REVERT: D 172 ASP cc_start: 0.8939 (m-30) cc_final: 0.8491 (t0) REVERT: D 219 GLU cc_start: 0.8872 (tt0) cc_final: 0.8471 (tp30) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2308 time to fit residues: 78.5313 Evaluate side-chains 196 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 8.9990 chunk 60 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.121630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.087722 restraints weight = 80304.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.092239 restraints weight = 42556.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092750 restraints weight = 24056.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093279 restraints weight = 21353.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093543 restraints weight = 20172.853| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4353 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= 0.119 Angle : 0.474 5.318 13948 Z= 0.262 Chirality : 0.041 0.147 1518 Planarity : 0.004 0.044 1829 Dihedral : 4.833 84.312 1399 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.22), residues: 1248 helix: 1.51 (0.31), residues: 262 sheet: 0.00 (0.25), residues: 362 loop : -0.40 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 321 TYR 0.021 0.001 TYR D 184 PHE 0.013 0.001 PHE D 147 TRP 0.007 0.001 TRP A 576 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00244 (10267) covalent geometry : angle 0.47429 (13944) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.86870 ( 4) hydrogen bonds : bond 0.03656 ( 473) hydrogen bonds : angle 5.54154 ( 1287) *********************** 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 241 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.565 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: A 222 ASP cc_start: 0.8611 (m-30) cc_final: 0.8169 (m-30) REVERT: A 371 GLN cc_start: 0.8071 (tp40) cc_final: 0.7777 (tp-100) REVERT: A 419 LYS cc_start: 0.8485 (tppt) cc_final: 0.8121 (mtmt) REVERT: A 586 PHE cc_start: 0.6891 (m-80) cc_final: 0.6049 (m-80) REVERT: A 780 LEU cc_start: 0.9183 (mt) cc_final: 0.8772 (tp) REVERT: B 287 ASN cc_start: 0.9312 (m-40) cc_final: 0.8976 (t0) REVERT: B 388 TYR cc_start: 0.6145 (m-80) cc_final: 0.5791 (m-80) REVERT: D 50 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8980 (tm-30) REVERT: D 131 ASP cc_start: 0.8207 (t0) cc_final: 0.7950 (t70) REVERT: D 146 ASP cc_start: 0.9165 (m-30) cc_final: 0.8888 (m-30) REVERT: D 167 LEU cc_start: 0.8985 (mm) cc_final: 0.8729 (tp) REVERT: D 172 ASP cc_start: 0.8940 (m-30) cc_final: 0.8460 (t0) REVERT: D 219 GLU cc_start: 0.8855 (tt0) cc_final: 0.8394 (tp30) REVERT: E 101 LEU cc_start: 0.8501 (tp) cc_final: 0.8293 (tp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2343 time to fit residues: 79.1952 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN D 54 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.120268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086226 restraints weight = 86476.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089463 restraints weight = 51831.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090961 restraints weight = 33105.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.092013 restraints weight = 25603.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.092581 restraints weight = 23969.424| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10269 Z= 0.195 Angle : 0.531 5.649 13948 Z= 0.297 Chirality : 0.041 0.144 1518 Planarity : 0.004 0.055 1829 Dihedral : 4.855 68.190 1399 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.22), residues: 1248 helix: 1.34 (0.31), residues: 261 sheet: -0.33 (0.25), residues: 368 loop : -0.66 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 132 TYR 0.020 0.002 TYR D 184 PHE 0.013 0.001 PHE D 147 TRP 0.008 0.001 TRP A 576 HIS 0.005 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00398 (10267) covalent geometry : angle 0.53077 (13944) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.85360 ( 4) hydrogen bonds : bond 0.03894 ( 473) hydrogen bonds : angle 5.71051 ( 1287) *********************** 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 238 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.540 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: A 222 ASP cc_start: 0.8701 (m-30) cc_final: 0.8323 (m-30) REVERT: A 306 ASP cc_start: 0.9063 (m-30) cc_final: 0.8856 (m-30) REVERT: A 367 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8318 (mtm-85) REVERT: A 419 