Starting phenix.real_space_refine on Sun Apr 5 06:29:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u6s_63921/04_2026/9u6s_63921.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u6s_63921/04_2026/9u6s_63921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u6s_63921/04_2026/9u6s_63921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u6s_63921/04_2026/9u6s_63921.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u6s_63921/04_2026/9u6s_63921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u6s_63921/04_2026/9u6s_63921.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 5687 2.51 5 N 1453 2.21 5 O 1462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8621 Number of models: 1 Model: "" Number of chains: 13 Chain: "N" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2511 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 15, 'TRANS': 302} Chain: "O" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "P" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Q" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 515 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "R" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "S" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "U" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "V" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "W" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "X" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 505 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Z" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Time building chain proxies: 2.03, per 1000 atoms: 0.24 Number of scatterers: 8621 At special positions: 0 Unit cell: (90.72, 100.8, 79.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 1462 8.00 N 1453 7.00 C 5687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.72 Conformation dependent library (CDL) restraints added in 413.5 milliseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 1 sheets defined 89.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'N' and resid 324 through 328 Processing helix chain 'N' and resid 329 through 335 removed outlier: 4.023A pdb=" N LEU N 333 " --> pdb=" O PRO N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 349 No H-bonds generated for 'chain 'N' and resid 347 through 349' Processing helix chain 'N' and resid 350 through 364 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 365 through 385 removed outlier: 3.791A pdb=" N LEU N 371 " --> pdb=" O GLY N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 400 through 424 removed outlier: 3.940A pdb=" N TRP N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 489 Processing helix chain 'N' and resid 491 through 516 Processing helix chain 'N' and resid 521 through 543 removed outlier: 4.305A pdb=" N MET N 541 " --> pdb=" O LEU N 537 " (cutoff:3.500A) Processing helix chain 'N' and resid 548 through 560 removed outlier: 4.510A pdb=" N PHE N 552 " --> pdb=" O ILE N 548 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 590 removed outlier: 3.558A pdb=" N ARG N 588 " --> pdb=" O ALA N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 632 removed outlier: 3.509A pdb=" N LEU N 595 " --> pdb=" O LEU N 591 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 3.954A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 48 removed outlier: 4.238A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 63 through 80 Processing helix chain 'P' and resid 10 through 48 removed outlier: 3.967A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 63 through 79 Processing helix chain 'Q' and resid 8 through 49 removed outlier: 3.670A pdb=" N GLY Q 13 " --> pdb=" O GLY Q 9 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 60 Processing helix chain 'Q' and resid 63 through 80 Processing helix chain 'R' and resid 10 through 49 removed outlier: 4.527A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 37 " --> pdb=" O ALA R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 Processing helix chain 'R' and resid 63 through 80 Processing helix chain 'S' and resid 10 through 48 removed outlier: 4.203A pdb=" N LEU S 14 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA S 39 " --> pdb=" O ALA S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 62 through 79 removed outlier: 4.252A pdb=" N VAL S 66 " --> pdb=" O PRO S 62 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE S 72 " --> pdb=" O PHE S 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 48 removed outlier: 3.545A pdb=" N LEU T 14 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY T 43 " --> pdb=" O ALA T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 Processing helix chain 'T' and resid 63 through 80 Processing helix chain 'U' and resid 9 through 49 removed outlier: 3.834A pdb=" N GLY U 13 " --> pdb=" O GLY U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 63 through 80 Processing helix chain 'V' and resid 9 through 49 removed outlier: 4.436A pdb=" N GLY V 13 " --> pdb=" O GLY V 9 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY V 43 " --> pdb=" O ALA V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 61 Processing helix chain 'V' and resid 62 through 64 No H-bonds generated for 'chain 'V' and resid 62 through 64' Processing helix chain 'V' and resid 65 through 80 removed outlier: 3.503A pdb=" N GLY V 69 " --> pdb=" O LEU V 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 49 removed outlier: 3.997A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 60 Processing helix chain 'W' and resid 63 through 80 Processing helix chain 'X' and resid 10 through 45 removed outlier: 3.922A pdb=" N LEU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.674A pdb=" N PHE X 58 " --> pdb=" O THR X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 80 Processing helix chain 'Y' and resid 9 through 48 removed outlier: 4.390A pdb=" N GLY Y 13 " --> pdb=" O GLY Y 9 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 63 through 80 Processing helix chain 'Z' and resid 9 through 49 removed outlier: 3.811A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY Z 43 " --> pdb=" O ALA Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 63 through 80 removed outlier: 3.649A pdb=" N ILE Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 389 through 391 removed outlier: 3.587A pdb=" N ILE N 391 " --> pdb=" O LEU N 396 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1408 1.32 - 1.44: 2121 1.44 - 1.57: 5184 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 8751 Sorted by residual: bond pdb=" C LEU T 61 " pdb=" N PRO T 62 " ideal model delta sigma weight residual 