Starting phenix.real_space_refine on Sun Jan 26 02:05:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x83_38134/01_2025/8x83_38134_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x83_38134/01_2025/8x83_38134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x83_38134/01_2025/8x83_38134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x83_38134/01_2025/8x83_38134.map" model { file = "/net/cci-nas-00/data/ceres_data/8x83_38134/01_2025/8x83_38134_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x83_38134/01_2025/8x83_38134_neut_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 72 5.16 5 Na 2 4.78 5 C 7820 2.51 5 N 2048 2.21 5 O 2116 1.98 5 H 12424 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24482 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' NA': 2, 'FRU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 15.27, per 1000 atoms: 0.62 Number of scatterers: 24482 At special positions: 0 Unit cell: (110.67, 110.67, 106.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 Na 2 11.00 O 2116 8.00 N 2048 7.00 C 7820 6.00 H 12424 1.00 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: 6.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 85.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 73 through 100 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.516A pdb=" N ASN A 123 " --> pdb=" O ASN A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.722A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 removed outlier: 3.516A pdb=" N TYR A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.329A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 357 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.740A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.963A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 425 removed outlier: 4.312A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 37 through 64 Processing helix chain 'B' and resid 73 through 100 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.516A pdb=" N ASN B 123 " --> pdb=" O ASN B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.722A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 removed outlier: 3.516A pdb=" N TYR B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.329A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 357 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 369 removed outlier: 3.740A pdb=" N ILE B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.963A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 425 removed outlier: 4.312A pdb=" N LEU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 37 through 64 Processing helix chain 'C' and resid 73 through 100 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.516A pdb=" N ASN C 123 " --> pdb=" O ASN C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.722A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 removed outlier: 3.516A pdb=" N TYR C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.329A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 357 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 369 removed outlier: 3.740A pdb=" N ILE C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.963A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 425 removed outlier: 4.312A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 37 through 64 Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 removed outlier: 3.516A pdb=" N ASN D 123 " --> pdb=" O ASN D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.722A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 removed outlier: 3.516A pdb=" N TYR D 179 " --> pdb=" O TYR D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.329A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 357 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 369 removed outlier: 3.740A pdb=" N ILE D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.963A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 425 removed outlier: 4.312A pdb=" N LEU D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.596A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.596A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.596A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.596A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3168 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: 11.63 Time building geometry restraints manager: 7.