Starting phenix.real_space_refine on Fri Jun 20 22:45:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x83_38134/06_2025/8x83_38134_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x83_38134/06_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_38134/06_2025/8x83_38134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x83_38134/06_2025/8x83_38134.map" model { file = "/net/cci-nas-00/data/ceres_data/8x83_38134/06_2025/8x83_38134_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x83_38134/06_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-5710/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: 16.04, per 1000 atoms: 0.66 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: 6.26 Conformation dependent library (CDL) restraints added in 1.9 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: 1.84 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: 9.13 Time building geometry restraints manager: 7.64 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: 0.870 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: 0.400 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 56.220 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.050 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.250 ------------------------------------------------------------------------------- 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= 0.319 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 Details of bonding type rmsd hydrogen bonds : bond 0.10124 ( 1056) hydrogen bonds : angle 4.81562 ( 3168) covalent geometry : bond 0.00510 (12284) covalent geometry : angle 0.59658 (16668) *********************** 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 : 1.683 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: 2.9944 time to fit residues: 439.7172 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 : 1.686 ------------------------------------------------------------------------------- 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 = 36625.925| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.52 r_work: 0.3079 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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= 0.203 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 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 1056) hydrogen bonds : angle 4.01141 ( 3168) covalent geometry : bond 0.00451 (12284) covalent geometry : angle 0.49470 (16668) *********************** 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 : 1.735 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: 0.8339 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 272 LYS cc_start: 0.7252 (tppt) cc_final: 0.6504 (tmmt) REVERT: B 305 LEU cc_start: 0.8490 (tt) cc_final: 0.8286 (tm) REVERT: B 354 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8104 (mm-30) REVERT: C 272 LYS cc_start: 0.7261 (tppt) cc_final: 0.6512 (tmmt) REVERT: C 305 LEU cc_start: 0.8483 (tt) cc_final: 0.8278 (tm) REVERT: C 354 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8108 (mm-30) REVERT: D 272 LYS cc_start: 0.7241 (tppt) cc_final: 0.6493 (tmmt) REVERT: D 354 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8089 (mm-30) outliers start: 20 outliers final: 8 residues processed: 160 average time/residue: 2.5263 time to fit residues: 442.3149 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 : 1.785 ------------------------------------------------------------------------------- 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: 1.