Starting phenix.real_space_refine on Thu Jan 23 07:30:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tsz_26105/01_2025/7tsz_26105.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tsz_26105/01_2025/7tsz_26105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tsz_26105/01_2025/7tsz_26105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tsz_26105/01_2025/7tsz_26105.map" model { file = "/net/cci-nas-00/data/ceres_data/7tsz_26105/01_2025/7tsz_26105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tsz_26105/01_2025/7tsz_26105.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 6345 2.51 5 N 1712 2.21 5 O 1964 1.98 5 H 9670 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19722 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9195 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 572} Chain breaks: 7 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 4930 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 11, 'TRANS': 320} Chain breaks: 6 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 676 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "E" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1371 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "P" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 160 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Time building chain proxies: 9.30, per 1000 atoms: 0.47 Number of scatterers: 19722 At special positions: 0 Unit cell: (112.751, 125.637, 139.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 O 1964 8.00 N 1712 7.00 C 6345 6.00 H 9670 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 24.9% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 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: 8.06 Time building geometry restraints manager: 6.29 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.400 Extract box with map and model: 0.790 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 43.200 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.010 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.230 ------------------------------------------------------------------------------- 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 10267 Z= 0.353 Angle : 0.886 8.944 13944 Z= 0.540 Chirality : 0.048 0.205 1518 Planarity : 0.005 0.048 1829 Dihedral : 11.128 89.114 3684 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1248 helix: 0.09 (0.29), residues: 247 sheet: 0.84 (0.24), residues: 389 loop : 0.58 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 73 HIS 0.009 0.003 HIS D 139 PHE 0.013 0.002 PHE A 570 TYR 0.015 0.002 TYR D 184 ARG 0.011 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8425 (mm) cc_final: 0.7996 (tp) REVERT: A 303 LYS cc_start: 0.9390 (tttm) cc_final: 0.8941 (ttpp) REVERT: A 304 MET cc_start: 0.8980 (mtm) cc_final: 0.8404 (ttm) REVERT: A 307 ASP cc_start: 0.8940 (m-30) cc_final: 0.8634 (m-30) REVERT: A 372 MET cc_start: 0.8224 (mtp) cc_final: 0.7911 (mtm) REVERT: A 441 GLN cc_start: 0.9052 (tt0) cc_final: 0.8822 (tp40) REVERT: A 449 TRP cc_start: 0.8513 (t60) cc_final: 0.7989 (t60) REVERT: A 450 LEU cc_start: 0.9366 (mt) cc_final: 0.8810 (tt) REVERT: A 461 THR cc_start: 0.7913 (t) cc_final: 0.7044 (t) REVERT: A 540 GLN cc_start: 0.8476 (tp40) cc_final: 0.8058 (tp40) REVERT: B 112 SER cc_start: 0.8165 (p) cc_final: 0.7682 (p) REVERT: B 150 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 369 THR cc_start: 0.7827 (p) cc_final: 0.7622 (p) REVERT: D 116 ASN cc_start: 0.9394 (m-40) cc_final: 0.8749 (m110) REVERT: D 172 ASP cc_start: 