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12392 1.02 - 1.22: 36 1.22 - 1.42: 4996 1.42 - 1.61: 7172 1.61 - 1.81: 112 Bond restraints: 24708 Sorted by residual: bond pdb=" C VAL D 417 " pdb=" N ALA D 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL A 417 " pdb=" N ALA A 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL B 417 " pdb=" N ALA B 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL C 417 " pdb=" N ALA C 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" NE ARG A 424 " pdb=" HE ARG A 424 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 24703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 43924 1.51 - 3.01: 584 3.01 - 4.52: 64 4.52 - 6.03: 32 6.03 - 7.53: 20 Bond angle restraints: 44624 Sorted by residual: angle pdb=" CA ALA A 418 " pdb=" C ALA A 418 " pdb=" N LEU A 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA B 418 " pdb=" C ALA B 418 " pdb=" N LEU B 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA D 418 " pdb=" C ALA D 418 " pdb=" N LEU D 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA C 418 " pdb=" C ALA C 418 " pdb=" N LEU C 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" O VAL A 417 " pdb=" C VAL A 417 " pdb=" N ALA A 418 " ideal model delta sigma weight residual 121.87 116.25 5.62 9.70e-01 1.06e+00 3.36e+01 ... (remaining 44619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 10295 16.56 - 33.11: 917 33.11 - 49.67: 204 49.67 - 66.23: 132 66.23 - 82.79: 16 Dihedral angle restraints: 11564 sinusoidal: 6244 harmonic: 5320 Sorted by residual: dihedral pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " pdb=" CG ASN B 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN A 120 " pdb=" CA ASN A 120 " pdb=" CB ASN A 120 " pdb=" CG ASN A 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN C 120 " pdb=" CA ASN C 120 " pdb=" CB ASN C 120 " pdb=" CG ASN C 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 11561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1492 0.035 - 0.069: 388 0.069 - 0.104: 100 0.104 - 0.139: 16 0.139 - 0.173: 8 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA VAL D 417 " pdb=" N VAL D 417 " pdb=" C VAL D 417 " pdb=" CB VAL D 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA VAL B 417 " pdb=" N VAL B 417 " pdb=" C VAL B 417 " pdb=" CB VAL B 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA VAL C 417 " pdb=" N VAL C 417 " pdb=" C VAL C 417 " pdb=" CB VAL C 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 2001 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN C 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN C 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN C 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN C 423 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN B 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN B 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN B 423 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN A 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN A 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN A 423 " -0.219 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1420 2.20 - 2.80: 51656 2.80 - 3.40: 71708 3.40 - 4.00: 92624 4.00 - 4.60: 146175 Nonbonded interactions: 363583 Sorted by model distance: nonbonded pdb=" OD1 ASN D 401 " pdb=" HG1 THR D 403 " model vdw 1.599 2.450 nonbonded pdb=" OD1 ASN C 401 " pdb=" HG1 THR C 403 " model vdw 1.599 2.450 nonbonded pdb=" OD1 ASN A 401 " pdb=" HG1 THR A 403 " model vdw 1.599 2.450 nonbonded pdb=" OD1 ASN B 401 " pdb=" HG1 THR B 403 " model vdw 