1.335 1.369 -0.034 9.40e-03 1.13e+04 1.30e+01 bond pdb=" C LEU X 61 " pdb=" N PRO X 62 " ideal model delta sigma weight residual 1.337 1.369 -0.032 1.11e-02 8.12e+03 8.45e+00 bond pdb=" C LYS N 399 " pdb=" N PRO N 400 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.83e+00 bond pdb=" CA LYS N 399 " pdb=" C LYS N 399 " ideal model delta sigma weight residual 1.524 1.552 -0.028 1.26e-02 6.30e+03 4.84e+00 bond pdb=" C VAL N 475 " pdb=" N PHE N 476 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.25e-02 6.40e+03 4.16e+00 ... (remaining 8746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 11616 3.99 - 7.97: 216 7.97 - 11.96: 32 11.96 - 15.94: 3 15.94 - 19.93: 3 Bond angle restraints: 11870 Sorted by residual: angle pdb=" CA LEU R 76 " pdb=" CB LEU R 76 " pdb=" CG LEU R 76 " ideal model delta sigma weight residual 116.30 136.23 -19.93 3.50e+00 8.16e-02 3.24e+01 angle pdb=" N PHE N 476 " pdb=" CA PHE N 476 " pdb=" CB PHE N 476 " ideal model delta sigma weight residual 109.94 118.42 -8.48 1.49e+00 4.50e-01 3.24e+01 angle pdb=" CA LYS N 399 " pdb=" C LYS N 399 " pdb=" N PRO N 400 " ideal model delta sigma weight residual 118.44 126.06 -7.62 1.59e+00 3.96e-01 2.30e+01 angle pdb=" CA LEU Z 25 " pdb=" CB LEU Z 25 " pdb=" CG LEU Z 25 " ideal model delta sigma weight residual 116.30 132.63 -16.33 3.50e+00 8.16e-02 2.18e+01 angle pdb=" C ILE R 75 " pdb=" N LEU R 76 " pdb=" CA LEU R 76 " ideal model delta sigma weight residual 122.06 113.49 8.57 1.86e+00 2.89e-01 2.12e+01 ... (remaining 11865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4515 17.11 - 34.22: 382 34.22 - 51.32: 50 51.32 - 68.43: 6 68.43 - 85.54: 3 Dihedral angle restraints: 4956 sinusoidal: 1786 harmonic: 3170 Sorted by residual: dihedral pdb=" CA TRP N 545 " pdb=" C TRP N 545 " pdb=" N LEU N 546 " pdb=" CA LEU N 546 " ideal model delta harmonic sigma weight residual 180.00 -143.75 -36.25 0 5.00e+00 4.00e-02 5.26e+01 dihedral pdb=" CA LEU N 546 " pdb=" C LEU N 546 " pdb=" N MET N 547 " pdb=" CA MET N 547 " ideal model delta harmonic sigma weight residual -180.00 -146.52 -33.48 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA LYS N 399 " pdb=" C LYS N 399 " pdb=" N PRO N 400 " pdb=" CA PRO N 400 " ideal model delta harmonic sigma weight residual 180.00 150.76 29.24 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 4953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1084 0.062 - 0.124: 306 0.124 - 0.186: 61 0.186 - 0.248: 11 0.248 - 0.311: 1 Chirality restraints: 1463 Sorted by residual: chirality pdb=" CA LYS N 399 " pdb=" N LYS N 399 " pdb=" C LYS N 399 " pdb=" CB LYS N 399 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL N 475 " pdb=" CA VAL N 475 " pdb=" CG1 VAL N 475 " pdb=" CG2 VAL N 475 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL N 472 " pdb=" CA VAL N 472 " pdb=" CG1 VAL N 472 " pdb=" CG2 VAL N 472 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1460 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 399 " 0.091 5.00e-02 4.00e+02 1.40e-01 3.13e+01 pdb=" N PRO N 400 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO N 400 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO N 400 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP N 358 " -0.036 2.00e-02 2.50e+03 2.31e-02 1.34e+01 pdb=" CG TRP N 358 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP N 358 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP N 358 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP N 358 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP N 358 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP N 358 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 358 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 358 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP N 358 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE W 68 " -0.018 2.00e-02 2.50e+03 2.38e-02 9.88e+00 pdb=" CG PHE W 68 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE W 68 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE W 68 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE W 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE W 68 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE W 68 " -0.000 2.00e-02 2.50e+03 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 849 2.73 - 3.28: 9670 3.28 - 3.82: 15119 3.82 - 4.36: 17592 4.36 - 4.90: 28162 Nonbonded interactions: 71392 Sorted by model distance: nonbonded pdb=" O ASP N 455 " pdb=" OG1 THR N 459 " model vdw 2.193 3.040 nonbonded pdb=" NE2 GLN V 34 " pdb=" O LEU V 59 " model vdw 2.257 3.120 nonbonded pdb=" OD1 ASN R 51 " pdb=" NH1 ARG S 49 " model vdw 2.285 3.120 nonbonded pdb=" O GLU N 550 " pdb=" NE2 GLN N 554 " model vdw 2.293 3.120 nonbonded pdb=" OD2 ASP Q 48 " pdb=" OG SER Q 50 " model vdw 2.300 3.040 ... (remaining 71387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.090 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 0.077 8751 Z= 0.264 Angle : 1.290 19.931 11870 Z= 0.633 Chirality : 0.059 0.311 1463 Planarity : 0.008 0.140 1495 Dihedral : 12.458 85.540 2978 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.24), residues: 1168 helix: -0.14 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -2.35 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 563 TYR 0.025 0.003 TYR N 565 PHE 0.055 0.003 PHE W 68 TRP 0.061 0.003 TRP N 358 HIS 0.009 0.002 HIS N 605 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 8751) covalent geometry : angle 1.29046 (11870) hydrogen bonds : bond 0.10680 ( 830) hydrogen bonds : angle 5.66746 ( 2478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.296 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: N 354 PHE cc_start: 0.9538 (m-80) cc_final: 0.9188 (m-80) REVERT: N 379 LEU cc_start: 0.9701 (tp) cc_final: 0.9480 (tp) REVERT: N 476 PHE cc_start: 0.9622 (m-80) cc_final: 0.9207 (m-80) REVERT: N 619 GLN cc_start: 0.9749 (mp10) cc_final: 0.9461 (mp10) REVERT: N 622 ARG cc_start: 0.9760 (tmt170) cc_final: 0.9315 (tmt170) REVERT: O 19 MET cc_start: 0.9301 (mtt) cc_final: 0.8652 (mtt) REVERT: O 47 GLU cc_start: 0.9446 (tp30) cc_final: 0.9134 (tp30) REVERT: P 19 MET cc_start: 0.9150 (mmt) cc_final: 0.8873 (mmt) REVERT: P 58 PHE cc_start: 0.9738 (m-10) cc_final: 0.9292 (m-80) REVERT: P 68 PHE cc_start: 0.9765 (m-80) cc_final: 0.9460 (m-80) REVERT: P 75 ILE cc_start: 0.9807 (tt) cc_final: 0.9497 (pt) REVERT: Q 19 MET cc_start: 0.8854 (mtt) cc_final: 0.8062 (ptp) REVERT: Q 70 LEU cc_start: 0.9705 (pp) cc_final: 0.9331 (pp) REVERT: Q 74 PHE cc_start: 0.9343 (m-80) cc_final: 0.8941 (m-80) REVERT: Q 76 LEU cc_start: 0.9369 (mt) cc_final: 