0.8765 (m-30) cc_final: 0.8422 (t0) REVERT: D 183 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8226 (pt0) REVERT: E 28 TYR cc_start: 0.8302 (t80) cc_final: 0.7999 (t80) REVERT: E 92 THR cc_start: 0.8936 (m) cc_final: 0.8678 (p) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.5516 time to fit residues: 250.7786 Evaluate side-chains 222 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 230 GLN E 36 ASN E 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.119499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080079 restraints weight = 89244.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084624 restraints weight = 41781.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087543 restraints weight = 27028.470| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10267 Z= 0.448 Angle : 0.723 8.363 13944 Z= 0.413 Chirality : 0.044 0.154 1518 Planarity : 0.006 0.078 1829 Dihedral : 5.605 82.129 1399 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1248 helix: 0.89 (0.31), residues: 251 sheet: -0.02 (0.24), residues: 385 loop : -0.20 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 73 HIS 0.016 0.002 HIS B 324 PHE 0.022 0.002 PHE D 147 TYR 0.024 0.002 TYR A 578 ARG 0.006 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.6714 (tt0) cc_final: 0.6450 (tt0) REVERT: A 284 ILE cc_start: 0.8411 (mm) cc_final: 0.7960 (tp) REVERT: A 303 LYS cc_start: 0.9372 (tttm) cc_final: 0.9118 (tttt) REVERT: A 307 ASP cc_start: 0.8925 (m-30) cc_final: 0.8607 (m-30) REVERT: A 367 ARG cc_start: 0.9223 (mtm180) cc_final: 0.8955 (mtm-85) REVERT: A 383 ASP cc_start: 0.8697 (m-30) cc_final: 0.8431 (m-30) REVERT: A 419 LYS cc_start: 0.9096 (tttt) cc_final: 0.8792 (tppt) REVERT: A 420 GLU cc_start: 0.8616 (pm20) cc_final: 0.8084 (pm20) REVERT: A 423 THR cc_start: 0.9378 (p) cc_final: 0.9167 (p) REVERT: A 449 TRP cc_start: 0.8321 (t60) cc_final: 0.8052 (t60) REVERT: A 450 LEU cc_start: 0.9436 (mt) cc_final: 0.8994 (tt) REVERT: A 521 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8247 (mt-10) REVERT: A 531 TYR cc_start: 0.8800 (p90) cc_final: 0.8563 (p90) REVERT: A 586 PHE cc_start: 0.6687 (m-80) cc_final: 0.5647 (m-10) REVERT: A 775 GLN cc_start: 0.9145 (tt0) cc_final: 0.8750 (tt0) REVERT: B 287 ASN cc_start: 0.9267 (m-40) cc_final: 0.8871 (t0) REVERT: B 388 TYR cc_start: 0.6085 (m-80) cc_final: 0.5665 (m-80) REVERT: D 50 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9148 (tm-30) REVERT: D 102 HIS cc_start: 0.8737 (t70) cc_final: 0.8073 (t70) REVERT: D 111 MET cc_start: 0.9143 (mmm) cc_final: 0.8743 (mtt) REVERT: D 116 ASN cc_start: 0.9339 (m-40) cc_final: 0.8312 (m110) REVERT: D 131 ASP cc_start: 0.8341 (t0) cc_final: 0.8089 (t0) REVERT: D 135 ARG cc_start: 0.7935 (mpt180) cc_final: 0.7681 (mtt90) REVERT: D 172 ASP cc_start: 0.9100 (m-30) cc_final: 0.8681 (t0) REVERT: E 42 ASP cc_start: 0.8523 (m-30) cc_final: 0.8286 (m-30) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.5262 time to fit residues: 182.9066 Evaluate side-chains 188 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 40.0000 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.120128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085463 restraints weight = 80732.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087301 restraints weight = 37560.