1.599 2.450 nonbonded pdb="HH22 ARG A 31 " pdb=" OD1 ASP A 110 " model vdw 1.674 2.450 ... (remaining 363578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 425) selection = (chain 'B' and resid 1 through 425) selection = (chain 'C' and resid 1 through 425) selection = (chain 'D' and resid 1 through 425) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.380 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.250 Process input model: 55.980 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 0.181 12284 Z= 0.298 Angle : 0.597 7.346 16668 Z= 0.375 Chirality : 0.034 0.173 2004 Planarity : 0.003 0.041 2032 Dihedral : 14.831 82.787 4452 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 12.23 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.21), residues: 1504 helix: 2.08 (0.14), residues: 1244 sheet: 0.86 (0.73), residues: 48 loop : -1.52 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 154 HIS 0.002 0.000 HIS A 278 PHE 0.010 0.001 PHE A 315 TYR 0.007 0.001 TYR C 312 ARG 0.002 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.850 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: A 399 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7274 (mpp-170) REVERT: B 399 ARG cc_start: 0.7523 (mmt180) cc_final: 0.7273 (mpp-170) REVERT: C 399 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7273 (mpp-170) REVERT: D 399 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7274 (mpp-170) outliers start: 16 outliers final: 4 residues processed: 136 average time/residue: 3.3151 time to fit residues: 485.7884 Evaluate side-chains 124 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112861 restraints weight = 36625.904| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.52 r_work: 0.3080 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12284 Z= 0.294 Angle : 0.495 4.385 16668 Z= 0.273 Chirality : 0.035 0.139 2004 Planarity : 0.003 0.035 2032 Dihedral : 4.987 56.289 1760 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.53 % Allowed : 11.01 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.21), residues: 1504 helix: 2.28 (0.14), residues: 1252 sheet: 0.48 (0.82), residues: 48 loop : -1.64 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 328 HIS 0.003 0.001 HIS C 337 PHE 0.013 0.002 PHE B 11 TYR 0.010 0.002 TYR A 56 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.910 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: A 272 LYS cc_start: 0.7238 (tppt) cc_final: 0.6490 (tmmt) REVERT: A 354 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8095 (mm-30) REVERT: B 272 LYS cc_start: 0.7251 (tppt) cc_final: 0.6503 (tmmt) REVERT: B 305 LEU cc_start: 0.8489 (tt) cc_final: 0.8285 (tm) REVERT: B 354 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8101 (mm-30) REVERT: C 272 LYS cc_start: 0.7261 (tppt) cc_final: 0.6512 (tmmt) REVERT: C 305 LEU cc_start: 0.8482 (tt) cc_final: 0.8277 (tm) REVERT: C 354 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8105 (mm-30) REVERT: D 272 LYS cc_start: 0.7241 (tppt) cc_final: 0.6492 (tmmt) REVERT: D 354 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8086 (mm-30) outliers start: 20 outliers final: 8 residues processed: 160 average time/residue: 2.6999 time to fit residues: 473.6875 Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.106919 restraints weight = 36239.355| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.65 r_work: 0.3023 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12284 Z= 0.334 Angle : 0.501 5.027 16668 Z= 0.276 Chirality : 0.036 0.148 2004 Planarity : 0.003 0.037 2032 Dihedral : 5.133 57.930 1760 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.83 % Allowed : 10.70 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.21), residues: 1504 helix: 2.21 (0.14), residues: 1256 sheet: 0.48 (0.82), residues: 48 loop : -1.55 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 154 HIS 0.004 0.001 HIS A 337 PHE 0.012 0.002 PHE A 11 TYR 0.011 0.002 TYR C 182 ARG 0.002 