Starting phenix.real_space_refine on Mon Sep 30 02:56:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/09_2024/8x83_38134_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/09_2024/8x83_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/09_2024/8x83_38134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/09_2024/8x83_38134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/09_2024/8x83_38134_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/09_2024/8x83_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-5461/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: 15.83, per 1000 atoms: 0.65 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: 6.78 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: 1.52 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: 9.52 Time building geometry restraints manager: 7.92 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: 0.580 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: 0.430 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 55.470 Find NCS groups from input model: 0.860 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: 0.010 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.600 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.732 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: 2.9926 time to fit residues: 439.6266 Evaluate side-chains 124 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.871 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: 0.7439 (tppt) cc_final: 0.6749 (tmmt) REVERT: A 354 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 272 LYS cc_start: 0.7440 (tppt) cc_final: 0.6749 (tmmt) REVERT: B 354 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8012 (mm-30) REVERT: C 272 LYS cc_start: 0.7441 (tppt) cc_final: 0.6751 (tmmt) REVERT: C 354 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8013 (mm-30) REVERT: D 272 LYS cc_start: 0.7440 (tppt) cc_final: 0.6750 (tmmt) REVERT: D 354 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8013 (mm-30) outliers start: 20 outliers final: 8 residues processed: 160 average time/residue: 2.5195 time to fit residues: 442.6199 Evaluate side-chains 152 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 76 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2048 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= 0.285 Angle : 0.476 4.540 16668 Z= 0.262 Chirality : 0.035 0.140 2004 Planarity : 0.003 0.037 2032 Dihedral : 4.979 57.676 1760 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.83 % Allowed : 10.09 % Favored : 88.07 % 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: 2.34 (0.14), residues: 1256 sheet: 0.49 (0.81), residues: 48 loop : -1.47 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.004 0.001 HIS B 337 PHE 0.013 0.002 PHE C 11 TYR 0.009 0.002 TYR D 56 ARG 0.002 0.000 ARG C 340 *********************** 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 176 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.810 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: 0.7585 (tppt) cc_final: 0.6868 (tmmt) REVERT: A 424 ARG cc_start: 0.6397 (mpt90) cc_final: 0.6189 (ttt90) REVERT: B 272 LYS cc_start: 0.7584 (tppt) cc_final: 0.6866 (tmmt) REVERT: B 424 ARG cc_start: 0.6397 (mpt90) cc_final: 0.6191 (ttt90) REVERT: C 272 LYS cc_start: 0.7582 (tppt) cc_final: 0.6865 (tmmt) REVERT: C 424 ARG cc_start: 0.6393 (mpt90) cc_final: 0.6188 (ttt90) REVERT: D 272 LYS cc_start: 0.7585 (tppt) cc_final: 0.6868 (tmmt) REVERT: D 424 ARG cc_start: 0.6395 (mpt90) cc_final: 0.6188 (ttt90) outliers start: 24 outliers final: 8 residues processed: 168 average time/residue: 2.4957 time to fit residues: 459.8753 Evaluate side-chains 152 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 136 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12284 Z= 0.144 Angle : 0.403 3.928 16668 Z= 0.221 Chirality : 0.033 0.131 2004 Planarity : 0.003 0.034 2032 Dihedral : 4.609 58.478 1760 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.53 % Allowed : 10.55 % Favored : 87.92 % 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: 3.38 (0.21), residues: 1504 helix: 2.78 (0.14), residues: 1256 sheet: 0.58 (0.78), residues: 48 loop : -1.15 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.003 0.001 HIS C 306 PHE 0.012 0.001 PHE A 11 TYR 0.005 0.001 TYR A 96 ARG 0.002 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 fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 2.107 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: 0.7676 (tppt) cc_final: 0.6973 (tmmt) REVERT: A 391 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.6076 (t0) REVERT: B 272 LYS cc_start: 0.7678 (tppt) cc_final: 0.6975 (tmmt) REVERT: B 391 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.6075 (t0) REVERT: C 272 LYS cc_start: 0.7675 (tppt) cc_final: 0.6973 (tmmt) REVERT: C 391 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.6074 (t0) REVERT: D 272 LYS cc_start: 0.7677 (tppt) cc_final: 0.6974 (tmmt) REVERT: D 391 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.6077 (t0) outliers start: 20 outliers final: 4 residues processed: 164 average time/residue: 2.4429 time to fit