0.9119 (pp) REVERT: S 19 MET cc_start: 0.9012 (mmt) cc_final: 0.8340 (mmm) REVERT: S 64 THR cc_start: 0.9696 (p) cc_final: 0.9277 (p) REVERT: T 59 LEU cc_start: 0.9712 (mm) cc_final: 0.9510 (mm) REVERT: T 64 THR cc_start: 0.9550 (p) cc_final: 0.8863 (p) REVERT: U 37 ILE cc_start: 0.9770 (mm) cc_final: 0.9527 (pt) REVERT: U 58 PHE cc_start: 0.9583 (m-10) cc_final: 0.9244 (m-80) REVERT: U 68 PHE cc_start: 0.9726 (m-80) cc_final: 0.9350 (m-80) REVERT: V 15 ILE cc_start: 0.9356 (pt) cc_final: 0.9104 (pt) REVERT: V 19 MET cc_start: 0.9409 (mtt) cc_final: 0.8895 (mmm) REVERT: V 74 PHE cc_start: 0.9548 (m-80) cc_final: 0.9325 (m-80) REVERT: V 76 LEU cc_start: 0.9733 (mt) cc_final: 0.9265 (mt) REVERT: W 19 MET cc_start: 0.9462 (mtt) cc_final: 0.8985 (mtt) REVERT: W 64 THR cc_start: 0.9690 (p) cc_final: 0.9333 (p) REVERT: X 15 ILE cc_start: 0.9536 (mt) cc_final: 0.9050 (mt) REVERT: X 19 MET cc_start: 0.9118 (mmt) cc_final: 0.8807 (mmm) REVERT: X 34 GLN cc_start: 0.9705 (mm-40) cc_final: 0.9074 (mm-40) REVERT: Y 19 MET cc_start: 0.8700 (mmt) cc_final: 0.8426 (mmt) REVERT: Y 68 PHE cc_start: 0.9580 (m-10) cc_final: 0.9292 (m-80) REVERT: Z 34 GLN cc_start: 0.9308 (mp10) cc_final: 0.8519 (mp10) REVERT: Z 64 THR cc_start: 0.9509 (p) cc_final: 0.8705 (p) REVERT: Z 68 PHE cc_start: 0.9478 (m-80) cc_final: 0.9253 (m-80) REVERT: Z 76 LEU cc_start: 0.9833 (mt) cc_final: 0.9592 (mt) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.0613 time to fit residues: 34.2622 Evaluate side-chains 317 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 554 GLN ** U 34 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 = 0.3195 r_free = 0.3195 target = 0.055427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.046068 restraints weight = 50843.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047055 restraints weight = 35932.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.047906 restraints weight = 28268.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048374 restraints weight = 22812.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048725 restraints weight = 19963.583| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8751 Z= 0.169 Angle : 0.861 11.986 11870 Z= 0.422 Chirality : 0.044 0.209 1463 Planarity : 0.006 0.123 1495 Dihedral : 5.667 34.217 1261 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.11 % Favored : 95.72 % Rotamer: Outliers : 0.61 % Allowed : 6.56 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1168 helix: 0.47 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -2.00 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 482 TYR 0.010 0.001 TYR N 515 PHE 0.022 0.002 PHE Q 68 TRP 0.020 0.002 TRP N 496 HIS 0.003 0.001 HIS N 605 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8751) covalent geometry : angle 0.86070 (11870) hydrogen bonds : bond 0.05711 ( 830) hydrogen bonds : angle 4.57009 ( 2478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 359 time to evaluate : 0.333 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: N 379 LEU cc_start: 0.9680 (tp) cc_final: 0.9455 (tp) REVERT: N 466 LEU cc_start: 0.9594 (pp) cc_final: 0.9310 (pp) REVERT: N 470 PHE cc_start: 0.9173 (m-10) cc_final: 0.8944 (m-80) REVERT: N 476 PHE cc_start: 0.9596 (m-80) cc_final: 0.9048 (m-80) REVERT: O 19 MET cc_start: 0.9275 (mtt) cc_final: 0.8664 (mtt) REVERT: P 19 MET cc_start: 0.9060 (mmt) cc_final: 0.8744 (mmt) REVERT: P 58 PHE cc_start: 0.9724 (m-10) cc_final: 0.9320 (m-80) REVERT: P 60 LEU cc_start: 0.9465 (mt) cc_final: 0.9258 (pp) REVERT: P 68 PHE cc_start: 0.9755 (m-80) cc_final: 0.9431 (m-80) REVERT: Q 34 GLN cc_start: 0.9646 (mt0) cc_final: 0.9416 (mt0) REVERT: Q 68 PHE cc_start: 0.9723 (m-80) cc_final: 0.9332 (m-80) REVERT: R 34 GLN cc_start: 0.9126 (mp10) cc_final: 0.8734 (mm-40) REVERT: S 19 MET cc_start: 0.9003 (mmt) cc_final: 0.8515 (mmt) REVERT: S 60 LEU cc_start: 0.9740 (mm) cc_final: 0.9532 (mm) REVERT: S 64 THR cc_start: 0.9680 (p) cc_final: 0.9259 (p) REVERT: T 59 LEU cc_start: 0.9711 (mm) cc_final: 0.9438 (mm) REVERT: T 64 THR cc_start: 0.9470 (p) cc_final: 0.8550 (p) REVERT: T 68 PHE cc_start: 0.9528 (m-80) cc_final: 0.9279 (m-80) REVERT: U 37 ILE cc_start: 0.9785 (mm) cc_final: 0.9542 (pt) REVERT: U 58 PHE cc_start: 0.9559 (m-10) cc_final: 0.9231 (m-80) REVERT: U 68 PHE cc_start: 0.9697 (m-80) cc_final: 0.9325 (m-80) REVERT: V 19 MET cc_start: 0.9426 (mtt) cc_final: 0.9009 (mmm) REVERT: V 58 PHE cc_start: 0.9484 (m-80) cc_final: 0.9009 (m-80) REVERT: V 74 PHE cc_start: 0.9461 (m-80) cc_final: 0.9089 (m-80) REVERT: V 76 LEU cc_start: 0.9733 (mt) cc_final: 0.9432 (mt) REVERT: W 64 THR cc_start: 0.9674 (p) cc_final: 0.9294 (p) REVERT: X 19 MET cc_start: 0.9238 (mmt) cc_final: 0.8688 (mmt) REVERT: X 30 THR cc_start: 0.9588 (t) cc_final: 0.9286 (t) REVERT: X 34 GLN cc_start: 0.9711 (mm-40) cc_final: 0.9117 (mm-40) REVERT: Y 68 PHE cc_start: 0.9615 (m-10) cc_final: 0.9321 (m-80) REVERT: Z 59 LEU cc_start: 0.9616 (pp) cc_final: 0.9388 (pp) REVERT: Z 64 THR cc_start: 0.9508 (p) cc_final: 0.8613 (p) REVERT: Z 68 PHE cc_start: 0.9450 (m-80) cc_final: 0.9212 (m-80) REVERT: Z 76 LEU cc_start: 0.9809 (mt) cc_final: 0.9584 (mt) outliers start: 5 outliers final: 0 residues processed: 360 average time/residue: 0.0604 time to fit residues: 33.6807 Evaluate side-chains 316 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.052864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043837 restraints weight = 54520.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.044852 restraints weight = 38347.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045534 restraints weight = 29604.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.046056 restraints weight = 24401.