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.791 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: A 5 GLN cc_start: 0.7798 (tp-100) cc_final: 0.6873 (tm-30) REVERT: A 272 LYS cc_start: 0.7556 (tppt) cc_final: 0.6803 (tmmt) REVERT: A 424 ARG cc_start: 0.6338 (mpt90) cc_final: 0.6004 (ttt90) REVERT: B 5 GLN cc_start: 0.7783 (tp-100) cc_final: 0.6857 (tm-30) REVERT: B 272 LYS cc_start: 0.7568 (tppt) cc_final: 0.6812 (tmmt) REVERT: B 424 ARG cc_start: 0.6353 (mpt90) cc_final: 0.6018 (ttt90) REVERT: C 5 GLN cc_start: 0.7794 (tp-100) cc_final: 0.6871 (tm-30) REVERT: C 272 LYS cc_start: 0.7568 (tppt) cc_final: 0.6810 (tmmt) REVERT: C 424 ARG cc_start: 0.6345 (mpt90) cc_final: 0.6015 (ttt90) REVERT: D 5 GLN cc_start: 0.7793 (tp-100) cc_final: 0.6873 (tm-30) REVERT: D 272 LYS cc_start: 0.7559 (tppt) cc_final: 0.6805 (tmmt) REVERT: D 424 ARG cc_start: 0.6351 (mpt90) cc_final: 0.6011 (ttt90) outliers start: 24 outliers final: 8 residues processed: 182 average time/residue: 2.4806 time to fit residues: 496.5313 Evaluate side-chains 156 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 130 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.138218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107511 restraints weight = 36464.612| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.66 r_work: 0.3036 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12284 Z= 0.262 Angle : 0.461 4.185 16668 Z= 0.254 Chirality : 0.035 0.137 2004 Planarity : 0.003 0.036 2032 Dihedral : 5.052 59.294 1760 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 11.62 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.21), residues: 1504 helix: 2.34 (0.14), residues: 1256 sheet: 0.51 (0.80), residues: 48 loop : -1.40 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 174 HIS 0.003 0.001 HIS C 337 PHE 0.012 0.002 PHE D 11 TYR 0.006 0.001 TYR C 326 ARG 0.001 0.000 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.835 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: A 272 LYS cc_start: 0.7598 (tppt) cc_final: 0.6820 (tmmt) REVERT: A 391 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5982 (t0) REVERT: A 424 ARG cc_start: 0.6277 (mpt90) cc_final: 0.6042 (ttt90) REVERT: B 272 LYS cc_start: 0.7608 (tppt) cc_final: 0.6831 (tmmt) REVERT: B 391 ASP cc_start: 0.6226 (OUTLIER) cc_final: 0.5975 (t0) REVERT: B 424 ARG cc_start: 0.6298 (mpt90) cc_final: 0.6064 (ttt90) REVERT: C 272 LYS cc_start: 0.7624 (tppt) cc_final: 0.6848 (tmmt) REVERT: C 391 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5964 (t0) REVERT: C 424 ARG cc_start: 0.6280 (mpt90) cc_final: 0.6048 (ttt90) REVERT: D 272 LYS cc_start: 0.7607 (tppt) cc_final: 0.6827 (tmmt) REVERT: D 391 ASP cc_start: 0.6243 (OUTLIER) cc_final: 0.5994 (t0) REVERT: D 424 ARG cc_start: 0.6292 (mpt90) cc_final: 0.6051 (ttt90) outliers start: 28 outliers final: 8 residues processed: 160 average time/residue: 2.5112 time to fit residues: 441.8366 Evaluate side-chains 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.106604 restraints weight = 36454.488| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.65 r_work: 0.3030 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12284 Z= 0.293 Angle : 0.480 4.178 16668 Z= 0.265 Chirality : 0.035 0.137 2004 Planarity : 0.003 0.036 2032 Dihedral : 5.138 59.914 1760 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.76 % Allowed : 12.92 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.21), residues: 1504 helix: 2.31 (0.14), residues: 1256 sheet: 0.54 (0.79), residues: 48 loop : -1.37 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 174 HIS 0.003 0.001 HIS D 337 PHE 0.011 0.002 PHE A 11 TYR 0.007 0.001 TYR A 122 ARG 0.002 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.799 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: A 272 LYS cc_start: 0.7685 (tppt) cc_final: 0.6944 (tmmt) REVERT: A 391 ASP cc_start: 0.6275 (OUTLIER) cc_final: 0.5982 (t0) REVERT: A 424 ARG cc_start: 0.6353 (mpt90) cc_final: 