residues: 441.7267 Evaluate side-chains 149 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 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 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12284 Z= 0.315 Angle : 0.473 4.282 16668 Z= 0.262 Chirality : 0.036 0.144 2004 Planarity : 0.003 0.036 2032 Dihedral : 5.105 59.631 1760 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 2.87 (0.21), residues: 1504 helix: 2.44 (0.14), residues: 1256 sheet: 0.49 (0.79), residues: 48 loop : -1.42 (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 C 337 PHE 0.010 0.002 PHE A 11 TYR 0.008 0.002 TYR C 56 ARG 0.002 0.000 ARG B 402 *********************** 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 168 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.876 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 272 LYS cc_start: 0.7690 (tppt) cc_final: 0.6958 (tmmt) REVERT: B 272 LYS cc_start: 0.7690 (tppt) cc_final: 0.6958 (tmmt) REVERT: C 272 LYS cc_start: 0.7689 (tppt) cc_final: 0.6958 (tmmt) REVERT: D 272 LYS cc_start: 0.7691 (tppt) cc_final: 0.6959 (tmmt) outliers start: 20 outliers final: 4 residues processed: 156 average time/residue: 2.2696 time to fit residues: 391.5258 Evaluate side-chains 150 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2494 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= 0.184 Angle : 0.418 4.099 16668 Z= 0.232 Chirality : 0.033 0.133 2004 Planarity : 0.003 0.034 2032 Dihedral : 4.861 59.670 1760 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.53 % Allowed : 12.08 % Favored : 86.39 % 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: 3.22 (0.21), residues: 1504 helix: 2.65 (0.14), residues: 1256 sheet: 0.58 (0.79), residues: 48 loop : -1.15 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 174 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.001 PHE D 11 TYR 0.005 0.001 TYR B 182 ARG 0.001 0.000 ARG C 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 170 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.853 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: 0.7939 (p) cc_final: 0.7675 (p) REVERT: A 272 LYS cc_start: 0.7723 (tppt) cc_final: 0.7019 (tmmt) REVERT: B 25 VAL cc_start: 0.7937 (p) cc_final: 0.7673 (p) REVERT: B 272 LYS cc_start: 0.7714 (tppt) cc_final: 0.7008 (tmmt) REVERT: C 25 VAL cc_start: 0.7937 (p) cc_final: 0.7673 (p) REVERT: C 272 LYS cc_start: 0.7714 (tppt) cc_final: 0.7008 (tmmt) REVERT: D 25 VAL cc_start: 0.7935 (p) cc_final: 0.7672 (p) REVERT: D 272 LYS cc_start: 0.7724 (tppt) cc_final: 0.7020 (tmmt) outliers start: 20 outliers final: 8 residues processed: 166 average time/residue: 2.2645 time to fit residues: 416.5689 Evaluate side-chains 153 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12284 Z= 0.138 Angle : 0.394 3.945 16668 Z= 0.217 Chirality : 0.032 0.134 2004 Planarity : 0.003 0.033 2032 Dihedral : 3.507 18.882 1752 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.22 % Allowed : 12.16 % Favored : 86.62 % 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: 3.62 (0.21), residues: 1504 helix: 2.93 (0.14), residues: 1256 sheet: 0.65 (0.77), residues: 48 loop : -0.96 (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 C 96 ARG 0.004 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 fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.699 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 209 MET cc_start: 0.7860 (ttt) cc_final: 0.7577 (ttm) REVERT: A 272 LYS cc_start: 0.7659 (tppt) cc_final: 0.7018 (tmmt) REVERT: B 209 MET cc_start: 0.7860 (ttt) cc_final: 0.7579 (ttm) REVERT: B 272 LYS cc_start: 0.7691 (tppt) cc_final: 0.7036 (tmmt) REVERT: C 209 MET cc_start: 0.7860 (ttt) cc_final: 0.7580 (ttm) REVERT: C 272 LYS cc_start: 0.7691 (tppt) cc_final: 0.7036 (tmmt) REVERT: D 209 MET cc_start: 0.7861 (ttt) cc_final: 0.7579 (ttm) REVERT: D 272 LYS cc_start: 0.7660 (tppt) cc_final: 0.7018 (tmmt) outliers start: 16 outliers final: 8 residues processed: 167 average time/residue: 2.6486 time to fit residues: 481.8735 Evaluate side-chains 162 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 B 421 GLN C 113 ASN D 113 ASN D 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2695 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= 0.241 Angle : 0.440 4.200 16668 Z= 0.244 Chirality : 0.034 0.136 2004 Planarity : 0.003 0.035 2032 Dihedral : 3.971 27.696 1752 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.22 % Allowed : 12.39 % Favored : 86.39 % 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: 3.31 (0.21), residues: 1504 helix: 2.73 (0.14), residues: 1256 sheet: 0.69 (0.78), residues: 48 loop : -1.20 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 174 HIS 0.003 0.001 HIS C 337 PHE 0.010 0.002 PHE B 11 TYR 0.007 0.001 TYR B 56 ARG 0.002 0.000 ARG C 129 *********************** 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 181 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.741 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: 0.7879 (p) cc_final: 0.7618 (p) REVERT: A 209 MET cc_start: 0.7873 (ttt) cc_final: 0.7585 (ttm) REVERT: A 272 LYS cc_start: 0.7707 (tppt) cc_final: 0.7042 (tmmt) REVERT: B 25 VAL cc_start: 0.7880 (p) cc_final: 0.7618 (p) REVERT: B 209 MET cc_start: 0.7871 (ttt) cc_final: 0.7584 (ttm) REVERT: B 272 LYS cc_start: 0.7709 (tppt) cc_final: 0.7043 (tmmt) REVERT: C 25 VAL cc_start: 0.7877 (p) cc_final: 0.7616 (p) REVERT: C 209 MET cc_start: 0.7874 (ttt) cc_final: 0.7587 (ttm) REVERT: C 272 LYS cc_start: 0.7706 (tppt) cc_final: 0.7043 (tmmt) REVERT: D 25 VAL cc_start: 0.7880 (p) cc_final: 0.7617 (p) REVERT: D 209 MET cc_start: 0.7875 (ttt) cc_final: 0.7586 (ttm) REVERT: D 272 LYS cc_start: 0.7707 (tppt) cc_final: 0.7040 (tmmt) outliers start: 16 outliers final: 12 residues processed: 177 average time/residue: 2.4526 time to fit residues: 476.3734 Evaluate side-chains 178 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 B residue 113 ASN Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN 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 D residue 113 ASN 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 128 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12284 Z= 0.173 Angle : 0.429 4.074 16668 Z= 0.237 Chirality : 0.033 0.137 2004 Planarity : 0.003 0.034 2032 Dihedral : 3.811 25.325 1752 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.61 % Allowed : 13.46 % Favored : 85.93 % 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: 3.45 (0.21), residues: 1504 helix: 2.82 (0.14), residues: 1256 sheet: 0.78 (0.77), residues: 48 loop : -1.12 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 174 HIS 0.003 0.001 HIS B 337 PHE 0.011 0.001 PHE D 11 TYR 0.005 0.001 TYR A 182 ARG 0.004 0.000 ARG A 129 *********************** 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 168 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.936 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 25 VAL cc_start: 0.7896 (p) cc_final: 0.7615 (p) REVERT: A 272 LYS cc_start: 0.7700 (tppt) cc_final: 0.7037 (tmmt) REVERT: B 25 VAL cc_start: 0.7895 (p) cc_final: 0.7614 (p) REVERT: B 272 LYS cc_start: 0.7700 (tppt) cc_final: 0.7037 (tmmt) REVERT: C 25 VAL cc_start: 0.7891 (p) cc_final: 0.7609 (p) REVERT: C 209 MET cc_start: 0.7875 (ttt) cc_final: 0.7589 (ttm) REVERT: C 272 LYS cc_start: 0.7702 (tppt) cc_final: 0.7038 (tmmt) REVERT: D 25 VAL cc_start: 0.7894 (p) cc_final: 0.7612 (p) REVERT: D 209 MET cc_start: 0.7874 (ttt) cc_final: 0.7587 (ttm) REVERT: D 272 LYS cc_start: 0.7702 (tppt) cc_final: 0.7038 (tmmt) outliers start: 8 outliers final: 8 residues processed: 168 average time/residue: 2.4806 time to fit residues: 458.2922 Evaluate side-chains 166 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 1.810 ------------------------------------------------------------------------------- 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 88 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2767 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= 0.157 Angle : 0.407 4.033 16668 Z= 0.224 Chirality : 0.033 0.132 2004 Planarity : 0.003 0.034 2032 Dihedral : 3.566 19.618 1752 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.61 % Allowed : 13.76 % Favored : 85.63 % 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: 3.65 (0.21), residues: 1504 helix: 2.95 (0.14), residues: 1256 sheet: 0.83 (0.76), residues: 48 loop : -1.03 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.001 PHE C 11 TYR 0.005 0.001 TYR D 96 ARG 0.003 0.000 ARG D 129 ********************** 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 fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7868 (p) cc_final: 0.7599 (p) REVERT: A 272 LYS cc_start: 0.7693 (tppt) cc_final: 0.7031 (tmmt) REVERT: B 25 VAL cc_start: 0.7868 (p) cc_final: 0.7598 (p) REVERT: B 272 LYS cc_start: 0.7692 (tppt) cc_final: 0.7030 (tmmt) REVERT: C 25 VAL cc_start: 0.7868 (p) cc_final: 0.7598 (p) REVERT: C 272 LYS cc_start: 0.7693 (tppt) cc_final: 0.7037 (tmmt) REVERT: D 25 VAL cc_start: 0.7868 (p) cc_final: 0.7597 (p) REVERT: D 272 LYS cc_start: 0.7693 (tppt) cc_final: 0.7035 (tmmt) outliers start: 8 outliers final: 8 residues processed: 170 average time/residue: 2.7835 time to fit residues: 515.2639 Evaluate side-chains 160 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 36 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.0010 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.141158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111675 restraints weight = 37647.736| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.63 r_work: 0.3087 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12284 Z= 0.141 Angle : 0.396 3.991 16668 Z= 0.218 Chirality : 0.032 0.136 2004 Planarity : 0.003 0.033 2032 Dihedral : 3.393 16.212 1752 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 14.22 % 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: 3.82 (0.21), residues: 1504 helix: 3.07 (0.14), residues: 1256 sheet: 0.85 (0.76), residues: 48 loop : -0.97 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 174 HIS 0.003 0.001 HIS D 306 PHE 0.010 0.001 PHE A 11 TYR 0.005 0.001 TYR B 96 ARG 0.003 0.000 ARG C 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7974.66 seconds wall clock time: 139 minutes 20.98 seconds (8360.98 seconds total)