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 0.0970 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.138444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107602 restraints weight = 36166.200| |-----------------------------------------------------------------------------| r_work (start): 0.3176 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: 3.76 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12284 Z= 0.205 Angle : 0.481 4.960 16668 Z= 0.265 Chirality : 0.035 0.145 2004 Planarity : 0.003 0.037 2032 Dihedral : 5.018 57.834 1760 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.83 % Allowed : 10.40 % Favored : 87.77 % 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: 2.69 (0.21), residues: 1504 helix: 2.32 (0.14), residues: 1256 sheet: 0.47 (0.81), residues: 48 loop : -1.49 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 154 HIS 0.004 0.001 HIS D 337 PHE 0.013 0.002 PHE C 11 TYR 0.010 0.002 TYR C 182 ARG 0.002 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 1056) hydrogen bonds : angle 3.96914 ( 3168) covalent geometry : bond 0.00454 (12284) covalent geometry : angle 0.48148 (16668) *********************** 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 186 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LYS cc_start: 0.7533 (tppt) cc_final: 0.6784 (tmmt) REVERT: A 424 ARG cc_start: 0.6294 (mpt90) cc_final: 0.6036 (ttt90) REVERT: B 272 LYS cc_start: 0.7537 (tppt) cc_final: 0.6784 (tmmt) REVERT: B 424 ARG cc_start: 0.6307 (mpt90) cc_final: 0.6047 (ttt90) REVERT: C 272 LYS cc_start: 0.7539 (tppt) cc_final: 0.6786 (tmmt) REVERT: C 424 ARG cc_start: 0.6302 (mpt90) cc_final: 0.6051 (ttt90) REVERT: D 272 LYS cc_start: 0.7536 (tppt) cc_final: 0.6784 (tmmt) REVERT: D 424 ARG cc_start: 0.6312 (mpt90) cc_final: 0.6047 (ttt90) outliers start: 24 outliers final: 8 residues processed: 178 average time/residue: 2.4095 time to fit residues: 472.5866 Evaluate side-chains 152 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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: 7.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.137614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106827 restraints weight = 36489.224| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.66 r_work: 0.3031 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12284 Z= 0.200 Angle : 0.471 4.208 16668 Z= 0.260 Chirality : 0.035 0.140 2004 Planarity : 0.003 0.036 2032 Dihedral : 5.114 59.358 1760 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.83 % Allowed : 11.93 % 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: 2.73 (0.21), residues: 1504 helix: 2.33 (0.14), residues: 1256 sheet: 0.56 (0.80), residues: 48 loop : -1.42 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 174 HIS 0.003 0.001 HIS C 337 PHE 0.012 0.002 PHE D 11 TYR 0.006 0.001 TYR D 326 ARG 0.001 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 1056) hydrogen bonds : angle 3.94711 ( 3168) covalent geometry : bond 0.00445 (12284) covalent geometry : angle 0.47105 (16668) *********************** 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: 24 poor density : 148 time to evaluate : 3.190 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: 0.7607 (tppt) cc_final: 0.6829 (tmmt) REVERT: A 391 ASP cc_start: 0.6250 (OUTLIER) cc_final: 0.5953 (t0) REVERT: A 424 ARG cc_start: 0.6321 (mpt90) cc_final: 0.6048 (ttt90) REVERT: B 272 LYS cc_start: 0.7610 (tppt) cc_final: 0.6833 (tmmt) REVERT: B 391 ASP cc_start: 0.6255 (OUTLIER) cc_final: 0.5955 (t0) REVERT: B 424 ARG cc_start: 0.6343 (mpt90) cc_final: 0.6076 (ttt90) REVERT: C 272 LYS cc_start: 0.7625 (tppt) cc_final: 0.6850 (tmmt) REVERT: C 391 ASP cc_start: 0.6234 (OUTLIER) cc_final: 0.5933 (t0) REVERT: C 424 ARG cc_start: 0.6322 (mpt90) cc_final: 0.6063 (ttt90) REVERT: D 272 LYS cc_start: 0.7606 (tppt) cc_final: 0.6828 (tmmt) REVERT: D 391 ASP cc_start: 0.6258 (OUTLIER) cc_final: 0.5961 (t0) REVERT: D 424 ARG cc_start: 0.6336 (mpt90) cc_final: 0.6057 (ttt90) outliers start: 24 outliers final: 8 residues processed: 160 average time/residue: 3.3924 time to fit residues: 607.1131 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 : 3.191 ------------------------------------------------------------------------------- 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: 4.9990 