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046419 restraints weight = 21223.617| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8751 Z= 0.260 Angle : 0.865 10.300 11870 Z= 0.451 Chirality : 0.045 0.213 1463 Planarity : 0.006 0.123 1495 Dihedral : 5.659 34.404 1261 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.46 % Rotamer: Outliers : 0.49 % Allowed : 5.22 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1168 helix: 0.71 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -2.02 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 563 TYR 0.015 0.002 TYR N 382 PHE 0.021 0.002 PHE U 74 TRP 0.012 0.002 TRP N 496 HIS 0.003 0.001 HIS N 489 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 8751) covalent geometry : angle 0.86468 (11870) hydrogen bonds : bond 0.05735 ( 830) hydrogen bonds : angle 4.76444 ( 2478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 342 time to evaluate : 0.318 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: N 354 PHE cc_start: 0.9502 (m-80) cc_final: 0.9125 (m-80) REVERT: N 379 LEU cc_start: 0.9767 (tp) cc_final: 0.9510 (tp) REVERT: N 466 LEU cc_start: 0.9618 (pp) cc_final: 0.9344 (pp) REVERT: N 476 PHE cc_start: 0.9649 (m-80) cc_final: 0.9102 (m-80) REVERT: N 622 ARG cc_start: 0.9780 (tmt170) cc_final: 0.9170 (tmt170) REVERT: O 19 MET cc_start: 0.9260 (mtt) cc_final: 0.8691 (mtt) REVERT: O 28 LEU cc_start: 0.9640 (mt) cc_final: 0.9398 (mt) REVERT: P 19 MET cc_start: 0.9189 (mmt) cc_final: 0.8922 (mmt) REVERT: P 58 PHE cc_start: 0.9752 (m-10) cc_final: 0.9346 (m-80) REVERT: P 60 LEU cc_start: 0.9507 (mt) cc_final: 0.9275 (pp) REVERT: P 68 PHE cc_start: 0.9761 (m-80) cc_final: 0.9391 (m-80) REVERT: P 75 ILE cc_start: 0.9701 (tt) cc_final: 0.9401 (pt) REVERT: Q 34 GLN cc_start: 0.9728 (mt0) cc_final: 0.9467 (mt0) REVERT: Q 68 PHE cc_start: 0.9693 (m-80) cc_final: 0.9369 (m-80) REVERT: Q 70 LEU cc_start: 0.9718 (pp) cc_final: 0.9283 (pp) REVERT: Q 74 PHE cc_start: 0.9290 (m-80) cc_final: 0.8811 (m-80) REVERT: Q 76 LEU cc_start: 0.9596 (mt) cc_final: 0.9359 (mt) REVERT: R 34 GLN cc_start: 0.9184 (mp10) cc_final: 0.8774 (mm-40) REVERT: S 19 MET cc_start: 0.9186 (mmt) cc_final: 0.8847 (mmt) REVERT: S 64 THR cc_start: 0.9667 (p) cc_final: 0.9285 (p) REVERT: T 59 LEU cc_start: 0.9721 (mm) cc_final: 0.9494 (mm) REVERT: T 64 THR cc_start: 0.9545 (p) cc_final: 0.8540 (p) REVERT: T 68 PHE cc_start: 0.9570 (m-80) cc_final: 0.9306 (m-80) REVERT: U 19 MET cc_start: 0.9524 (mtt) cc_final: 0.9065 (mmm) REVERT: U 58 PHE cc_start: 0.9593 (m-10) cc_final: 0.9248 (m-80) REVERT: U 68 PHE cc_start: 0.9724 (m-80) cc_final: 0.9348 (m-80) REVERT: V 58 PHE cc_start: 0.9572 (m-80) cc_final: 0.9126 (m-80) REVERT: V 74 PHE cc_start: 0.9515 (m-80) cc_final: 0.9141 (m-80) REVERT: V 76 LEU cc_start: 0.9728 (mt) cc_final: 0.9511 (mt) REVERT: W 15 ILE cc_start: 0.9232 (mp) cc_final: 0.9007 (mp) REVERT: W 19 MET cc_start: 0.9431 (mtt) cc_final: 0.9076 (mtt) REVERT: W 28 LEU cc_start: 0.9758 (tp) cc_final: 0.9341 (mt) REVERT: W 64 THR cc_start: 0.9713 (p) cc_final: 0.9325 (p) REVERT: W 65 LEU cc_start: 0.9676 (mm) cc_final: 0.9439 (mm) REVERT: X 19 MET cc_start: 0.9227 (mmt) cc_final: 0.8837 (mmt) REVERT: X 30 THR cc_start: 0.9615 (t) cc_final: 0.9372 (t) REVERT: X 34 GLN cc_start: 0.9749 (mm-40) cc_final: 0.9158 (mm-40) REVERT: Y 59 LEU cc_start: 0.9767 (tt) cc_final: 0.9517 (pp) REVERT: Y 68 PHE cc_start: 0.9606 (m-10) cc_final: 0.9329 (m-80) REVERT: Z 15 ILE cc_start: 0.9305 (mt) cc_final: 0.9093 (mt) REVERT: Z 64 THR cc_start: 0.9554 (p) cc_final: 0.8794 (p) REVERT: Z 68 PHE cc_start: 0.9501 (m-80) cc_final: 0.9267 (m-80) outliers start: 4 outliers final: 0 residues processed: 342 average time/residue: 0.0602 time to fit residues: 31.7879 Evaluate side-chains 297 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 434 HIS ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045355 restraints weight = 50760.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046335 restraints weight = 36108.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.047095 restraints weight = 28008.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047638 restraints weight = 23074.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048078 restraints weight = 19885.264| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8751 Z= 0.167 Angle : 0.889 14.066 11870 Z= 0.423 Chirality : 0.044 0.239 1463 Planarity : 0.005 0.125 1495 Dihedral : 5.494 33.073 1261 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.20 % Favored : 95.63 % Rotamer: Outliers : 0.24 % Allowed : 6.44 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1168 helix: 0.76 (0.16), residues: 1033 sheet: None (None), residues: 0 loop : -2.00 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 49 TYR 0.008 0.001 TYR N 565 PHE 0.036 0.002 PHE N 357 TRP 0.008 0.001 TRP N 496 HIS 0.003 0.001 HIS N 605 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8751) covalent geometry : angle 0.88902 (11870) hydrogen bonds : bond 0.05613 ( 830) hydrogen bonds : angle 4.49515 ( 2478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 354 time to evaluate : 0.330 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: N 354 PHE cc_start: 0.9552 (m-80) cc_final: 0.9134 (m-80) REVERT: N 379 LEU cc_start: 0.9708 (tp) cc_final: 0.9501 (tp) REVERT: N 622 ARG cc_start: 0.9757 (tmt170) cc_final: 0.9095 (tmt170) REVERT: O 19 MET cc_start: 0.9239 (mtt) cc_final: 0.8814 (mtt) REVERT: P 19 MET cc_start: 0.9183 (mmt) cc_final: 0.8754 (mmt) REVERT: P 58 PHE cc_start: 0.9678 (m-10) cc_final: 0.9228 (m-80) REVERT: P 60 LEU cc_start: 0.9478 (mt) cc_final: 0.9245 (pp) REVERT: P 68 PHE cc_start: 0.9755 (m-80) cc_final: 0.9368 (m-80) REVERT: P 76 LEU cc_start: 0.9572 (tt) cc_final: 0.9332 (tt) REVERT: Q 34 GLN cc_start: 0.9664 (mt0) cc_final: 0.9438 (mt0) REVERT: Q 68 PHE cc_start: 0.9676 (m-80) cc_final: 0.9343 (m-80) REVERT: Q 70 LEU cc_start: 0.9705 (pp) cc_final: 0.9235 (pp) REVERT: Q 74 PHE cc_start: 0.9229 (m-80) cc_final: 0.8948 (m-80) REVERT: Q 76 LEU cc_start: 0.9544 (mt) cc_final: 0.9271 (mt) REVERT: R 68 PHE cc_start: 0.9388 (m-80) cc_final: 0.9150 (m-80) REVERT: S 19 MET cc_start: 0.9070 (mmt) cc_final: 0.8712 (mmt) REVERT: S 60 LEU cc_start: 0.9734 (mm) cc_final: 0.9534 (mm) REVERT: S 68 PHE cc_start: 0.9270 (m-80) cc_final: 0.9005 (m-80) REVERT: T 64 THR cc_start: 0.9548 (p) cc_final: 0.8563 (p) REVERT: T 68 PHE cc_start: 0.9551 (m-80) cc_final: 0.9272 (m-80) REVERT: U 58 PHE cc_start: 0.9588 (m-10) cc_final: 0.9225 (m-80) REVERT: U 68 PHE cc_start: 0.9704 (m-80) cc_final: 0.9321 (m-80) REVERT: V 58 PHE cc_start: 0.9496 (m-80) cc_final: 0.9046 (m-80) REVERT: V 74 PHE cc_start: 0.9496 (m-80) cc_final: 0.9107 (m-80) REVERT: W 64 THR cc_start: 0.9666 (p) cc_final: 0.9145 (p) REVERT: X 15 ILE cc_start: 0.9520 (mt) cc_final: 0.9119 (mt) REVERT: X 19 MET cc_start: 0.9207 (mmt) cc_final: 0.8940 (mmm) REVERT: X 30 THR cc_start: 0.9483 (t) cc_final: 0.9260 (t) REVERT: X 34 GLN cc_start: 0.9517 (mm-40) cc_final: 0.9049 (mm-40) REVERT: Y 19 MET cc_start: 0.8687 (mmt) cc_final: 0.8484 (mmt) REVERT: Y 59 LEU cc_start: 0.9770 (tt) cc_final: 0.9505 (pp) REVERT: Y 68 PHE cc_start: 0.9578 (m-10) cc_final: 0.9327 (m-80) REVERT: Z 59 LEU cc_start: 0.9623 (pp) cc_final: 0.9360 (pp) REVERT: Z 64 THR cc_start: 0.9542 (p) cc_final: 0.8705 (p) REVERT: Z 68 PHE cc_start: 0.9468 (m-80) cc_final: 0.9206 (m-80) REVERT: Z 76 LEU cc_start: 0.9803 (mt) cc_final: 0.9567 (mt) outliers start: 2 outliers final: 1 residues processed: 355 average time/residue: 0.0665 time to fit residues: 36.3322 Evaluate side-chains 316 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 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 = 0.3162 r_free = 0.3162 target = 0.054257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044958 restraints weight = 52561.