Starting phenix.real_space_refine on Fri Jul 3 18:01:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnr_32046/07_2026/7vnr_32046_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnr_32046/07_2026/7vnr_32046.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/7vnr_32046/07_2026/7vnr_32046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnr_32046/07_2026/7vnr_32046.map" model { file = "/net/cci-nas-00/data/ceres_data/7vnr_32046/07_2026/7vnr_32046_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnr_32046/07_2026/7vnr_32046_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 84 5.16 5 C 9892 2.51 5 N 2620 2.21 5 O 2744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15343 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2706 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 6, 'TRANS': 326} Chain breaks: 2 Chain: "C" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2706 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 6, 'TRANS': 326} Chain breaks: 2 Chain: "E" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2706 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 6, 'TRANS': 326} Chain breaks: 2 Chain: "G" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2706 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 6, 'TRANS': 326} Chain breaks: 2 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "F" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 19 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.19 Number of scatterers: 15343 At special positions: 0 Unit cell: (120.54, 120.54, 120.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 84 16.00 O 2744 8.00 N 2620 7.00 C 9892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 850.8 milliseconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 78.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 74 through 93 Processing helix chain 'A' and resid 99 through 119 Processing helix chain 'A' and resid 126 through 154 removed outlier: 3.528A pdb=" N CYS A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 175 through 190 removed outlier: 4.057A pdb=" N PHE A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 234 through 261 Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.703A pdb=" N SER A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 334 removed outlier: 5.185A pdb=" N SER A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.511A pdb=" N ALA A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'A' and resid 557 through 586 removed outlier: 4.013A pdb=" N VAL A 561 " --> pdb=" O ASP A 557 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 93 Processing helix chain 'C' and resid 99 through 119 Processing helix chain 'C' and resid 126 through 154 removed outlier: 3.528A pdb=" N CYS C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 175 through 190 removed outlier: 4.058A pdb=" N PHE C 179 " --> pdb=" O CYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 216 Processing helix chain 'C' and resid 221 through 234 Processing helix chain 'C' and resid 234 through 261 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.703A pdb=" N SER C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 334 removed outlier: 5.186A pdb=" N SER C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Proline residue: C 314 - end of helix Processing helix chain 'C' and resid 339 through 355 removed outlier: 3.699A pdb=" N ILE C 346 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 554 removed outlier: 4.224A pdb=" N LEU C 553 " --> pdb=" O PHE C 549 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 586 removed outlier: 3.970A pdb=" N VAL C 561 " --> pdb=" O ASP C 557 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 562 " --> pdb=" O VAL C 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 93 Processing helix chain 'E' and resid 99 through 119 Processing helix chain 'E' and resid 126 through 154 removed outlier: 3.529A pdb=" N CYS E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 Processing helix chain 'E' and resid 175 through 190 removed outlier: 4.058A pdb=" N PHE E 179 " --> pdb=" O CYS E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 216 Processing helix chain 'E' and resid 221 through 234 Processing helix chain 'E' and resid 234 through 261 Processing helix chain 'E' and resid 269 through 282 removed outlier: 3.702A pdb=" N SER E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 335 removed outlier: 5.185A pdb=" N SER E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE E 310 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Proline residue: E 314 - end of helix removed outlier: 3.551A pdb=" N PHE E 335 " --> pdb=" O ARG E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 355 removed outlier: 3.756A pdb=" N ALA E 343 " --> pdb=" O ARG