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.089213 restraints weight = 25816.157| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10267 Z= 0.202 Angle : 0.547 6.623 13944 Z= 0.306 Chirality : 0.043 0.174 1518 Planarity : 0.004 0.057 1829 Dihedral : 5.142 73.949 1399 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1248 helix: 1.18 (0.31), residues: 260 sheet: 0.04 (0.25), residues: 367 loop : -0.33 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 739 HIS 0.007 0.001 HIS D 139 PHE 0.014 0.001 PHE D 147 TYR 0.024 0.001 TYR D 184 ARG 0.004 0.000 ARG D 49 *********************** 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 251 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.6593 (tt0) cc_final: 0.6340 (tt0) REVERT: A 303 LYS cc_start: 0.9313 (tttm) cc_final: 0.8985 (ttpt) REVERT: A 305 GLU cc_start: 0.8851 (tt0) cc_final: 0.8611 (tt0) REVERT: A 307 ASP cc_start: 0.8886 (m-30) cc_final: 0.8583 (m-30) REVERT: A 367 ARG cc_start: 0.9191 (mtm180) cc_final: 0.8929 (mtm-85) REVERT: A 419 LYS cc_start: 0.9030 (tttt) cc_final: 0.8703 (tppt) REVERT: A 420 GLU cc_start: 0.8651 (pm20) cc_final: 0.8065 (pm20) REVERT: A 449 TRP cc_start: 0.8334 (t60) cc_final: 0.8005 (t60) REVERT: A 450 LEU cc_start: 0.9460 (mt) cc_final: 0.8965 (tt) REVERT: A 586 PHE cc_start: 0.6713 (m-80) cc_final: 0.6010 (m-10) REVERT: A 775 GLN cc_start: 0.9145 (tt0) cc_final: 0.8796 (tt0) REVERT: B 111 LEU cc_start: 0.8700 (mt) cc_final: 0.8500 (mp) REVERT: B 287 ASN cc_start: 0.9338 (m-40) cc_final: 0.8913 (t0) REVERT: B 388 TYR cc_start: 0.6096 (m-80) cc_final: 0.5759 (m-80) REVERT: D 50 GLN cc_start: 0.9368 (tm-30) cc_final: 0.9126 (tm-30) REVERT: D 102 HIS cc_start: 0.8734 (t70) cc_final: 0.7943 (t70) REVERT: D 131 ASP cc_start: 0.8345 (t0) cc_final: 0.8103 (t70) REVERT: D 172 ASP cc_start: 0.9038 (m-30) cc_final: 0.8639 (t0) REVERT: E 36 ASN cc_start: 0.8100 (m-40) cc_final: 0.7820 (m-40) REVERT: E 42 ASP cc_start: 0.8578 (m-30) cc_final: 0.8355 (m-30) REVERT: E 50 MET cc_start: 0.8889 (mtm) cc_final: 0.8511 (mtm) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.5183 time to fit residues: 179.6570 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 : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.119262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086280 restraints weight = 82274.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088683 restraints weight = 46783.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089987 restraints weight = 33369.998| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10267 Z= 0.234 Angle : 0.532 6.059 13944 Z= 0.298 Chirality : 0.041 0.150 1518 Planarity : 0.004 0.047 1829 Dihedral : 4.838 55.101 1399 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1248 helix: 1.16 (0.31), residues: 261 sheet: -0.16 (0.25), residues: 363 loop : -0.58 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 739 HIS 0.005 0.001 HIS B 324 PHE 0.019 0.001 PHE D 95 TYR 0.022 0.002 TYR D 184 ARG 0.003 0.000 ARG D 135 *********************** 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 237 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.784 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: 0.8623 (m-30) cc_final: 0.8215 (m-30) REVERT: A 303 LYS cc_start: 0.9325 (tttm) cc_final: 0.8996 (ttpt) REVERT: A 304 MET cc_start: 0.8981 (mtm) cc_final: 0.8392 (ttm) REVERT: A 307 ASP cc_start: 0.8824 (m-30) cc_final: 0.8543 (m-30) REVERT: A 368 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8745 (mm-30) REVERT: A 419 LYS cc_start: 0.9027 (tttt) cc_final: 0.8704 (tppt) REVERT: A 420 GLU cc_start: 0.8716 (pm20) cc_final: 0.8084 (pm20) REVERT: A 449 TRP cc_start: 0.8392 (t60) cc_final: 0.8157 (t60) REVERT: A 450 LEU cc_start: 0.9441 (mt) cc_final: 0.9080 (mm) REVERT: A 586 PHE