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.045912 restraints weight = 37497.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046724 restraints weight = 29033.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047242 restraints weight = 23307.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047689 restraints weight = 20118.334| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8751 Z= 0.203 Angle : 0.870 12.178 11870 Z= 0.438 Chirality : 0.045 0.250 1463 Planarity : 0.005 0.123 1495 Dihedral : 5.522 33.019 1261 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1168 helix: 0.82 (0.16), residues: 1033 sheet: None (None), residues: 0 loop : -2.07 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 563 TYR 0.012 0.001 TYR N 515 PHE 0.027 0.002 PHE N 357 TRP 0.061 0.002 TRP N 496 HIS 0.009 0.001 HIS N 434 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8751) covalent geometry : angle 0.87039 (11870) hydrogen bonds : bond 0.05510 ( 830) hydrogen bonds : angle 4.63422 ( 2478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.318 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: N 379 LEU cc_start: 0.9736 (tp) cc_final: 0.9496 (tp) REVERT: N 466 LEU cc_start: 0.9622 (pp) cc_final: 0.9364 (pp) REVERT: N 622 ARG cc_start: 0.9759 (tmt170) cc_final: 0.9067 (tmt170) REVERT: O 19 MET cc_start: 0.9256 (mtt) cc_final: 0.8861 (mtt) REVERT: P 19 MET cc_start: 0.9020 (mmt) cc_final: 0.8677 (mmt) REVERT: P 58 PHE cc_start: 0.9715 (m-10) cc_final: 0.9289 (m-80) REVERT: P 63 GLU cc_start: 0.9594 (mm-30) cc_final: 0.9338 (mp0) REVERT: P 68 PHE cc_start: 0.9736 (m-80) cc_final: 0.9356 (m-80) REVERT: P 76 LEU cc_start: 0.9560 (tt) cc_final: 0.9339 (tt) REVERT: Q 34 GLN cc_start: 0.9679 (mt0) cc_final: 0.9432 (mt0) REVERT: Q 68 PHE cc_start: 0.9676 (m-80) cc_final: 0.9321 (m-80) REVERT: Q 70 LEU cc_start: 0.9722 (pp) cc_final: 0.9242 (pp) REVERT: Q 74 PHE cc_start: 0.9279 (m-80) cc_final: 0.9003 (m-80) REVERT: R 34 GLN cc_start: 0.9065 (mp10) cc_final: 0.8695 (mm-40) REVERT: R 68 PHE cc_start: 0.9422 (m-80) cc_final: 0.9150 (m-80) REVERT: S 19 MET cc_start: 0.9166 (mmt) cc_final: 0.8787 (mmt) REVERT: S 60 LEU cc_start: 0.9721 (mm) cc_final: 0.9495 (mm) REVERT: S 68 PHE cc_start: 0.9239 (m-80) cc_final: 0.8964 (m-80) REVERT: T 64 THR cc_start: 0.9566 (p) cc_final: 0.8507 (p) REVERT: T 68 PHE cc_start: 0.9564 (m-80) cc_final: 0.9289 (m-80) REVERT: U 15 ILE cc_start: 0.9488 (mt) cc_final: 0.9179 (mt) REVERT: U 19 MET cc_start: 0.9521 (mtt) cc_final: 0.8473 (mmm) REVERT: U 68 PHE cc_start: 0.9714 (m-80) cc_final: 0.9331 (m-80) REVERT: V 58 PHE cc_start: 0.9522 (m-80) cc_final: 0.9068 (m-80) REVERT: V 64 THR cc_start: 0.9680 (p) cc_final: 0.9458 (p) REVERT: V 74 PHE cc_start: 0.9494 (m-10) cc_final: 0.9131 (m-80) REVERT: V 76 LEU cc_start: 0.9735 (mt) cc_final: 0.9489 (mt) REVERT: W 15 ILE cc_start: 0.9214 (mp) cc_final: 0.8956 (mp) REVERT: W 19 MET cc_start: 0.9467 (mtt) cc_final: 0.9049 (mtt) REVERT: W 28 LEU cc_start: 0.9736 (tp) cc_final: 0.9344 (mt) REVERT: W 34 GLN cc_start: 0.9532 (mp10) cc_final: 0.9270 (mp10) REVERT: W 64 THR cc_start: 0.9653 (p) cc_final: 0.9150 (p) REVERT: W 65 LEU cc_start: 0.9619 (mm) cc_final: 0.9392 (mm) REVERT: X 19 MET cc_start: 0.9177 (mmt) cc_final: 0.8880 (mmt) REVERT: X 28 LEU cc_start: 0.9741 (mm) cc_final: 0.9533 (mm) REVERT: X 34 GLN cc_start: 0.9570 (mm-40) cc_final: 0.9117 (mm-40) REVERT: Y 19 MET cc_start: 0.8617 (mmt) cc_final: 0.8307 (mmt) REVERT: Y 68 PHE cc_start: 0.9555 (m-10) cc_final: 0.9317 (m-80) REVERT: Z 64 THR cc_start: 0.9554 (p) cc_final: 0.8743 (p) REVERT: Z 68 PHE cc_start: 0.9479 (m-80) cc_final: 0.9228 (m-80) REVERT: Z 76 LEU cc_start: 0.9805 (mt) cc_final: 0.9558 (mt) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.0692 time to fit residues: 37.7562 Evaluate side-chains 296 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 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 = 0.3183 r_free = 0.3183 target = 0.055314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.045820 restraints weight = 50913.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046839 restraints weight = 35936.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047514 restraints weight = 28040.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048053 restraints weight = 23307.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048481 restraints weight = 20272.488| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8751 Z= 0.171 Angle : 0.908 14.194 11870 Z= 0.435 Chirality : 0.045 0.257 1463 Planarity : 0.005 0.124 1495 Dihedral : 5.464 32.419 1261 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.28 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1168 helix: 0.81 (0.16), residues: 1031 sheet: None (None), residues: 0 loop : -2.01 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 49 TYR 0.012 0.001 TYR N 515 PHE 0.022 0.002 PHE N 357 TRP 0.069 0.002 TRP N 496 HIS 0.006 0.001 HIS N 434 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8751) covalent geometry : angle 0.90850 (11870) hydrogen bonds : bond 0.05451 ( 830) hydrogen bonds : angle 4.50914 ( 2478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.336 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: N 476 PHE cc_start: 0.9386 (m-10) cc_final: 0.8919 (m-80) REVERT: N 563 ARG cc_start: 0.8800 (ptt180) cc_final: 0.7489 (ptt90) REVERT: N 619 GLN cc_start: 0.9764 (mp10) cc_final: 0.9369 (mp10) REVERT: N 622 ARG cc_start: 0.9775 (tmt170) cc_final: 0.9125 (ptm-80) REVERT: O 19 MET cc_start: 0.9240 (mtt) cc_final: 0.8911 (mtt) REVERT: P 19 MET cc_start: 0.8982 (mmt) cc_final: 0.8644 (mmt) REVERT: P 58 PHE cc_start: 0.9693 (m-10) cc_final: 0.9270 (m-80) REVERT: P 61 LEU cc_start: 0.9679 (mt) cc_final: 0.9473 (mt) REVERT: P 68 PHE cc_start: 0.9736 (m-80) cc_final: 0.9350 (m-80) REVERT: Q 19 MET cc_start: 0.9072 (ptp) cc_final: 0.8461 (mtt) REVERT: Q 34 GLN cc_start: 0.9659 (mt0) cc_final: 0.9403 (mt0) REVERT: Q 47 GLU cc_start: 0.8684 (tt0) cc_final: 0.8314 (tm-30) REVERT: Q 51 ASN cc_start: 0.9377 (m-40) cc_final: 0.8949 (m110) REVERT: Q 68 PHE cc_start: 0.9671 (m-80) cc_final: 0.9405 (m-80) REVERT: Q 70 LEU cc_start: 0.9701 (pp) cc_final: 0.9212 (pp) REVERT: Q 74 PHE cc_start: 0.9272 (m-80) cc_final: 