0.6094 (ttt90) REVERT: B 272 LYS cc_start: 0.7697 (tppt) cc_final: 0.6955 (tmmt) REVERT: B 391 ASP cc_start: 0.6286 (OUTLIER) cc_final: 0.5994 (t0) REVERT: B 424 ARG cc_start: 0.6361 (mpt90) cc_final: 0.6105 (ttt90) REVERT: C 272 LYS cc_start: 0.7712 (tppt) cc_final: 0.6971 (tmmt) REVERT: C 391 ASP cc_start: 0.6271 (OUTLIER) cc_final: 0.5976 (t0) REVERT: C 424 ARG cc_start: 0.6351 (mpt90) cc_final: 0.6099 (ttt90) REVERT: D 272 LYS cc_start: 0.7700 (tppt) cc_final: 0.6957 (tmmt) REVERT: D 391 ASP cc_start: 0.6296 (OUTLIER) cc_final: 0.6003 (t0) REVERT: D 424 ARG cc_start: 0.6357 (mpt90) cc_final: 0.6091 (ttt90) outliers start: 23 outliers final: 11 residues processed: 172 average time/residue: 2.5343 time to fit residues: 481.1409 Evaluate side-chains 155 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN C 27 ASN D 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106607 restraints weight = 36448.093| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.58 r_work: 0.3023 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12284 Z= 0.315 Angle : 0.484 4.276 16668 Z= 0.268 Chirality : 0.036 0.139 2004 Planarity : 0.003 0.037 2032 Dihedral : 4.439 34.339 1752 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.22 % Allowed : 12.54 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.21), residues: 1504 helix: 2.23 (0.14), residues: 1256 sheet: 0.76 (0.77), residues: 48 loop : -1.37 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 174 HIS 0.003 0.001 HIS A 337 PHE 0.011 0.002 PHE A 11 TYR 0.007 0.002 TYR C 122 ARG 0.002 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.720 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: A 5 GLN cc_start: 0.7766 (tp-100) cc_final: 0.6708 (tm-30) REVERT: A 272 LYS cc_start: 0.7592 (tppt) cc_final: 0.6818 (tmmt) REVERT: A 391 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5838 (t0) REVERT: A 424 ARG cc_start: 0.6209 (mpt90) cc_final: 0.5882 (ttt90) REVERT: B 5 GLN cc_start: 0.7764 (tp-100) cc_final: 0.6709 (tm-30) REVERT: B 272 LYS cc_start: 0.7602 (tppt) cc_final: 0.6824 (tmmt) REVERT: B 391 ASP cc_start: 0.6163 (OUTLIER) cc_final: 0.5856 (t0) REVERT: B 424 ARG cc_start: 0.6219 (mpt90) cc_final: 0.5893 (ttt90) REVERT: C 5 GLN cc_start: 0.7766 (tp-100) cc_final: 0.6712 (tm-30) REVERT: C 272 LYS cc_start: 0.7608 (tppt) cc_final: 0.6829 (tmmt) REVERT: C 391 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5829 (t0) REVERT: C 424 ARG cc_start: 0.6210 (mpt90) cc_final: 0.5885 (ttt90) REVERT: D 5 GLN cc_start: 0.7766 (tp-100) cc_final: 0.6712 (tm-30) REVERT: D 272 LYS cc_start: 0.7595 (tppt) cc_final: 0.6817 (tmmt) REVERT: D 391 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5852 (t0) REVERT: D 424 ARG cc_start: 0.6223 (mpt90) cc_final: 0.5888 (ttt90) outliers start: 29 outliers final: 13 residues processed: 170 average time/residue: 2.5837 time to fit residues: 482.7910 Evaluate side-chains 155 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 113 ASN B 27 ASN B 113 ASN C 27 ASN C 113 ASN D 27 ASN D 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107980 restraints weight = 36218.155| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.65 r_work: 0.3053 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12284 Z= 0.208 Angle : 0.440 4.060 16668 Z= 0.244 Chirality : 0.034 0.135 2004 Planarity : 0.003 0.035 2032 Dihedral : 4.086 28.694 1752 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.76 % Allowed : 13.76 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.21), residues: 1504 helix: 2.49 (0.14), residues: 1256 sheet: 0.79 (0.74), residues: 48 loop : -1.17 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 174 HIS 0.003 0.001 HIS D 337 PHE 0.012 0.001 PHE D 11 TYR 0.006 0.001 TYR B 122 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 2.089 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: A 272 LYS cc_start: 0.7723 (tppt) cc_final: 0.6989 (tmmt) REVERT: A 391 ASP cc_start: 0.6120 (OUTLIER) cc_final: 