E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 554 removed outlier: 4.223A pdb=" N LEU E 553 " --> pdb=" O PHE E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 586 removed outlier: 4.135A pdb=" N VAL E 561 " --> pdb=" O ASP E 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 93 Processing helix chain 'G' and resid 99 through 119 Processing helix chain 'G' and resid 126 through 154 removed outlier: 3.529A pdb=" N CYS G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 170 Processing helix chain 'G' and resid 175 through 190 removed outlier: 4.059A pdb=" N PHE G 179 " --> pdb=" O CYS G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 216 Processing helix chain 'G' and resid 221 through 234 Processing helix chain 'G' and resid 234 through 261 Processing helix chain 'G' and resid 269 through 282 removed outlier: 3.704A pdb=" N SER G 273 " --> pdb=" O SER G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 334 removed outlier: 5.186A pdb=" N SER G 309 " --> pdb=" O LEU G 305 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N PHE G 310 " --> pdb=" O LEU G 306 " (cutoff:3.500A) Proline residue: G 314 - end of helix Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 533 through 554 removed outlier: 4.224A pdb=" N LEU G 553 " --> pdb=" O PHE G 549 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG G 554 " --> pdb=" O LYS G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 586 removed outlier: 4.128A pdb=" N VAL G 561 " --> pdb=" O ASP G 557 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 562 " --> pdb=" O VAL G 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.605A pdb=" N PHE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 78 through 92 removed outlier: 4.072A pdb=" N PHE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.604A pdb=" N PHE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 39 Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 78 through 92 removed outlier: 4.072A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'F' and resid 8 through 20 removed outlier: 3.605A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 44 through 54 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 78 through 92 removed outlier: 4.072A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 117 through 128 Processing helix chain 'F' and resid 138 through 146 Processing helix chain 'H' and resid 8 through 20 removed outlier: 3.605A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 Processing helix chain 'H' and resid 44 through 54 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 78 through 92 removed outlier: 4.073A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 117 through 128 Processing helix chain 'H' and resid 138 through 146 Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AA5, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=AA6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AA7, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=AA8, first strand: chain 'H' and resid 99 through 101 1112 hydrogen bonds defined for protein. 3324 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: 2.31 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2488 1.30 - 1.43: 4295 1.43 - 1.56: 8725 1.56 - 1.69: 12 1.69 - 1.82: 144 Bond restraints: 15664 Sorted by residual: bond pdb=" C04 7YV A1101 " pdb=" C05 7YV A1101 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C04 7YV C1101 " pdb=" C05 7YV C1101 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C04 7YV E1101 " pdb=" C05 7YV E1101 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C04 7YV G1101 " pdb=" C05 7YV G1101 " ideal model delta sigma weight residual 1.531 1.297 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C03 7YV E1101 " pdb=" C05 7YV E1101 " ideal model delta sigma weight residual 1.531 1.304 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 15659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 20372 2.29 - 4.58: 649 4.58 - 6.87: 84 6.87 - 9.16: 23 9.16 - 11.45: 16 Bond angle restraints: 21144 Sorted by residual: angle pdb=" C ARG G 554 " pdb=" N PRO G 555 " pdb=" CA PRO G 555 " ideal model delta sigma weight residual 119.82 114.66 5.16 9.80e-01 1.04e+00 2.78e+01 angle pdb=" N LYS A 559 " pdb=" CA LYS A 559 " pdb=" C LYS A 559 " ideal model delta sigma weight residual 111.82 105.71 6.11 1.16e+00 7.43e-01 2.77e+01 angle pdb=" N ARG A 554 " pdb=" CA ARG A 554 " pdb=" C ARG A 554 " ideal model delta sigma weight residual 109.81 121.26 -11.45 2.21e+00 2.05e-01 2.69e+01 angle pdb=" N ARG C 554 " pdb=" CA ARG C 554 " pdb=" C ARG C 554 " ideal model delta sigma weight residual 109.81 121.18 -11.37 2.21e+00 2.05e-01 2.65e+01 angle pdb=" C MET G 340 " pdb=" N PRO G 341 " pdb=" CA PRO G 341 " ideal model delta sigma weight residual 119.32 113.57 5.75 1.14e+00 7.69e-01 