0.8965 (m-80) REVERT: Q 76 LEU cc_start: 0.9473 (mt) cc_final: 0.9121 (mt) REVERT: R 34 GLN cc_start: 0.8989 (mp10) cc_final: 0.8595 (mm-40) REVERT: R 68 PHE cc_start: 0.9462 (m-80) cc_final: 0.9123 (m-80) REVERT: S 19 MET cc_start: 0.9043 (mmt) cc_final: 0.8370 (mmm) REVERT: S 60 LEU cc_start: 0.9709 (mm) cc_final: 0.9506 (mm) REVERT: S 68 PHE cc_start: 0.9268 (m-80) cc_final: 0.8953 (m-80) REVERT: T 64 THR cc_start: 0.9553 (p) cc_final: 0.8513 (p) REVERT: T 68 PHE cc_start: 0.9541 (m-80) cc_final: 0.9291 (m-80) REVERT: U 19 MET cc_start: 0.9543 (mtt) cc_final: 0.9150 (mmm) REVERT: U 68 PHE cc_start: 0.9703 (m-80) cc_final: 0.9312 (m-80) REVERT: V 15 ILE cc_start: 0.9346 (pt) cc_final: 0.9126 (pt) REVERT: V 19 MET cc_start: 0.9349 (mtt) cc_final: 0.8886 (mmm) REVERT: V 64 THR cc_start: 0.9663 (p) cc_final: 0.9413 (p) REVERT: V 74 PHE cc_start: 0.9496 (m-10) cc_final: 0.9033 (m-80) REVERT: V 76 LEU cc_start: 0.9736 (mt) cc_final: 0.9448 (mt) REVERT: W 64 THR cc_start: 0.9650 (p) cc_final: 0.9215 (p) REVERT: X 19 MET cc_start: 0.9205 (mmt) cc_final: 0.8859 (mmt) REVERT: X 30 THR cc_start: 0.9587 (t) cc_final: 0.9279 (t) REVERT: X 34 GLN cc_start: 0.9700 (mm-40) cc_final: 0.9112 (mm-40) REVERT: Y 19 MET cc_start: 0.8623 (mmt) cc_final: 0.8344 (mmt) REVERT: Y 68 PHE cc_start: 0.9526 (m-10) cc_final: 0.9304 (m-80) REVERT: Z 59 LEU cc_start: 0.9601 (pp) cc_final: 0.9356 (pp) REVERT: Z 64 THR cc_start: 0.9533 (p) cc_final: 0.8746 (p) REVERT: Z 76 LEU cc_start: 0.9806 (mt) cc_final: 0.9417 (mt) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.0679 time to fit residues: 38.3844 Evaluate side-chains 308 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 106 optimal weight: 0.0040 chunk 107 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 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 = 0.3195 r_free = 0.3195 target = 0.055897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046358 restraints weight = 50398.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047419 restraints weight = 35415.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048130 restraints weight = 27874.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048665 restraints weight = 23117.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049059 restraints weight = 20193.356| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8751 Z= 0.171 Angle : 0.937 14.730 11870 Z= 0.446 Chirality : 0.046 0.257 1463 Planarity : 0.005 0.125 1495 Dihedral : 5.473 31.977 1261 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1168 helix: 0.73 (0.16), residues: 1037 sheet: None (None), residues: 0 loop : -2.29 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 482 TYR 0.013 0.001 TYR N 515 PHE 0.026 0.002 PHE U 74 TRP 0.072 0.002 TRP N 496 HIS 0.004 0.001 HIS N 434 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8751) covalent geometry : angle 0.93660 (11870) hydrogen bonds : bond 0.05413 ( 830) hydrogen bonds : angle 4.54584 ( 2478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.290 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: N 379 LEU cc_start: 0.9704 (tp) cc_final: 0.9497 (tp) REVERT: N 476 PHE cc_start: 0.9387 (m-10) cc_final: 0.9160 (m-10) REVERT: N 563 ARG cc_start: 0.8838 (ptt180) cc_final: 0.7806 (ptt90) REVERT: N 619 GLN cc_start: 0.9687 (mp10) cc_final: 0.9322 (mp10) REVERT: N 622 ARG cc_start: 0.9774 (tmt170) cc_final: 0.8979 (ptm-80) REVERT: P 19 MET cc_start: 0.8902 (mmt) cc_final: 0.8524 (mmt) REVERT: P 58 PHE cc_start: 0.9671 (m-10) cc_final: 0.9251 (m-80) REVERT: P 68 PHE cc_start: 0.9730 (m-80) cc_final: 0.9349 (m-80) REVERT: P 76 LEU cc_start: 0.9607 (tt) cc_final: 0.9396 (tt) REVERT: Q 19 MET cc_start: 0.9026 (ptp) cc_final: 0.8444 (mtt) REVERT: Q 34 GLN cc_start: 0.9645 (mt0) cc_final: 0.9426 (mt0) REVERT: Q 51 ASN cc_start: 0.9411 (m-40) cc_final: 0.8992 (m110) REVERT: Q 68 PHE cc_start: 0.9641 (m-80) cc_final: 0.9425 (m-80) REVERT: Q 70 LEU cc_start: 0.9709 (pp) cc_final: 0.9206 (pp) REVERT: Q 74 PHE cc_start: 0.9256 (m-80) cc_final: 0.8964 (m-80) REVERT: Q 76 LEU cc_start: 0.9459 (mt) cc_final: 0.9100 (mt) REVERT: R 68 PHE cc_start: 0.9488 (m-80) cc_final: 0.9142 (m-80) REVERT: S 19 MET cc_start: 0.8915 (mmt) cc_final: 0.8258 (mmm) REVERT: S 68 PHE cc_start: 0.9237 (m-80) cc_final: 0.8931 (m-80) REVERT: T 64 THR cc_start: 0.9549 (p) cc_final: 0.8904 (p) REVERT: U 19 MET cc_start: 0.9514 (mtt) cc_final: 0.8994 (mmm) REVERT: U 64 THR cc_start: 0.9387 (p) cc_final: 0.8612 (p) REVERT: U 68 PHE cc_start: 0.9714 (m-80) cc_final: 0.9307 (m-80) REVERT: V 64 THR cc_start: 0.9649 (p) cc_final: 0.9393 (p) REVERT: V 74 PHE cc_start: 0.9516 (m-10) cc_final: 0.9076 (m-80) REVERT: V 76 LEU cc_start: 0.9727 (mt) cc_final: 0.9367 (mt) REVERT: W 19 MET cc_start: 0.9452 (mtt) cc_final: 0.8892 (mtt) REVERT: X 19 MET cc_start: 0.9168 (mmt) cc_final: 0.8786 (mmt) REVERT: X 34 GLN cc_start: 0.9509 (mm-40) cc_final: 0.9072 (mm-40) REVERT: Y 59 LEU cc_start: 0.9782 (tt) cc_final: 0.9513 (pp) REVERT: Y 68 PHE cc_start: 0.9534 (m-10) cc_final: 0.9279 (m-80) REVERT: Z 15 ILE cc_start: 0.9373 (mt) cc_final: 0.8811 (mt) REVERT: Z 34 GLN cc_start: 0.9224 (mp10) cc_final: 0.8816 (mp10) REVERT: Z 52 PHE cc_start: 0.8789 (p90) cc_final: 0.8415 (p90) REVERT: Z 64 THR cc_start: 0.9214 (p) cc_final: 0.8890 (p) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.0670 time to fit residues: 36.8551 Evaluate side-chains 313 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 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 = 0.3217 r_free = 0.3217 target = 0.056340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047015 restraints weight = 51231.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048072 restraints weight = 36571.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048839 restraints weight = 28542.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049330 restraints weight = 23954.