cc_start: 0.6721 (m-80) cc_final: 0.6051 (m-10) REVERT: A 774 LEU cc_start: 0.8844 (tp) cc_final: 0.8631 (tp) REVERT: A 775 GLN cc_start: 0.8954 (tt0) cc_final: 0.8674 (tt0) REVERT: A 780 LEU cc_start: 0.9234 (mt) cc_final: 0.8807 (tp) REVERT: B 42 PHE cc_start: 0.6250 (t80) cc_final: 0.5964 (t80) REVERT: B 111 LEU cc_start: 0.8702 (mt) cc_final: 0.8486 (mp) REVERT: B 287 ASN cc_start: 0.9306 (m-40) cc_final: 0.9030 (t0) REVERT: B 388 TYR cc_start: 0.6289 (m-80) cc_final: 0.6001 (m-80) REVERT: D 50 GLN cc_start: 0.9265 (tm-30) cc_final: 0.9031 (tm-30) REVERT: D 172 ASP cc_start: 0.8980 (m-30) cc_final: 0.8513 (t0) REVERT: E 36 ASN cc_start: 0.8159 (m110) cc_final: 0.7850 (m-40) REVERT: E 42 ASP cc_start: 0.8561 (m-30) cc_final: 0.8307 (m-30) REVERT: E 50 MET cc_start: 0.8914 (mtm) cc_final: 0.8599 (mtm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.5413 time to fit residues: 177.9997 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 : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.121052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082866 restraints weight = 81872.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.087565 restraints weight = 37565.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090621 restraints weight = 23817.372| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10267 Z= 0.138 Angle : 0.480 5.014 13944 Z= 0.264 Chirality : 0.042 0.151 1518 Planarity : 0.004 0.041 1829 Dihedral : 4.586 48.277 1399 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1248 helix: 1.38 (0.31), residues: 263 sheet: -0.14 (0.25), residues: 364 loop : -0.50 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 376 HIS 0.004 0.001 HIS B 165 PHE 0.012 0.001 PHE D 147 TYR 0.022 0.001 TYR D 184 ARG 0.002 0.000 ARG D 49 *********************** 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 237 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.491 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: 0.8620 (m-30) cc_final: 0.8215 (m-30) REVERT: A 367 ARG cc_start: 0.9219 (mtm180) cc_final: 0.8720 (mtm-85) REVERT: A 449 TRP cc_start: 0.8351 (t60) cc_final: 0.8109 (t60) REVERT: A 450 LEU cc_start: 0.9386 (mt) cc_final: 0.9062 (mm) REVERT: A 533 HIS cc_start: 0.8027 (t-90) cc_final: 0.7777 (t-90) REVERT: A 774 LEU cc_start: 0.8777 (tp) cc_final: 0.8547 (tp) REVERT: A 780 LEU cc_start: 0.9191 (mt) cc_final: 0.8808 (tp) REVERT: B 42 PHE cc_start: 0.6511 (t80) cc_final: 0.6165 (t80) REVERT: B 134 LEU cc_start: 0.9237 (mp) cc_final: 0.8861 (mp) REVERT: B 287 ASN cc_start: 0.9399 (m-40) cc_final: 0.8997 (t0) REVERT: B 388 TYR cc_start: 0.6092 (m-80) cc_final: 0.5801 (m-80) REVERT: D 50 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9114 (tm-30) REVERT: D 172 ASP cc_start: 0.9011 (m-30) cc_final: 0.8540 (t0) REVERT: D 219 GLU cc_start: 0.8847 (tt0) cc_final: 0.8520 (tp30) REVERT: E 36 ASN cc_start: 0.8439 (m-40) cc_final: 0.8115 (m-40) REVERT: E 42 ASP cc_start: 0.8378 (m-30) cc_final: 0.8161 (m-30) REVERT: E 50 MET cc_start: 0.8735 (mtm) cc_final: 0.8479 (mtm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.5086 time to fit residues: 166.4354 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 : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 765 ASN D 54 GLN E 36 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085716 restraints weight = 83056.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087420 restraints weight = 50122.