LYS cc_start: 0.8648 (tppt) cc_final: 0.8273 (mtmt) REVERT: A 586 PHE cc_start: 0.7073 (m-80) cc_final: 0.6168 (m-80) REVERT: A 741 MET cc_start: 0.6638 (pmm) cc_final: 0.6429 (pmm) REVERT: B 42 PHE cc_start: 0.6610 (t80) cc_final: 0.6256 (t80) REVERT: B 287 ASN cc_start: 0.9365 (m-40) cc_final: 0.9010 (t0) REVERT: B 388 TYR cc_start: 0.6285 (m-80) cc_final: 0.5895 (m-80) REVERT: D 50 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9114 (tm-30) REVERT: D 131 ASP cc_start: 0.8151 (t0) cc_final: 0.7667 (t70) REVERT: D 146 ASP cc_start: 0.9231 (m-30) cc_final: 0.8959 (m-30) REVERT: D 172 ASP cc_start: 0.9049 (m-30) cc_final: 0.8599 (t0) REVERT: E 101 LEU cc_start: 0.8635 (tp) cc_final: 0.8412 (tp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2556 time to fit residues: 83.4076 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 : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 69 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.121846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088143 restraints weight = 85760.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091065 restraints weight = 48332.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092470 restraints weight = 32893.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093387 restraints weight = 24795.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093735 restraints weight = 22897.184| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10269 Z= 0.106 Angle : 0.469 5.390 13948 Z= 0.258 Chirality : 0.041 0.144 1518 Planarity : 0.004 0.041 1829 Dihedral : 4.518 57.118 1399 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.23), residues: 1248 helix: 1.60 (0.32), residues: 262 sheet: -0.28 (0.25), residues: 363 loop : -0.58 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 132 TYR 0.022 0.001 TYR D 184 PHE 0.016 0.001 PHE D 95 TRP 0.006 0.001 TRP A 739 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00222 (10267) covalent geometry : angle 0.46886 (13944) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.76415 ( 4) hydrogen bonds : bond 0.03453 ( 473) hydrogen bonds : angle 5.39764 ( 1287) *********************** 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 : 0.565 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: A 222 ASP cc_start: 0.8654 (m-30) cc_final: 0.8184 (m-30) REVERT: A 223 LEU cc_start: 0.9543 (mp) cc_final: 0.8886 (tt) REVERT: A 305 GLU cc_start: 0.8852 (tt0) cc_final: 0.8591 (tt0) REVERT: A 306 ASP cc_start: 0.9071 (m-30) cc_final: 0.8848 (m-30) REVERT: A 307 ASP cc_start: 0.8879 (m-30) cc_final: 0.8524 (m-30) REVERT: A 419 LYS cc_start: 0.8579 (tppt) cc_final: 0.8224 (mtmt) REVERT: A 533 HIS cc_start: 0.8151 (t-90) cc_final: 0.7939 (t-90) REVERT: A 586 PHE cc_start: 0.6995 (m-80) cc_final: 0.5761 (m-80) REVERT: A 780 LEU cc_start: 0.9219 (mt) cc_final: 0.8828 (tp) REVERT: B 42 PHE cc_start: 0.6653 (t80) cc_final: 0.6291 (t80) REVERT: B 287 ASN cc_start: 0.9379 (m-40) cc_final: 0.8985 (t0) REVERT: B 388 TYR cc_start: 0.6273 (m-80) cc_final: 0.5862 (m-80) REVERT: D 50 GLN cc_start: 0.9294 (tm-30) cc_final: 0.9047 (tm-30) REVERT: D 131 ASP cc_start: 0.8104 (t0) cc_final: 0.7649 (t70) REVERT: D 172 ASP cc_start: 0.9007 (m-30) cc_final: 0.8542 (t0) REVERT: D 219 GLU cc_start: 0.8870 (tt0) cc_final: 0.8362 (tp30) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2591 time to fit residues: 83.4469 Evaluate side-chains 195 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.118934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080591 restraints weight = 82531.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085069 restraints weight = 38659.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087955 restraints weight = 24812.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089693 restraints weight = 19093.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.090809 restraints weight = 16379.667| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10269 Z= 0.200 Angle : 0.526 6.255 13948 Z= 0.296 Chirality : 0.041 0.148 1518 Planarity : 0.004 0.048 1829 Dihedral : 4.600 43.320 1399 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.23), residues: 1248 helix: 1.23 (0.31), residues: 264 sheet: -0.39 (0.25), residues: 367 loop : -0.72 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 132 TYR 0.022 0.002 TYR D 159 PHE 0.010 0.001 PHE A 791 TRP 0.007 0.001 TRP A 745 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00409 (10267) covalent geometry : angle 0.52623 (13944) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.73921 ( 4) hydrogen bonds : bond 0.03828 ( 473) hydrogen bonds : angle 5.66576 ( 1287) *********************** 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 223 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.434 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: A 222 ASP cc_start: 0.8663 (m-30) cc_final: 0.8292 (m-30) REVERT: A 224 GLU cc_start: 0.9083 (mp0) cc_final: 0.8799 (mp0) REVERT: A 232 ASP cc_start: 0.7744 (m-30) cc_final: 0.7521 (m-30) REVERT: A 307 ASP cc_start: 0.8832 (m-30) cc_final: 0.8518 (m-30) REVERT: A 419 LYS cc_start: 0.8500 (tppt) cc_final: 0.8188 (mtmt) REVERT: A 533 HIS cc_start: 0.8074 (t-90) cc_final: 0.7850 (t-90) REVERT: A 586 PHE cc_start: 0.7106 (m-80) cc_final: 0.6865 (m-10) REVERT: A 618 TYR cc_start: 0.7640 (m-80) cc_final: 0.7274 (m-80) REVERT: A 735 THR cc_start: 0.9127 (m) cc_final: 0.8857 (p) REVERT: A 780 LEU cc_start: 0.9175 (mt) cc_final: 0.8796 (tp) REVERT: B 42 PHE cc_start: 0.6671 (t80) cc_final: 0.6322 (t80) REVERT: B 287 ASN cc_start: 0.9394 (m-40) cc_final: 0.8942 (t0) REVERT: B 388 TYR cc_start: 0.6306 (m-80) cc_final: 0.5920 (m-80) REVERT: D 50 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9167 (tm-30) REVERT: D 131 ASP cc_start: 0.7948 (t0) cc_final: 0.7581 (t70) REVERT: D 146 ASP cc_start: 0.9233 (m-30) cc_final: 0.8985 (m-30) REVERT: E 41 ASN cc_start: 0.9510 (p0) cc_final: 0.9147 (p0) REVERT: E 101 LEU cc_start: 0.8502 (tp) cc_final: 0.8264 (tp) REVERT: P 1293 ASN cc_start: 0.9154 (p0) cc_final: 0.8894 (p0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2345 time to fit residues: 71.7831 Evaluate side-chains 192 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN E 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.120064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.087543 restraints weight = 81014.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089368 restraints weight = 48320.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.091213 restraints weight = 35228.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091669 restraints weight = 24861.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.092370 restraints weight = 23505.937| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10269 Z= 0.128 Angle : 0.482 5.508 13948 Z= 0.267 Chirality : 0.041 0.148 1518 Planarity : 0.004 0.044 1829 Dihedral : 4.438 37.519 1399 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.23), residues: 1248 helix: 1.36 (0.32), residues: 266 sheet: -0.45 (0.25), residues: 374 loop : -0.63 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 132 TYR 0.025 0.001 TYR D 159 PHE 0.009 0.001 PHE D 147 TRP 0.018 0.001 TRP A 739 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00263 (10267) covalent geometry : angle 0.48214 (13944) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.75215 ( 4) hydrogen bonds : bond 0.03559 ( 473) hydrogen bonds : angle 5.46544 ( 1287) *********************** 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 221 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.529 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: A 222 ASP cc_start: 0.8534 (m-30) cc_final: 0.8164 (m-30) REVERT: A 223 LEU cc_start: 0.9572 (mt) cc_final: 0.9296 (tt) REVERT: A 232 ASP cc_start: 0.7662 (m-30) cc_final: 0.7437 (m-30) REVERT: A 306 ASP cc_start: 0.8975 (m-30) cc_final: 0.8768 (m-30) REVERT: A 307 ASP cc_start: 0.8786 (m-30) cc_final: 0.8468 (m-30) REVERT: A 367 ARG cc_start: 0.8958 (mtm-85) cc_final: 0.8051 (mtm-85) REVERT: A 419 LYS cc_start: 0.8543 (tppt) cc_final: 0.8244 (mtmt) REVERT: A 470 GLU cc_start: 0.8201 (tt0) cc_final: 0.7948 (tt0) REVERT: A 533 HIS cc_start: 0.7907 (t-90) cc_final: 0.7642 (t-90) REVERT: A 586 PHE cc_start: 0.7011 (m-80) cc_final: 0.6767 (m-10) REVERT: A 618 TYR cc_start: 0.7490 (m-80) cc_final: 0.7127 (m-80) REVERT: A 735 THR cc_start: 0.9122 (m) cc_final: 0.8852 (p) REVERT: A 780 LEU cc_start: 0.9172 (mt) cc_final: 0.8796 (tp) REVERT: B 42 PHE cc_start: 0.6620 (t80) cc_final: 0.6337 (t80) REVERT: B 287 ASN cc_start: 0.9314 (m-40) cc_final: 0.8972 (t0) REVERT: B 388 TYR cc_start: 0.6381 (m-80) cc_final: 0.6045 (m-80) REVERT: D 50 GLN cc_start: 0.9284 (tm-30) cc_final: 0.9080 (tm-30) REVERT: D 131 ASP cc_start: 0.8026 (t0) cc_final: 0.7667 (t70) REVERT: D 146 ASP cc_start: 0.9123 (m-30) cc_final: 0.8903 (m-30) REVERT: D 172 ASP cc_start: 0.8879 (m-30) cc_final: 0.8464 (t0) REVERT: E 41 ASN cc_start: 0.9548 (p0) cc_final: 0.9207 (p0) REVERT: E 101 LEU cc_start: 0.8580 (tp) cc_final: 0.8289 (tp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2303 time to fit residues: 70.3419 Evaluate side-chains 190 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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: 6.9990 chunk 125 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.120144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087575 restraints weight = 81370.