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.137054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107764 restraints weight = 36682.180| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.54 r_work: 0.3028 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12284 Z= 0.246 Angle : 0.506 4.283 16668 Z= 0.280 Chirality : 0.037 0.145 2004 Planarity : 0.003 0.037 2032 Dihedral : 5.304 59.644 1760 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.83 % Allowed : 12.84 % 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: 2.48 (0.21), residues: 1504 helix: 2.16 (0.14), residues: 1256 sheet: 0.54 (0.81), residues: 48 loop : -1.47 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 174 HIS 0.003 0.001 HIS A 337 PHE 0.011 0.002 PHE A 11 TYR 0.009 0.002 TYR D 182 ARG 0.002 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 1056) hydrogen bonds : angle 4.04228 ( 3168) covalent geometry : bond 0.00556 (12284) covalent geometry : angle 0.50638 (16668) *********************** 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 180 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.768 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: 0.7810 (tp-100) cc_final: 0.6796 (tm-30) REVERT: A 272 LYS cc_start: 0.7544 (tppt) cc_final: 0.6761 (tmmt) REVERT: A 391 ASP cc_start: 0.6223 (OUTLIER) cc_final: 0.5904 (t0) REVERT: A 424 ARG cc_start: 0.6286 (mpt90) cc_final: 0.6016 (ttt90) REVERT: B 5 GLN cc_start: 0.7820 (tp-100) cc_final: 0.6804 (tm-30) REVERT: B 272 LYS cc_start: 0.7551 (tppt) cc_final: 0.6767 (tmmt) REVERT: B 391 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.5964 (t0) REVERT: B 424 ARG cc_start: 0.6289 (mpt90) cc_final: 0.6020 (ttt90) REVERT: C 5 GLN cc_start: 0.7823 (tp-100) cc_final: 0.6808 (tm-30) REVERT: C 272 LYS cc_start: 0.7565 (tppt) cc_final: 0.6782 (tmmt) REVERT: C 391 ASP cc_start: 0.6176 (OUTLIER) cc_final: 0.5906 (t0) REVERT: C 424 ARG cc_start: 0.6280 (mpt90) cc_final: 0.6015 (ttt90) REVERT: D 5 GLN cc_start: 0.7808 (tp-100) cc_final: 0.6796 (tm-30) REVERT: D 272 LYS cc_start: 0.7554 (tppt) cc_final: 0.6770 (tmmt) REVERT: D 391 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5919 (t0) REVERT: D 424 ARG cc_start: 0.6287 (mpt90) cc_final: 0.6009 (ttt90) outliers start: 24 outliers final: 11 residues processed: 172 average time/residue: 2.3979 time to fit residues: 453.6328 Evaluate side-chains 163 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR 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 75 THR 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: 0.7980 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.139381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108741 restraints weight = 36198.805| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.65 r_work: 0.3061 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12284 Z= 0.140 Angle : 0.427 4.051 16668 Z= 0.236 Chirality : 0.033 0.137 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.016 28.562 1752 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 13.00 % Favored : 85.17 % 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: 2.54 (0.14), residues: 1256 sheet: 0.55 (0.78), residues: 48 loop : -1.18 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 174 HIS 0.003 0.001 HIS D 337 PHE 0.012 0.001 PHE A 11 TYR 0.006 0.001 TYR D 182 ARG 0.002 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 1056) hydrogen bonds : angle 3.77938 ( 3168) covalent geometry : bond 0.00296 (12284) covalent geometry : angle 0.42715 (16668) *********************** 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: 24 poor density : 158 time to evaluate : 1.766 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: 0.7752 (p) cc_final: 0.7513 (p) REVERT: A 272 LYS cc_start: 0.7689 (tppt) cc_final: 0.6957 (tmmt) REVERT: A 391 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5882 (t0) REVERT: A 424 ARG cc_start: 0.6359 (mpt90) cc_final: 0.6149 (ttt90) REVERT: B 25 VAL cc_start: 0.7747 (p) cc_final: 0.7511 (p) REVERT: B 272 LYS cc_start: 0.7705 (tppt) cc_final: 0.6972 (tmmt) REVERT: B 391 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5904 (t0) REVERT: B 424 ARG cc_start: 0.6376 (mpt90) cc_final: 0.6166 (ttt90) REVERT: C 25 VAL cc_start: 0.7758 (p) cc_final: 0.7519 (p) REVERT: C 272 LYS cc_start: 0.7711 (tppt) cc_final: 0.6977 (tmmt) REVERT: C 391 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5890 (t0) REVERT: C 424 ARG cc_start: 0.6376 (mpt90) cc_final: 0.6169 (ttt90) REVERT: D 25 VAL cc_start: 0.7760 (p) cc_final: 0.7519 (p) REVERT: D 272 LYS cc_start: 0.7698 (tppt) cc_final: 0.6964 (tmmt) REVERT: D 391 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5884 (t0) REVERT: D 424 ARG cc_start: 0.6372 (mpt90) cc_final: 0.6158 (ttt90) outliers start: 24 outliers final: 8 residues processed: 174 average time/residue: 2.4197 time to fit residues: 462.9071 Evaluate side-chains 150 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 391 ASP 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 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 391 ASP 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: 0.0070 chunk 101 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- 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 27 ASN D 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107858 restraints weight = 36331.772| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.65 r_work: 0.3049 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2534 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= 0.163 Angle : 0.445 4.150 16668 Z= 0.246 Chirality : 0.034 0.135 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.064 28.511 1752 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.53 % Allowed : 13.46 % Favored : 85.02 % 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: 3.05 (0.21), residues: 1504 helix: 2.53 (0.14), residues: 1256 sheet: 1.01 (0.77), residues: 48 loop : -1.27 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 174 HIS 0.003 0.001 HIS D 337 PHE 0.011 0.001 PHE A 11 TYR 0.007 0.001 TYR D 182 ARG 0.002 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 1056) hydrogen bonds : angle 3.80080 ( 3168) covalent geometry : bond 0.00353 (12284) covalent geometry : angle 0.44512 (16668) *********************** 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 178 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.763 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: A 272 LYS cc_start: 0.7666 (tppt) cc_final: 0.6963 (tmmt) REVERT: A 424 ARG cc_start: 0.6381 (mpt90) cc_final: 0.6155 (ttt90) REVERT: B 272 LYS cc_start: 0.7681 (tppt) cc_final: 0.6976 (tmmt) REVERT: B 391 ASP cc_start: 0.5954 (OUTLIER) cc_final: 0.5740 (t0) REVERT: B 424 ARG cc_start: 0.6372 (mpt90) cc_final: 0.6165 (ttt90) REVERT: C 209 MET cc_start: 0.7900 (ttt) cc_final: 0.7623 (ttp) REVERT: C 272 LYS cc_start: 0.7691 (tppt) cc_final: 0.6993 (tmmt) REVERT: C 391 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.5727 (t0) REVERT: C 424 ARG cc_start: 0.6387 (mpt90) cc_final: 0.6173 (ttt90) REVERT: D 209 MET cc_start: 0.7892 (ttt) cc_final: 0.7615 (ttp) REVERT: D 272 LYS cc_start: 0.7684 (tppt) cc_final: 0.6981 (tmmt) REVERT: D 424 ARG cc_start: 0.6394 (mpt90) cc_final: 0.6159 (ttt90) outliers start: 20 outliers final: 14 residues processed: 170 average time/residue: 2.4910 time to fit residues: 466.2159 Evaluate side-chains 165 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 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 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 391 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108127 restraints weight = 37779.917| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.63 r_work: 0.3034 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12284 Z= 0.158 Angle : 0.449 4.148 16668 Z= 0.248 Chirality : 0.034 0.134 2004 Planarity : 