2.54e+01 ... (remaining 21139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8243 17.87 - 35.75: 715 35.75 - 53.62: 242 53.62 - 71.50: 59 71.50 - 89.37: 17 Dihedral angle restraints: 9276 sinusoidal: 3800 harmonic: 5476 Sorted by residual: dihedral pdb=" C ARG C 554 " pdb=" N ARG C 554 " pdb=" CA ARG C 554 " pdb=" CB ARG C 554 " ideal model delta harmonic sigma weight residual -122.60 -133.95 11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N ARG C 554 " pdb=" C ARG C 554 " pdb=" CA ARG C 554 " pdb=" CB ARG C 554 " ideal model delta harmonic sigma weight residual 122.80 134.12 -11.32 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" N ARG G 554 " pdb=" C ARG G 554 " pdb=" CA ARG G 554 " pdb=" CB ARG G 554 " ideal model delta harmonic sigma weight residual 122.80 133.35 -10.55 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 9273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2305 0.151 - 0.302: 24 0.302 - 0.453: 1 0.453 - 0.605: 2 0.605 - 0.756: 8 Chirality restraints: 2340 Sorted by residual: chirality pdb=" C03 7YV C1101 " pdb=" C05 7YV C1101 " pdb=" C06 7YV C1101 " pdb=" C08 7YV C1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C03 7YV A1101 " pdb=" C05 7YV A1101 " pdb=" C06 7YV A1101 " pdb=" C08 7YV A1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C03 7YV E1101 " pdb=" C05 7YV E1101 " pdb=" C06 7YV E1101 " pdb=" C08 7YV E1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 2337 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 237 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" CD GLU A 237 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU A 237 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 237 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 237 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" CD GLU E 237 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU E 237 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU E 237 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 237 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" CD GLU C 237 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU C 237 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 237 " -0.016 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 4104 2.80 - 3.39: 18259 3.39 - 3.97: 29939 3.97 - 4.56: 41851 4.56 - 5.14: 57869 Nonbonded interactions: 152022 Sorted by model distance: nonbonded pdb=" OG1 THR B 28 " pdb=" OE1 GLU B 31 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR D 28 " pdb=" OE1 GLU D 31 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR F 28 " pdb=" OE1 GLU F 31 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR H 28 " pdb=" OE1 GLU H 31 " model vdw 2.217 3.040 nonbonded pdb=" O THR A 282 " pdb=" OG1 THR A 283 " model vdw 2.239 3.040 ... (remaining 152017 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 74 through 1101) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.00 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: 2.110 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.920 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 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 : 0.011 0.235 15664 Z= 0.532 Angle : 1.008 11.454 21144 Z= 0.583 Chirality : 0.067 0.756 2340 Planarity : 0.005 0.058 2664 Dihedral : 16.106 89.373 5740 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.38 % Favored : 93.40 % Rotamer: Outliers : 5.60 % Allowed : 6.41 % Favored : 88.00 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 1864 helix: -0.18 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.95 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 351 TYR 0.020 0.002 TYR C 565 PHE 0.024 0.003 PHE C 251 TRP 0.028 0.003 TRP C 86 HIS 0.005 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01099 / 0.53 (15664) covalent geometry : angle 1.00786 / 0.58 (21144) hydrogen bonds : bond 0.15685 / 10.37 ( 1112) hydrogen bonds : angle 5.85537 / 4.30 ( 3324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 455 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8525 (t80) cc_final: 0.8286 (t80) REVERT: A 112 CYS cc_start: 0.7777 (t) cc_final: 0.7525 (t) REVERT: A 218 ASP cc_start: 0.7690 (m-30) cc_final: 0.7254 (m-30) REVERT: A 225 LYS cc_start: 0.8875 (mttt) cc_final: 0.8621 (mttm) REVERT: A 557 ASP cc_start: 0.0513 (OUTLIER) cc_final: 0.0167 (p0) REVERT: C 218 ASP cc_start: 0.7678 (m-30) cc_final: 0.7292 (m-30) REVERT: C 225 LYS cc_start: 0.8831 (mttt) cc_final: 0.8584 (mttm) REVERT: E 130 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6419 (tp30) REVERT: E 218 ASP cc_start: 0.7754 (m-30) cc_final: 0.7463 (m-30) REVERT: E 225 LYS cc_start: 0.8839 (mttt) cc_final: 0.8607 (mttm) REVERT: G 218 ASP cc_start: 0.7701 (m-30) cc_final: 0.7466 (m-30) REVERT: G 225 LYS cc_start: 0.8808 (mttt) cc_final: 