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089198 restraints weight = 35430.914| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10267 Z= 0.241 Angle : 0.525 6.282 13944 Z= 0.293 Chirality : 0.041 0.149 1518 Planarity : 0.004 0.048 1829 Dihedral : 4.622 38.678 1399 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.23), residues: 1248 helix: 1.25 (0.31), residues: 263 sheet: -0.33 (0.25), residues: 368 loop : -0.65 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 739 HIS 0.004 0.001 HIS B 324 PHE 0.011 0.001 PHE D 147 TYR 0.021 0.002 TYR D 184 ARG 0.022 0.001 ARG D 132 *********************** 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 232 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8598 (m-30) cc_final: 0.8199 (m-30) REVERT: A 304 MET cc_start: 0.8669 (mtp) cc_final: 0.8229 (ttm) REVERT: A 307 ASP cc_start: 0.8852 (m-30) cc_final: 0.8538 (m-30) REVERT: A 368 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8614 (mm-30) REVERT: A 420 GLU cc_start: 0.8717 (pm20) cc_final: 0.8314 (pm20) REVERT: A 450 LEU cc_start: 0.9473 (mt) cc_final: 0.9093 (mm) REVERT: A 533 HIS cc_start: 0.7885 (t-90) cc_final: 0.7628 (t-90) REVERT: A 586 PHE cc_start: 0.7058 (m-80) cc_final: 0.5908 (m-80) REVERT: A 735 THR cc_start: 0.9187 (m) cc_final: 0.8965 (p) REVERT: A 774 LEU cc_start: 0.8904 (tp) cc_final: 0.8633 (tp) REVERT: A 780 LEU cc_start: 0.9250 (mt) cc_final: 0.8851 (tp) REVERT: B 42 PHE cc_start: 0.6570 (t80) cc_final: 0.6233 (t80) REVERT: B 287 ASN cc_start: 0.9361 (m-40) cc_final: 0.9047 (t0) REVERT: B 388 TYR cc_start: 0.6317 (m-80) cc_final: 0.5973 (m-80) REVERT: D 50 GLN cc_start: 0.9296 (tm-30) cc_final: 0.9053 (tm-30) REVERT: D 131 ASP cc_start: 0.8145 (t0) cc_final: 0.7716 (t70) REVERT: D 172 ASP cc_start: 0.8988 (m-30) cc_final: 0.8514 (t0) REVERT: D 219 GLU cc_start: 0.8958 (tt0) cc_final: 0.8531 (tp30) REVERT: E 36 ASN cc_start: 0.8253 (m110) cc_final: 0.7948 (m-40) REVERT: E 42 ASP cc_start: 0.8521 (m-30) cc_final: 0.8256 (m-30) REVERT: E 50 MET cc_start: 0.8801 (mtm) cc_final: 0.8544 (mtm) REVERT: E 101 LEU cc_start: 0.8597 (tp) cc_final: 0.8364 (tp) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.5359 time to fit residues: 171.0376 Evaluate side-chains 185 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.118755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085732 restraints weight = 81914.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088073 restraints weight = 49037.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089465 restraints weight = 33697.633| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10267 Z= 0.198 Angle : 0.497 5.687 13944 Z= 0.276 Chirality : 0.041 0.149 1518 Planarity : 0.004 0.045 1829 Dihedral : 4.501 29.428 1399 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1248 helix: 1.33 (0.32), residues: 262 sheet: -0.47 (0.25), residues: 377 loop : -0.69 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 739 HIS 0.004 0.001 HIS B 165 PHE 0.011 0.001 PHE D 147 TYR 0.022 0.001 TYR D 184 ARG 0.013 0.001 ARG D 132 *********************** 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 236 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.501 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: A 222 ASP cc_start: 0.8591 (m-30) cc_final: 0.8222 (m-30) REVERT: A 307 ASP cc_start: 0.8815 (m-30) cc_final: 0.8516 (m-30) REVERT: A 368 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8642 (mm-30) REVERT: A 470 GLU cc_start: 0.8111 (tt0) cc_final: 0.7606 (tt0) REVERT: A 533 HIS cc_start: 0.7869 (t-90) cc_final: 0.7580 (t-90) REVERT: A 548 TYR cc_start: 0.8101 (m-80) cc_final: 0.7820 (m-80) REVERT: A 586 PHE cc_start: 0.7079 (m-80) cc_final: 0.6123 (m-10) REVERT: A 735 THR cc_start: 0.9163 (m) cc_final: 0.8958 (p) REVERT: A 780 LEU cc_start: 0.9252 (mt) cc_final: 0.8872 (tp) REVERT: B 42 PHE cc_start: 0.6640 (t80) cc_final: 0.6300 (t80) REVERT: B 287 ASN cc_start: 0.9363 (m-40) cc_final: 0.9046 (t0) REVERT: B 388 TYR cc_start: 0.6384 (m-80) cc_final: 0.6077 (m-80) REVERT: D 50 GLN cc_start: 0.9297 (tm-30) cc_final: 0.9038 (tm-30) REVERT: D 131 ASP cc_start: 0.8161 (t0) cc_final: 0.7761 (t70) REVERT: D 172 ASP cc_start: 0.8999 (m-30) cc_final: 0.8517 (t0) REVERT: D 219 GLU cc_start: 0.8968 (tt0) cc_final: 0.8566 (tp30) REVERT: E 42 ASP cc_start: 0.8502 (m-30) cc_final: 0.8235 (m-30) REVERT: E 50 MET cc_start: 0.8814 (mtm) cc_final: 0.8574 (mtm) REVERT: E 101 LEU cc_start: 0.8639 (tp) cc_final: 0.8403 (tp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.5085 time to fit residues: 165.5918 Evaluate side-chains 188 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.118963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.085382 restraints weight = 82883.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087767 restraints weight = 49950.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.089160 restraints weight = 33326.278| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10267 Z= 0.175 Angle : 0.475 5.314 13944 Z= 0.263 Chirality : 0.041 0.150 1518 Planarity : 0.004 0.045 1829 Dihedral : 4.385 29.010 1399 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1248 helix: 1.52 (0.31), residues: 261 sheet: -0.47 (0.25), residues: 377 loop : -0.66 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 739 HIS 0.003 0.001 HIS B 165 PHE 0.010 0.001 PHE D 147 TYR 0.022 0.001 TYR D 184 ARG 0.011 0.000 ARG D 132 *********************** 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 227 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.519 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: A 222 ASP cc_start: 0.8565 (m-30) cc_final: 0.8188 (m-30) REVERT: A 307 ASP cc_start: 0.8821 (m-30) cc_final: 0.8505 (m-30) REVERT: A 368 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8682 (mm-30) REVERT: A 470 GLU cc_start: 0.8108 (tt0) cc_final: 0.7613 (tt0) REVERT: A 533 HIS cc_start: 0.7887 (t-90) cc_final: 0.7599 (t-90) REVERT: A 548 TYR cc_start: 0.8061 (m-80) cc_final: 0.7790 (m-80) REVERT: A 586 PHE cc_start: 0.7100 (m-80) cc_final: 0.6895 (m-80) REVERT: B 42 PHE cc_start: 0.6718 (t80) cc_final: 0.6409 (t80) REVERT: B 287 ASN cc_start: 0.9378 (m-40) cc_final: 0.9037 (t0) REVERT: B 388 TYR cc_start: 0.6362 (m-80) cc_final: 0.5990 (m-80) REVERT: D 50 GLN cc_start: 0.9305 (tm-30) cc_final: 0.9099 (tm-30) REVERT: D 116 ASN cc_start: 0.9339 (m-40) cc_final: 0.8686 (m110) REVERT: D 131 ASP cc_start: 0.8087 (t0) cc_final: 0.7709 (t70) REVERT: D 172 ASP cc_start: 0.8994 (m-30) cc_final: 0.8503 (t0) REVERT: D 219 GLU cc_start: 0.8917 (tt0) cc_final: 0.8517 (tp30) REVERT: D 225 MET cc_start: 0.9017 (mmt) cc_final: 0.8766 (mmm) REVERT: C 42 LEU cc_start: 0.9357 (mt) cc_final: 0.9124 (mt) REVERT: E 36 ASN cc_start: 0.8430 (m110) cc_final: 0.8155 (m-40) REVERT: E 42 ASP cc_start: 0.8521 (m-30) cc_final: 0.8262 (m-30) REVERT: E 101 LEU cc_start: 0.8673 (tp) cc_final: 0.8425 (tp) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.5196 time to fit residues: 162.3102 Evaluate side-chains 186 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.120758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080747 restraints weight = 88241.