0.003 0.035 2032 Dihedral : 4.022 27.608 1752 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.30 % Allowed : 14.07 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.21), residues: 1504 helix: 2.54 (0.14), residues: 1256 sheet: 0.87 (0.78), residues: 48 loop : -1.19 (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 0.011 0.001 PHE D 11 TYR 0.007 0.001 TYR D 182 ARG 0.001 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 1056) hydrogen bonds : angle 3.75702 ( 3168) covalent geometry : bond 0.00339 (12284) covalent geometry : angle 0.44866 (16668) *********************** 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 170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.717 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 127 ARG cc_start: 0.6866 (ttt180) cc_final: 0.6595 (ttt180) REVERT: A 272 LYS cc_start: 0.7688 (tppt) cc_final: 0.6970 (tmmt) REVERT: A 424 ARG cc_start: 0.6308 (mpt90) cc_final: 0.6076 (ttt90) REVERT: B 272 LYS cc_start: 0.7697 (tppt) cc_final: 0.6978 (tmmt) REVERT: B 391 ASP cc_start: 0.5996 (OUTLIER) cc_final: 0.5778 (t0) REVERT: B 424 ARG cc_start: 0.6309 (mpt90) cc_final: 0.6067 (ttt90) REVERT: C 127 ARG cc_start: 0.6864 (ttt180) cc_final: 0.6597 (ttt180) REVERT: C 272 LYS cc_start: 0.7690 (tppt) cc_final: 0.6971 (tmmt) REVERT: C 391 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5739 (t0) REVERT: C 424 ARG cc_start: 0.6336 (mpt90) cc_final: 0.6093 (ttt90) REVERT: D 127 ARG cc_start: 0.6858 (ttt180) cc_final: 0.6589 (ttt180) REVERT: D 272 LYS cc_start: 0.7704 (tppt) cc_final: 0.6986 (tmmt) REVERT: D 424 ARG cc_start: 0.6318 (mpt90) cc_final: 0.6082 (ttt90) outliers start: 17 outliers final: 9 residues processed: 166 average time/residue: 2.7802 time to fit residues: 502.1470 Evaluate side-chains 159 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 B residue 391 ASP 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 182 TYR Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.140170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110550 restraints weight = 37531.063| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.63 r_work: 0.3070 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.002 0.028 12284 Z= 0.117 Angle : 0.410 3.961 16668 Z= 0.225 Chirality : 0.033 0.137 2004 Planarity : 0.003 0.034 2032 Dihedral : 3.597 19.812 1752 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.69 % Allowed : 15.14 % Favored : 84.17 % 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: 3.48 (0.21), residues: 1504 helix: 2.82 (0.14), residues: 1256 sheet: 0.80 (0.76), residues: 48 loop : -1.03 (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 A 306 PHE 0.011 0.001 PHE D 11 TYR 0.005 0.001 TYR B 96 ARG 0.001 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 1056) hydrogen bonds : angle 3.59775 ( 3168) covalent geometry : bond 0.00239 (12284) covalent geometry : angle 0.40987 (16668) *********************** 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 165 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.739 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: A 127 ARG cc_start: 0.6875 (ttt180) cc_final: 0.6624 (ttt180) REVERT: A 209 MET cc_start: 0.7886 (ttt) cc_final: 0.7576 (ttm) REVERT: A 272 LYS cc_start: 0.7671 (tppt) cc_final: 0.6967 (tmmt) REVERT: B 127 ARG cc_start: 0.6871 (ttt180) cc_final: 0.6615 (ttt180) REVERT: B 209 MET cc_start: 0.7900 (ttt) cc_final: 0.7592 (ttm) REVERT: B 272 LYS cc_start: 0.7676 (tppt) cc_final: 0.6972 (tmmt) REVERT: B 391 ASP cc_start: 0.5978 (m-30) cc_final: 0.5742 (t0) REVERT: C 127 ARG cc_start: 0.6874 (ttt180) cc_final: 0.6622 (ttt180) REVERT: C 272 LYS cc_start: 0.7670 (tppt) cc_final: 0.6963 (tmmt) REVERT: C 391 ASP cc_start: 0.5971 (m-30) cc_final: 0.5738 (t0) REVERT: C 424 ARG cc_start: 0.6313 (mpt90) cc_final: 0.6090 (ttt90) REVERT: D 25 VAL cc_start: 0.7506 (p) cc_final: 0.7243 (p) REVERT: D 127 ARG cc_start: 0.6856 (ttt180) cc_final: 