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089781 restraints weight = 48192.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.091384 restraints weight = 35005.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091973 restraints weight = 24805.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092607 restraints weight = 23344.765| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10269 Z= 0.124 Angle : 0.475 5.503 13948 Z= 0.263 Chirality : 0.041 0.149 1518 Planarity : 0.004 0.046 1829 Dihedral : 4.317 30.789 1399 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.23), residues: 1248 helix: 1.48 (0.32), residues: 266 sheet: -0.47 (0.25), residues: 374 loop : -0.63 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 132 TYR 0.023 0.001 TYR D 159 PHE 0.008 0.001 PHE A 791 TRP 0.018 0.001 TRP A 739 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00256 (10267) covalent geometry : angle 0.47528 (13944) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.72472 ( 4) hydrogen bonds : bond 0.03459 ( 473) hydrogen bonds : angle 5.41039 ( 1287) ********************** 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 219 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.332 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: A 222 ASP cc_start: 0.8503 (m-30) cc_final: 0.8159 (m-30) REVERT: A 223 LEU cc_start: 0.9594 (mt) cc_final: 0.9307 (tt) REVERT: A 232 ASP cc_start: 0.7686 (m-30) cc_final: 0.7453 (m-30) REVERT: A 307 ASP cc_start: 0.8801 (m-30) cc_final: 0.8468 (m-30) REVERT: A 419 LYS cc_start: 0.8510 (tppt) cc_final: 0.8233 (mtmt) REVERT: A 470 GLU cc_start: 0.8165 (tt0) cc_final: 0.7948 (tt0) REVERT: A 533 HIS cc_start: 0.7844 (t-90) cc_final: 0.7579 (t-90) REVERT: A 547 ARG cc_start: 0.8260 (ptm160) cc_final: 0.7896 (ptm160) REVERT: A 586 PHE cc_start: 0.6990 (m-80) cc_final: 0.6754 (m-10) REVERT: A 735 THR cc_start: 0.9045 (m) cc_final: 0.8787 (p) REVERT: A 780 LEU cc_start: 0.9169 (mt) cc_final: 0.8788 (tp) REVERT: B 42 PHE cc_start: 0.6728 (t80) cc_final: 0.6476 (t80) REVERT: B 287 ASN cc_start: 0.9334 (m-40) cc_final: 0.9012 (t0) REVERT: B 388 TYR cc_start: 0.6322 (m-80) cc_final: 0.5912 (m-80) REVERT: D 50 GLN cc_start: 0.9252 (tm-30) cc_final: 0.9011 (tm-30) REVERT: D 131 ASP cc_start: 0.7973 (t0) cc_final: 0.7655 (t70) REVERT: D 146 ASP cc_start: 0.9116 (m-30) cc_final: 0.8878 (m-30) REVERT: D 172 ASP cc_start: 0.8891 (m-30) cc_final: 0.8452 (t0) REVERT: E 41 ASN cc_start: 0.9555 (p0) cc_final: 0.9199 (p0) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2445 time to fit residues: 73.5051 Evaluate side-chains 192 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 115 optimal weight: 0.0980 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.121094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088053 restraints weight = 81333.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.090764 restraints weight = 47804.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.092234 restraints weight = 31561.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092559 restraints weight = 24477.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.092926 restraints weight = 23096.847| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10269 Z= 0.098 Angle : 0.468 5.165 13948 Z= 0.256 Chirality : 0.041 0.150 1518 Planarity : 0.004 0.042 1829 Dihedral : 4.190 28.541 1399 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.23), residues: 1248 helix: 1.51 (0.31), residues: 266 sheet: -0.46 (0.25), residues: 372 loop : -0.55 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 132 TYR 0.022 0.001 TYR D 184 PHE 0.008 0.001 PHE A 395 TRP 0.017 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00207 (10267) covalent geometry : angle 0.46807 (13944) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.71667 ( 4) hydrogen bonds : bond 0.03353 ( 473) hydrogen bonds : angle 5.24935 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3549.26 seconds wall clock time: 61 minutes 10.79 seconds (3670.79 seconds total)