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049750 restraints weight = 20704.185| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8751 Z= 0.177 Angle : 0.966 14.885 11870 Z= 0.460 Chirality : 0.047 0.257 1463 Planarity : 0.005 0.128 1495 Dihedral : 5.439 31.808 1261 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.54 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1168 helix: 0.66 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -2.36 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 49 TYR 0.016 0.002 TYR N 565 PHE 0.056 0.002 PHE T 68 TRP 0.082 0.002 TRP N 496 HIS 0.003 0.001 HIS N 434 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8751) covalent geometry : angle 0.96583 (11870) hydrogen bonds : bond 0.05411 ( 830) hydrogen bonds : angle 4.65340 ( 2478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.231 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: N 476 PHE cc_start: 0.9457 (m-10) cc_final: 0.9221 (m-10) REVERT: N 528 MET cc_start: 0.9528 (mmp) cc_final: 0.9322 (mmm) REVERT: N 554 GLN cc_start: 0.9494 (mp10) cc_final: 0.8978 (mp10) REVERT: N 619 GLN cc_start: 0.9725 (mp10) cc_final: 0.9362 (mp10) REVERT: O 19 MET cc_start: 0.9099 (mtt) cc_final: 0.8494 (mtt) REVERT: P 19 MET cc_start: 0.8873 (mmt) cc_final: 0.8459 (mmt) REVERT: P 58 PHE cc_start: 0.9683 (m-10) cc_final: 0.9253 (m-80) REVERT: P 68 PHE cc_start: 0.9711 (m-80) cc_final: 0.9337 (m-80) REVERT: Q 19 MET cc_start: 0.8999 (ptp) cc_final: 0.8406 (mtt) REVERT: Q 34 GLN cc_start: 0.9618 (mt0) cc_final: 0.9369 (mt0) REVERT: Q 68 PHE cc_start: 0.9637 (m-80) cc_final: 0.9402 (m-80) REVERT: Q 70 LEU cc_start: 0.9719 (pp) cc_final: 0.9212 (pp) REVERT: Q 74 PHE cc_start: 0.9240 (m-80) cc_final: 0.8951 (m-80) REVERT: Q 76 LEU cc_start: 0.9456 (mt) cc_final: 0.9061 (mt) REVERT: R 68 PHE cc_start: 0.9498 (m-80) cc_final: 0.9139 (m-80) REVERT: S 19 MET cc_start: 0.8811 (mmt) cc_final: 0.8116 (mmm) REVERT: S 64 THR cc_start: 0.9591 (p) cc_final: 0.9354 (p) REVERT: S 68 PHE cc_start: 0.9301 (m-80) cc_final: 0.9014 (m-80) REVERT: T 64 THR cc_start: 0.9554 (p) cc_final: 0.8944 (p) REVERT: T 68 PHE cc_start: 0.9492 (m-80) cc_final: 0.9251 (m-80) REVERT: U 19 MET cc_start: 0.9489 (mtt) cc_final: 0.9230 (mtt) REVERT: U 64 THR cc_start: 0.9428 (p) cc_final: 0.8644 (p) REVERT: U 68 PHE cc_start: 0.9692 (m-80) cc_final: 0.9279 (m-80) REVERT: U 72 ILE cc_start: 0.9764 (mm) cc_final: 0.9514 (mm) REVERT: V 19 MET cc_start: 0.9285 (mtt) cc_final: 0.8972 (mmm) REVERT: V 34 GLN cc_start: 0.9627 (mm-40) cc_final: 0.9032 (mm-40) REVERT: V 64 THR cc_start: 0.9641 (p) cc_final: 0.9388 (p) REVERT: V 74 PHE cc_start: 0.9482 (m-10) cc_final: 0.9021 (m-80) REVERT: V 76 LEU cc_start: 0.9715 (mt) cc_final: 0.9356 (mt) REVERT: W 15 ILE cc_start: 0.9125 (mp) cc_final: 0.8863 (mp) REVERT: W 19 MET cc_start: 0.9434 (mtt) cc_final: 0.8855 (mtt) REVERT: W 64 THR cc_start: 0.9732 (p) cc_final: 0.9367 (p) REVERT: W 65 LEU cc_start: 0.9610 (mm) cc_final: 0.9409 (mm) REVERT: X 19 MET cc_start: 0.9101 (mmt) cc_final: 0.8839 (mmt) REVERT: X 34 GLN cc_start: 0.9541 (mm-40) cc_final: 0.9104 (mm-40) REVERT: Y 59 LEU cc_start: 0.9710 (tt) cc_final: 0.9508 (pp) REVERT: Y 68 PHE cc_start: 0.9490 (m-10) cc_final: 0.9207 (m-80) REVERT: Z 64 THR cc_start: 0.9539 (p) cc_final: 0.8688 (p) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.0654 time to fit residues: 36.6823 Evaluate side-chains 319 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 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 = 0.3218 r_free = 0.3218 target = 0.056761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047592 restraints weight = 50529.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048697 restraints weight = 35715.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049438 restraints weight = 27638.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050026 restraints weight = 22724.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050431 restraints weight = 19563.081| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8751 Z= 0.178 Angle : 0.973 15.880 11870 Z= 0.460 Chirality : 0.047 0.260 1463 Planarity : 0.005 0.128 1495 Dihedral : 5.451 32.250 1261 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1168 helix: 0.68 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -2.11 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 377 TYR 0.014 0.001 TYR N 515 PHE 0.035 0.002 PHE T 68 TRP 0.077 0.003 TRP N 496 HIS 0.003 0.001 HIS N 434 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8751) covalent geometry : angle 0.97250 (11870) hydrogen bonds : bond 0.05326 ( 830) hydrogen bonds : angle 4.63974 ( 2478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.281 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: N 354 PHE cc_start: 0.9515 (m-80) cc_final: 0.9120 (m-80) REVERT: N 372 PHE cc_start: 0.9576 (m-80) cc_final: 0.9365 (m-80) REVERT: N 476 PHE cc_start: 0.9490 (m-10) cc_final: 0.9231 (m-10) REVERT: N 477 PHE cc_start: 0.9648 (t80) cc_final: 0.9359 (t80) REVERT: N 496 TRP cc_start: 0.9236 (m-90) cc_final: 0.8982 (m100) REVERT: N 619 GLN cc_start: 0.9698 (mp10) cc_final: 0.9335 (mp10) REVERT: N 622 ARG cc_start: 0.9780 (tmt170) cc_final: 0.9209 (ptm-80) REVERT: O 19 MET cc_start: 0.9014 (mtt) cc_final: 0.8454 (mtt) REVERT: O 28 LEU cc_start: 0.9618 (mt) cc_final: 0.9376 (mt) REVERT: P 58 PHE cc_start: 0.9692 (m-10) cc_final: 0.9252 (m-80) REVERT: P 68 PHE cc_start: 0.9696 (m-80) cc_final: 0.9325 (m-80) REVERT: Q 19 MET cc_start: 0.8987 (ptp) cc_final: 0.8387 (mtt) REVERT: Q 34 GLN cc_start: 0.9630 (mt0) cc_final: 0.9395 (mt0) REVERT: Q 47 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8437 (tm-30) REVERT: Q 51 ASN cc_start: 0.9338 (m-40) cc_final: 0.9041 (m-40) REVERT: Q 68 PHE cc_start: 0.9647 (m-80) cc_final: 0.9399 (m-80) REVERT: Q 70 LEU cc_start: 0.9715 (pp) cc_final: 0.9214 (pp) REVERT: Q 74 PHE cc_start: 0.9219 (m-80) cc_final: 0.8946 (m-80) REVERT: Q 76 LEU cc_start: 0.9421 (mt) cc_final: 0.9007 (mt) REVERT: R 68 PHE cc_start: 0.9464 (m-80) cc_final: 0.9175 (m-80) REVERT: S 19 MET cc_start: 0.8746 (mmt) cc_final: 0.8112 (mmm) REVERT: S 64 THR cc_start: 0.9585 (p) cc_final: 0.9331 (p) REVERT: S 68 PHE cc_start: 0.9269 (m-80) cc_final: 0.8989 (m-80) REVERT: T 64 THR cc_start: 0.9513 (p) cc_final: 0.8918 (p) REVERT: T 68 PHE cc_start: 0.9480 (m-80) cc_final: 0.9238 (m-80) REVERT: U 37 ILE cc_start: 0.9774 (mm) cc_final: 0.9571 (pt) REVERT: U 56 LEU cc_start: 0.9494 (mt) cc_final: 0.9292 (pp) REVERT: U 64 THR cc_start: 0.9356 (p) cc_final: 0.8460 (p) REVERT: U 68 PHE cc_start: 0.9702 (m-80) cc_final: 0.9289 (m-80) REVERT: V 64 THR cc_start: 0.9628 (p) cc_final: 0.9365 (p) REVERT: V 74 PHE cc_start: 0.9498 (m-10) cc_final: 0.9044 (m-80) REVERT: V 76 LEU cc_start: 0.9715 (mt) cc_final: 0.9490 (mt) REVERT: W 15 ILE cc_start: 0.9130 (mp) cc_final: 0.8843 (mp) REVERT: W 19 MET cc_start: 0.9413 (mtt) cc_final: 0.8849 (mtt) REVERT: W 34 GLN cc_start: 0.9497 (mp10) cc_final: 0.9098 (mp10) REVERT: W 64 THR cc_start: 0.9750 (p) cc_final: 0.9341 (p) REVERT: W 65 LEU cc_start: 0.9616 (mm) cc_final: 0.9405 (mm) REVERT: X 19 MET cc_start: 0.9101 (mmt) cc_final: 0.8817 (mmt) REVERT: X 30 THR cc_start: 0.9590 (t) cc_final: 0.9297 (t) REVERT: X 34 GLN cc_start: 0.9710 (mm-40) cc_final: 0.9071 (mm-40) REVERT: Y 59 LEU cc_start: 0.9711 (tt) cc_final: 0.9487 (pp) REVERT: Y 68 PHE cc_start: 0.9521 (m-10) cc_final: 0.9227 (m-80) REVERT: Z 34 GLN cc_start: 0.9239 (mp10) cc_final: 0.8802 (mp10) REVERT: Z 64 THR cc_start: 0.9514 (p) cc_final: 0.8737 (p) REVERT: Z 74 PHE cc_start: 0.8641 (t80) cc_final: 0.8278 (t80) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.0636 time to fit residues: 35.4928 Evaluate side-chains 322 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 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 = 0.3226 r_free = 0.3226 target = 0.057238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.047850 restraints weight = 50327.