0.6601 (ttt180) REVERT: D 272 LYS cc_start: 0.7680 (tppt) cc_final: 0.6974 (tmmt) outliers start: 9 outliers final: 9 residues processed: 165 average time/residue: 3.0098 time to fit residues: 536.1079 Evaluate side-chains 155 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.139089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109319 restraints weight = 37820.448| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.64 r_work: 0.3051 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12284 Z= 0.135 Angle : 0.422 4.108 16668 Z= 0.234 Chirality : 0.033 0.135 2004 Planarity : 0.003 0.034 2032 Dihedral : 3.680 21.141 1752 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.76 % Allowed : 15.21 % Favored : 84.02 % 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: 3.40 (0.21), residues: 1504 helix: 2.77 (0.14), residues: 1256 sheet: 0.78 (0.77), residues: 48 loop : -1.06 (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 A 337 PHE 0.011 0.001 PHE D 11 TYR 0.006 0.001 TYR C 182 ARG 0.001 0.000 ARG D 424 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 1056) hydrogen bonds : angle 3.62973 ( 3168) covalent geometry : bond 0.00284 (12284) covalent geometry : angle 0.42199 (16668) ********************** 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 170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 2.140 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: A 127 ARG cc_start: 0.6906 (ttt180) cc_final: 0.6664 (ttt180) REVERT: A 209 MET cc_start: 0.7904 (ttt) cc_final: 0.7596 (ttm) REVERT: A 272 LYS cc_start: 0.7682 (tppt) cc_final: 0.6977 (tmmt) REVERT: B 25 VAL cc_start: 0.7654 (p) cc_final: 0.7413 (p) REVERT: B 127 ARG cc_start: 0.6900 (ttt180) cc_final: 0.6652 (ttt180) REVERT: B 209 MET cc_start: 0.7909 (ttt) cc_final: 0.7599 (ttm) REVERT: B 272 LYS cc_start: 0.7683 (tppt) cc_final: 0.6981 (tmmt) REVERT: B 391 ASP cc_start: 0.5964 (m-30) cc_final: 0.5729 (t0) REVERT: C 25 VAL cc_start: 0.7660 (p) cc_final: 0.7420 (p) REVERT: C 127 ARG cc_start: 0.6909 (ttt180) cc_final: 0.6662 (ttt180) REVERT: C 209 MET cc_start: 0.8035 (ttt) cc_final: 0.7721 (ttm) REVERT: C 272 LYS cc_start: 0.7679 (tppt) cc_final: 0.6974 (tmmt) REVERT: C 391 ASP cc_start: 0.5960 (m-30) cc_final: 0.5725 (t0) REVERT: C 424 ARG cc_start: 0.6367 (mpt90) cc_final: 0.6163 (ttt90) REVERT: D 25 VAL cc_start: 0.7475 (p) cc_final: 0.7244 (p) REVERT: D 127 ARG cc_start: 0.6886 (ttt180) cc_final: 0.6622 (ttt180) REVERT: D 209 MET cc_start: 0.8032 (ttt) cc_final: 0.7719 (ttm) REVERT: D 272 LYS cc_start: 0.7680 (tppt) cc_final: 0.6974 (tmmt) outliers start: 10 outliers final: 10 residues processed: 170 average time/residue: 2.6037 time to fit residues: 484.0039 Evaluate side-chains 162 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 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: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108082 restraints weight = 37854.854| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.63 r_work: 0.3036 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12284 Z= 0.157 Angle : 0.435 4.154 16668 Z= 0.241 Chirality : 0.034 0.136 2004 Planarity : 0.003 0.034 2032 Dihedral : 3.924 26.833 1752 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.38 % Allowed : 14.76 % Favored : 83.87 % 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: 3.27 (0.21), residues: 1504 helix: 2.69 (0.14), residues: 1256 sheet: 0.72 (0.78), residues: 48 loop : -1.15 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 174 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.001 PHE A 11 TYR 0.007 0.001 TYR D 182 ARG 0.002 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 1056) hydrogen bonds : angle 3.69597 ( 3168) covalent geometry : bond 0.00338 (12284) covalent geometry : angle 0.43475 (16668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16102.86 seconds wall clock time: 276 minutes 48.49 seconds (16608.49 seconds total)