0.5841 (t0) REVERT: A 424 ARG cc_start: 0.6381 (mpt90) cc_final: 0.6163 (ttt90) REVERT: B 272 LYS cc_start: 0.7730 (tppt) cc_final: 0.6996 (tmmt) REVERT: B 391 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5852 (t0) REVERT: B 424 ARG cc_start: 0.6412 (mpt90) cc_final: 0.6190 (ttt90) REVERT: C 272 LYS cc_start: 0.7744 (tppt) cc_final: 0.7016 (tmmt) REVERT: C 391 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5834 (t0) REVERT: C 424 ARG cc_start: 0.6412 (mpt90) cc_final: 0.6187 (ttt90) REVERT: D 272 LYS cc_start: 0.7730 (tppt) cc_final: 0.6996 (tmmt) REVERT: D 391 ASP cc_start: 0.6126 (OUTLIER) cc_final: 0.5848 (t0) REVERT: D 424 ARG cc_start: 0.6405 (mpt90) cc_final: 0.6169 (ttt90) outliers start: 23 outliers final: 15 residues processed: 159 average time/residue: 2.5229 time to fit residues: 441.7542 Evaluate side-chains 159 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107725 restraints weight = 36269.407| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.65 r_work: 0.3059 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12284 Z= 0.232 Angle : 0.454 4.049 16668 Z= 0.252 Chirality : 0.034 0.142 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.063 28.000 1752 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.07 % Allowed : 14.14 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.21), residues: 1504 helix: 2.49 (0.14), residues: 1256 sheet: 0.87 (0.73), residues: 48 loop : -1.21 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 174 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.002 PHE D 11 TYR 0.006 0.001 TYR D 182 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.760 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: A 272 LYS cc_start: 0.7714 (tppt) cc_final: 0.7003 (tmmt) REVERT: A 391 ASP cc_start: 0.6083 (m-30) cc_final: 0.5799 (t0) REVERT: A 424 ARG cc_start: 0.6375 (mpt90) cc_final: 0.6155 (ttt90) REVERT: B 272 LYS cc_start: 0.7717 (tppt) cc_final: 0.7011 (tmmt) REVERT: B 391 ASP cc_start: 0.6094 (m-30) cc_final: 0.5809 (t0) REVERT: B 424 ARG cc_start: 0.6385 (mpt90) cc_final: 0.6162 (ttt90) REVERT: C 272 LYS cc_start: 0.7726 (tppt) cc_final: 0.7019 (tmmt) REVERT: C 391 ASP cc_start: 0.6073 (m-30) cc_final: 0.5788 (t0) REVERT: C 424 ARG cc_start: 0.6388 (mpt90) cc_final: 0.6164 (ttt90) REVERT: D 272 LYS cc_start: 0.7716 (tppt) cc_final: 0.7007 (tmmt) REVERT: D 391 ASP cc_start: 0.6088 (m-30) cc_final: 0.5807 (t0) REVERT: D 424 ARG cc_start: 0.6385 (mpt90) cc_final: 0.6157 (ttt90) outliers start: 14 outliers final: 11 residues processed: 150 average time/residue: 2.6983 time to fit residues: 446.1971 Evaluate side-chains 144 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109820 restraints weight = 37568.196| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.65 r_work: 0.3061 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12284 Z= 0.164 Angle : 0.418 3.943 16668 Z= 0.229 Chirality : 0.033 0.133 2004 Planarity : 0.003 0.035 2032 Dihedral : 3.703 21.327 1752 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.69 % Allowed : 16.28 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.21), residues: 1504 helix: 2.74 (0.14), residues: 1256 sheet: 0.98 (0.70), residues: 48 loop : -1.00 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 174 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.001 PHE C 11 TYR 0.005 0.001 TYR C 96 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.943 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: A 25 VAL cc_start: 0.7514 (p) cc_final: 0.7280 (p) REVERT: A 127 ARG cc_start: 0.6820 (ttt180) cc_final: 0.6564 (ttt180) REVERT: A 272 LYS cc_start: 0.7684 (tppt) cc_final: 0.6973 (tmmt) REVERT: A 391 ASP cc_start: 0.5995 (m-30) cc_final: 0.5754 (t0) REVERT: B 25 VAL cc_start: 0.7491 (p) cc_final: 0.7263 (p) REVERT: B 127 ARG cc_start: 0.6828 (ttt180) cc_final: 0.6581 (ttt180) REVERT: B 272 LYS cc_start: 0.7687 (tppt) cc_final: 0.6981 (tmmt) REVERT: B 391 ASP cc_start: 0.6008 (m-30) cc_final: 