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048959 restraints weight = 35402.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049756 restraints weight = 27233.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050298 restraints weight = 22425.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050737 restraints weight = 19297.472| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8751 Z= 0.178 Angle : 1.000 16.061 11870 Z= 0.472 Chirality : 0.049 0.273 1463 Planarity : 0.005 0.128 1495 Dihedral : 5.485 31.606 1261 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.97 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1168 helix: 0.62 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -1.93 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 563 TYR 0.014 0.001 TYR N 515 PHE 0.032 0.002 PHE W 68 TRP 0.073 0.002 TRP N 496 HIS 0.003 0.001 HIS N 605 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8751) covalent geometry : angle 0.99993 (11870) hydrogen bonds : bond 0.05326 ( 830) hydrogen bonds : angle 4.70628 ( 2478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.375 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: N 372 PHE cc_start: 0.9618 (m-80) cc_final: 0.9386 (m-80) REVERT: N 476 PHE cc_start: 0.9539 (m-10) cc_final: 0.9302 (m-10) REVERT: N 477 PHE cc_start: 0.9622 (t80) cc_final: 0.9353 (t80) REVERT: N 496 TRP cc_start: 0.9310 (m-90) cc_final: 0.9030 (m100) REVERT: N 528 MET cc_start: 0.9522 (mmp) cc_final: 0.9296 (mmm) REVERT: N 547 MET cc_start: 0.8704 (mpp) cc_final: 0.8497 (mpp) REVERT: N 554 GLN cc_start: 0.9466 (mp10) cc_final: 0.9039 (mp10) REVERT: N 622 ARG cc_start: 0.9812 (tmt170) cc_final: 0.9267 (ptm-80) REVERT: O 19 MET cc_start: 0.9060 (mtt) cc_final: 0.8561 (mtt) REVERT: O 28 LEU cc_start: 0.9615 (mt) cc_final: 0.9397 (mt) REVERT: O 47 GLU cc_start: 0.9330 (tp30) cc_final: 0.8633 (pp20) REVERT: P 19 MET cc_start: 0.9104 (mmt) cc_final: 0.8292 (mmt) REVERT: P 58 PHE cc_start: 0.9677 (m-10) cc_final: 0.9253 (m-80) REVERT: P 68 PHE cc_start: 0.9716 (m-80) cc_final: 0.9368 (m-80) REVERT: P 76 LEU cc_start: 0.9586 (tp) cc_final: 0.9211 (tp) REVERT: Q 19 MET cc_start: 0.9005 (ptp) cc_final: 0.8364 (mtt) REVERT: Q 34 GLN cc_start: 0.9610 (mt0) cc_final: 0.9363 (mt0) REVERT: Q 47 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8455 (tm-30) REVERT: Q 68 PHE cc_start: 0.9659 (m-80) cc_final: 0.9411 (m-80) REVERT: Q 70 LEU cc_start: 0.9686 (pp) cc_final: 0.9190 (pp) REVERT: Q 74 PHE cc_start: 0.9266 (m-80) cc_final: 0.8978 (m-80) REVERT: Q 76 LEU cc_start: 0.9477 (mt) cc_final: 0.9072 (mt) REVERT: R 68 PHE cc_start: 0.9496 (m-80) cc_final: 0.9225 (m-80) REVERT: S 19 MET cc_start: 0.8890 (mmt) cc_final: 0.8164 (mmm) REVERT: S 64 THR cc_start: 0.9568 (p) cc_final: 0.9347 (p) REVERT: S 68 PHE cc_start: 0.9250 (m-80) cc_final: 0.8979 (m-80) REVERT: T 19 MET cc_start: 0.8975 (mtt) cc_final: 0.8591 (mmt) REVERT: T 64 THR cc_start: 0.9480 (p) cc_final: 0.8835 (p) REVERT: T 68 PHE cc_start: 0.9525 (m-80) cc_final: 0.9294 (m-80) REVERT: U 19 MET cc_start: 0.9548 (mtt) cc_final: 0.9265 (mmt) REVERT: U 47 GLU cc_start: 0.8830 (tp30) cc_final: 0.8626 (tp30) REVERT: U 64 THR cc_start: 0.9323 (p) cc_final: 0.8475 (p) REVERT: U 68 PHE cc_start: 0.9681 (m-80) cc_final: 0.9290 (m-80) REVERT: V 34 GLN cc_start: 0.9686 (mm-40) cc_final: 0.9078 (mm-40) REVERT: V 64 THR cc_start: 0.9641 (p) cc_final: 0.9390 (p) REVERT: V 74 PHE cc_start: 0.9543 (m-10) cc_final: 0.9080 (m-80) REVERT: V 76 LEU cc_start: 0.9723 (mt) cc_final: 0.9491 (mt) REVERT: W 15 ILE cc_start: 0.9175 (mp) cc_final: 0.8899 (mp) REVERT: W 19 MET cc_start: 0.9502 (mtt) cc_final: 0.8912 (mtt) REVERT: W 64 THR cc_start: 0.9762 (p) cc_final: 0.9365 (p) REVERT: X 19 MET cc_start: 0.9237 (mmt) cc_final: 0.9025 (mmt) REVERT: X 30 THR cc_start: 0.9602 (t) cc_final: 0.9352 (t) REVERT: X 34 GLN cc_start: 0.9700 (mm-40) cc_final: 0.9112 (mm-40) REVERT: Y 59 LEU cc_start: 0.9724 (tt) cc_final: 0.9514 (pp) REVERT: Y 68 PHE cc_start: 0.9488 (m-10) cc_final: 0.9179 (m-80) REVERT: Z 14 LEU cc_start: 0.9810 (mm) cc_final: 0.9597 (tp) REVERT: Z 19 MET cc_start: 0.8884 (mmt) cc_final: 0.8604 (mmt) REVERT: Z 34 GLN cc_start: 0.9222 (mp10) cc_final: 0.8796 (mp10) REVERT: Z 59 LEU cc_start: 0.9632 (pp) cc_final: 0.9239 (pp) REVERT: Z 64 THR cc_start: 0.9503 (p) cc_final: 0.8732 (p) REVERT: Z 74 PHE cc_start: 0.8658 (t80) cc_final: 0.8361 (t80) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.0663 time to fit residues: 37.0149 Evaluate side-chains 315 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 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 = 0.3231 r_free = 0.3231 target = 0.057346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047912 restraints weight = 50433.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.049002 restraints weight = 35431.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049780 restraints weight = 27501.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050325 restraints weight = 22745.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050756 restraints weight = 19652.125| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8751 Z= 0.177 Angle : 1.007 16.107 11870 Z= 0.474 Chirality : 0.049 0.271 1463 Planarity : 0.005 0.128 1495 Dihedral : 5.452 30.293 1261 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1168 helix: 0.58 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -1.96 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 563 TYR 0.021 0.001 TYR N 515 PHE 0.031 0.002 PHE W 68 TRP 0.069 0.002 TRP N 496 HIS 0.003 0.001 HIS N 605 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8751) covalent geometry : angle 1.00707 (11870) hydrogen bonds : bond 0.05263 ( 830) hydrogen bonds : angle 4.72656 ( 2478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1444.27 seconds wall clock time: 25 minutes 39.71 seconds (1539.71 seconds total)