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085402 restraints weight = 41185.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088371 restraints weight = 26717.727| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10267 Z= 0.180 Angle : 0.479 5.458 13944 Z= 0.265 Chirality : 0.041 0.149 1518 Planarity : 0.004 0.045 1829 Dihedral : 4.367 31.965 1399 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1248 helix: 1.57 (0.32), residues: 261 sheet: -0.42 (0.25), residues: 372 loop : -0.75 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 739 HIS 0.003 0.001 HIS B 324 PHE 0.009 0.001 PHE D 147 TYR 0.023 0.001 TYR D 159 ARG 0.009 0.000 ARG D 132 *********************** 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 223 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8684 (m-30) cc_final: 0.8348 (m-30) REVERT: A 307 ASP cc_start: 0.8866 (m-30) cc_final: 0.8543 (m-30) REVERT: A 470 GLU cc_start: 0.8196 (tt0) cc_final: 0.7780 (tt0) REVERT: A 533 HIS cc_start: 0.8249 (t-90) cc_final: 0.7999 (t-90) REVERT: A 548 TYR cc_start: 0.8336 (m-80) cc_final: 0.7808 (m-80) REVERT: A 586 PHE cc_start: 0.7086 (m-80) cc_final: 0.6005 (m-10) REVERT: B 42 PHE cc_start: 0.7115 (t80) cc_final: 0.6722 (t80) REVERT: B 287 ASN cc_start: 0.9442 (m-40) cc_final: 0.8967 (t0) REVERT: B 388 TYR cc_start: 0.6286 (m-80) cc_final: 0.5930 (m-80) REVERT: D 50 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9177 (tm-30) REVERT: D 116 ASN cc_start: 0.9329 (m-40) cc_final: 0.8650 (m110) REVERT: D 131 ASP cc_start: 0.8093 (t0) cc_final: 0.7729 (t70) REVERT: D 159 TYR cc_start: 0.8283 (p90) cc_final: 0.8073 (p90) REVERT: D 172 ASP cc_start: 0.9119 (m-30) cc_final: 0.8652 (t0) REVERT: E 42 ASP cc_start: 0.8538 (m-30) cc_final: 0.8253 (m-30) REVERT: E 101 LEU cc_start: 0.8643 (tp) cc_final: 0.8357 (tp) REVERT: P 1293 ASN cc_start: 0.9197 (p0) cc_final: 0.8985 (p0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.5324 time to fit residues: 163.1553 Evaluate side-chains 186 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.118597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085544 restraints weight = 82435.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089298 restraints weight = 51533.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090744 restraints weight = 33688.182| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10267 Z= 0.274 Angle : 0.537 6.065 13944 Z= 0.301 Chirality : 0.041 0.147 1518 Planarity : 0.005 0.053 1829 Dihedral : 4.626 37.986 1399 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1248 helix: 1.15 (0.31), residues: 265 sheet: -0.56 (0.26), residues: 371 loop : -0.96 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 739 HIS 0.003 0.001 HIS B 324 PHE 0.011 0.001 PHE A 791 TYR 0.024 0.002 TYR D 159 ARG 0.009 0.001 ARG D 132 ********************** 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 210 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8594 (m-30) cc_final: 0.8187 (m-30) REVERT: A 223 LEU cc_start: 0.9581 (mt) cc_final: 0.9019 (tt) REVERT: A 306 ASP cc_start: 0.8993 (m-30) cc_final: 0.8749 (m-30) REVERT: A 307 ASP cc_start: 0.8791 (m-30) cc_final: 0.8511 (m-30) REVERT: A 368 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8514 (mm-30) REVERT: A 533 HIS cc_start: 0.7912 (t-90) cc_final: 0.7629 (t-90) REVERT: A 586 PHE cc_start: 0.7109 (m-80) cc_final: 0.5971 (m-10) REVERT: A 618 TYR cc_start: 0.7586 (m-80) cc_final: 0.7194 (m-80) REVERT: B 287 ASN cc_start: 0.9399 (m-40) cc_final: 0.9053 (t0) REVERT: B 388 TYR cc_start: 0.6496 (m-80) cc_final: 