0.5769 (t0) REVERT: B 424 ARG cc_start: 0.6268 (mpt90) cc_final: 0.5999 (ttt90) REVERT: C 25 VAL cc_start: 0.7486 (p) cc_final: 0.7258 (p) REVERT: C 127 ARG cc_start: 0.6831 (ttt180) cc_final: 0.6579 (ttt180) REVERT: C 272 LYS cc_start: 0.7683 (tppt) cc_final: 0.6977 (tmmt) REVERT: C 391 ASP cc_start: 0.5992 (m-30) cc_final: 0.5754 (t0) REVERT: C 424 ARG cc_start: 0.6289 (mpt90) cc_final: 0.6029 (ttt90) REVERT: D 25 VAL cc_start: 0.7471 (p) cc_final: 0.7243 (p) REVERT: D 127 ARG cc_start: 0.6816 (ttt180) cc_final: 0.6559 (ttt180) REVERT: D 272 LYS cc_start: 0.7692 (tppt) cc_final: 0.6984 (tmmt) REVERT: D 391 ASP cc_start: 0.6000 (m-30) cc_final: 0.5759 (t0) outliers start: 9 outliers final: 8 residues processed: 157 average time/residue: 3.0384 time to fit residues: 517.4580 Evaluate side-chains 146 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 0.0470 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109862 restraints weight = 37664.821| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.66 r_work: 0.3061 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12284 Z= 0.162 Angle : 0.410 3.945 16668 Z= 0.227 Chirality : 0.033 0.134 2004 Planarity : 0.003 0.035 2032 Dihedral : 3.586 18.520 1752 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.61 % Allowed : 15.67 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.21), residues: 1504 helix: 2.82 (0.14), residues: 1256 sheet: 1.20 (0.70), residues: 48 loop : -0.99 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.003 0.001 HIS D 337 PHE 0.011 0.001 PHE A 11 TYR 0.005 0.001 TYR A 96 ARG 0.001 0.000 ARG C 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 1.750 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: A 25 VAL cc_start: 0.7537 (p) cc_final: 0.7305 (p) REVERT: A 127 ARG cc_start: 0.6876 (ttt180) cc_final: 0.6620 (ttt180) REVERT: A 209 MET cc_start: 0.7913 (ttt) cc_final: 0.7609 (ttm) REVERT: A 272 LYS cc_start: 0.7690 (tppt) cc_final: 0.6983 (tmmt) REVERT: A 391 ASP cc_start: 0.5998 (m-30) cc_final: 0.5700 (t0) REVERT: B 25 VAL cc_start: 0.7529 (p) cc_final: 0.7298 (p) REVERT: B 127 ARG cc_start: 0.6886 (ttt180) cc_final: 0.6636 (ttt180) REVERT: B 209 MET cc_start: 0.7913 (ttt) cc_final: 0.7608 (ttm) REVERT: B 272 LYS cc_start: 0.7684 (tppt) cc_final: 0.6990 (tmmt) REVERT: B 391 ASP cc_start: 0.5998 (m-30) cc_final: 0.5703 (t0) REVERT: B 424 ARG cc_start: 0.6337 (mpt90) cc_final: 0.6118 (ttt90) REVERT: C 25 VAL cc_start: 0.7532 (p) cc_final: 0.7303 (p) REVERT: C 127 ARG cc_start: 0.6888 (ttt180) cc_final: 0.6637 (ttt180) REVERT: C 272 LYS cc_start: 0.7688 (tppt) cc_final: 0.6982 (tmmt) REVERT: C 391 ASP cc_start: 0.6000 (m-30) cc_final: 0.5704 (t0) REVERT: D 25 VAL cc_start: 0.7501 (p) cc_final: 0.7273 (p) REVERT: D 127 ARG cc_start: 0.6873 (ttt180) cc_final: 0.6608 (ttt180) REVERT: D 272 LYS cc_start: 0.7694 (tppt) cc_final: 0.6993 (tmmt) REVERT: D 391 ASP cc_start: 0.6001 (m-30) cc_final: 0.5703 (t0) outliers start: 8 outliers final: 8 residues processed: 150 average time/residue: 3.0179 time to fit residues: 491.4821 Evaluate side-chains 147 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107251 restraints weight = 37996.475| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.64 r_work: 0.3022 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12284 Z= 0.261 Angle : 0.458 4.163 16668 Z= 0.254 Chirality : 0.034 0.136 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.138 29.851 1752 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.76 % Allowed : 16.13 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.21), residues: 1504 helix: 2.53 (0.14), residues: 1256 sheet: 0.98 (0.74), residues: 48 loop : -1.24 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 174 HIS 0.004 0.001 HIS C 337 PHE 0.010 0.002 PHE B 392 TYR 0.008 0.001 TYR B 56 ARG 0.002 0.000 ARG D 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14700.42 seconds wall clock time: 263 minutes 48.71 seconds (15828.71 seconds total)