0.6207 (m-80) REVERT: D 50 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9124 (tm-30) REVERT: D 219 GLU cc_start: 0.8934 (tt0) cc_final: 0.8531 (tp30) REVERT: C 81 ASP cc_start: 0.8333 (m-30) cc_final: 0.8113 (m-30) REVERT: E 42 ASP cc_start: 0.8534 (m-30) cc_final: 0.8244 (m-30) REVERT: E 101 LEU cc_start: 0.8733 (tp) cc_final: 0.8418 (tp) REVERT: P 1293 ASN cc_start: 0.9174 (p0) cc_final: 0.8918 (p0) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.5165 time to fit residues: 149.9742 Evaluate side-chains 175 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9474 > 50: distance: 173 - 182: 30.527 distance: 182 - 183: 31.493 distance: 182 - 191: 12.831 distance: 183 - 184: 39.375 distance: 184 - 199: 39.652 distance: 190 - 198: 35.805 distance: 199 - 206: 39.117 distance: 200 - 201: 39.819 distance: 200 - 203: 40.537 distance: 200 - 207: 40.054 distance: 203 - 205: 3.360 distance: 205 - 210: 25.935 distance: 205 - 211: 41.739 distance: 205 - 212: 36.997 distance: 213 - 214: 40.961 distance: 213 - 222: 40.605 distance: 214 - 215: 39.415 distance: 214 - 217: 40.465 distance: 214 - 223: 23.750 distance: 215 - 228: 22.776 distance: 217 - 218: 37.010 distance: 217 - 224: 40.740 distance: 217 - 225: 3.464 distance: 218 - 219: 39.917 distance: 218 - 226: 33.553 distance: 219 - 221: 41.179 distance: 228 - 229: 22.515 distance: 228 - 234: 11.413 distance: 229 - 230: 56.546 distance: 229 - 232: 40.065 distance: 229 - 235: 20.599 distance: 230 - 242: 53.098 distance: 232 - 233: 7.339 distance: 232 - 236: 40.490 distance: 232 - 237: 15.152 distance: 233 - 234: 34.700 distance: 233 - 238: 42.839 distance: 233 - 239: 56.994 distance: 234 - 240: 13.847 distance: 234 - 241: 26.588 distance: 242 - 243: 45.125 distance: 242 - 249: 4.339 distance: 242 - 338: 34.757 distance: 243 - 244: 41.270 distance: 243 - 246: 26.961 distance: 243 - 250: 13.508 distance: 244 - 258: 21.553 distance: 245 - 335: 32.992 distance: 246 - 247: 44.223 distance: 246 - 248: 28.109 distance: 246 - 251: 21.260 distance: 247 - 252: 42.636 distance: 247 - 253: 24.390 distance: 247 - 254: 37.736 distance: 248 - 255: 25.709 distance: 248 - 256: 15.362 distance: 248 - 257: 14.582 distance: 258 - 259: 45.558 distance: 258 - 263: 43.989 distance: 259 - 262: 45.535 distance: 260 - 261: 39.253 distance: 260 - 268: 10.217 distance: 262 - 265: 23.486 distance: 262 - 266: 17.324 distance: 262 - 267: 17.209 distance: 268 - 269: 8.088 distance: 268 - 273: 30.981 distance: 268 - 300: 30.697 distance: 269 - 270: 41.129 distance: 270 - 271: 21.364 distance: 270 - 278: 31.604 distance: 271 - 297: 18.247 distance: 272 - 275: 6.840 distance: 272 - 277: 39.939 distance: 278 - 279: 8.995 distance: 278 - 286: 29.891 distance: 279 - 282: 36.690 distance: 280 - 290: 14.267 distance: 282 - 283: 11.545 distance: 282 - 288: 3.042 distance: 282 - 289: 7.914 distance: 283 - 284: 24.942 distance: 283 - 285: 14.359 distance: 290 - 291: 42.134 distance: 290 - 294: 7.175 distance: 291 - 292: 44.998 distance: 291 - 295: 27.618 distance: 292 - 293: 26.463 distance: 292 - 297: 45.327 distance: 297 - 298: 42.949 distance: 298 - 299: 16.389 distance: 298 - 301: 61.716 distance: 298 - 307: 40.845 distance: 299 - 300: 33.840 distance: 299 - 319: 25.508 distance: 301 - 302: 23.138 distance: 301 - 308: 10.283 distance: 302 - 303: 60.549 distance: 302 - 310: 26.387 distance: 302 - 311: 40.954 distance: 303 - 304: 24.459 distance: 303 - 313: 40.472 distance: 304 - 305: 25.481 distance: 304 - 314: 42.608 distance: 304 - 315: 20.982 distance: 305 - 318: 20.181