0.8556 (mttm) outliers start: 90 outliers final: 14 residues processed: 514 average time/residue: 0.6116 time to fit residues: 340.1609 Evaluate side-chains 276 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain G residue 551 GLU Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 586 ILE Chi-restraints excluded: chain G residue 587 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS A 585 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN G 332 GLN ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN H 111 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.221601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.124187 restraints weight = 27820.629| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.95 r_work: 0.3253 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15664 Z= 0.197 Angle : 0.858 14.002 21144 Z= 0.429 Chirality : 0.043 0.176 2340 Planarity : 0.006 0.093 2664 Dihedral : 6.114 59.071 2194 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 4.10 % Allowed : 19.40 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 1864 helix: 1.08 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 207 TYR 0.028 0.001 TYR C 565 PHE 0.024 0.002 PHE D 16 TRP 0.022 0.002 TRP G 350 HIS 0.005 0.001 HIS G 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (15664) covalent geometry : angle 0.85849 / 0.43 (21144) hydrogen bonds : bond 0.05397 / 3.60 ( 1112) hydrogen bonds : angle 4.97525 / 3.67 ( 3324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 322 time to evaluate : 0.415 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 551 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7827 (tp30) REVERT: A 565 TYR cc_start: 0.8152 (t80) cc_final: 0.7656 (t80) REVERT: A 575 ARG cc_start: 0.8056 (ptp-170) cc_final: 0.7108 (mtt180) REVERT: C 139 MET cc_start: 0.7016 (tmm) cc_final: 0.6346 (ttm) REVERT: C 344 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7574 (p0) REVERT: C 572 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: C 573 LEU cc_start: 0.8214 (mp) cc_final: 0.7845 (tp) REVERT: E 139 MET cc_start: 0.6972 (tmm) cc_final: 0.6267 (ttm) REVERT: E 547 ARG cc_start: 0.9145 (tpp-160) cc_final: 0.8754 (tpm-80) REVERT: G 139 MET cc_start: 0.6661 (tmm) cc_final: 0.5887 (ttm) REVERT: G 547 ARG cc_start: 0.9176 (tpp-160) cc_final: 0.8585 (tpm-80) REVERT: G 563 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9099 (pp20) REVERT: B 145 MET cc_start: 0.6605 (mmm) cc_final: 0.6373 (mmt) REVERT: D 68 PHE cc_start: 0.7941 (t80) cc_final: 0.7426 (t80) REVERT: D 69 LEU cc_start: 0.9203 (pp) cc_final: 0.8984 (mp) REVERT: D 71 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7864 (mpt) REVERT: D 76 MET cc_start: 0.5108 (mtt) cc_final: 0.4526 (pmm) REVERT: D 87 GLU cc_start: 0.9389 (tp30) cc_final: 0.9139 (tp30) REVERT: D 112 LEU cc_start: 0.8064 (mm) cc_final: 0.7793 (tp) REVERT: F 53 ASN cc_start: 0.8517 (t0) cc_final: 0.8216 (p0) REVERT: F 68 PHE cc_start: 0.8243 (t80) cc_final: 0.7785 (t80) REVERT: F 71 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7920 (mpt) REVERT: F 72 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7677 (mmm) REVERT: F 76 MET cc_start: 0.4808 (mtt) cc_final: 0.3941 (pmm) REVERT: H 68 PHE cc_start: 0.8000 (t80) cc_final: 0.7609 (t80) REVERT: H 71 MET cc_start: 0.8644 (mtt) cc_final: 0.7957 (mpt) REVERT: H 76 MET cc_start: 0.5293 (mtt) cc_final: 0.4901 (pmm) REVERT: H 121 VAL cc_start: 0.7659 (p) cc_final: 0.7387 (m) outliers start: 66 outliers final: 18 residues processed: 356 average time/residue: 0.4880 time to fit residues: 192.1590 Evaluate side-chains 287 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain G residue 578 SER Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 143 optimal weight: 0.0270 chunk 124 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.217497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123513 restraints weight = 27938.249| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.98 r_work: 0.3178 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15664 Z= 0.165 Angle : 0.791 15.619 21144 Z= 0.391 Chirality : 0.042 0.219 2340 Planarity : 0.005 0.069 2664 Dihedral : 4.318 33.245 2163 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.81 % Favored : 95.98 % Rotamer: Outliers : 4.17 % Allowed : 21.33 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 1864 helix: 1.46 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 207 TYR 0.026 0.001 TYR C 565 PHE 0.031 0.002 PHE E 169 TRP 0.019 0.001 TRP G 350 HIS 0.008 0.001 HIS C 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (15664) covalent geometry : angle 0.79144 / 0.39 (21144) hydrogen bonds : bond 0.04585 / 3.06 ( 1112) hydrogen bonds : angle 4.82176 / 3.56 ( 3324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 307 time to evaluate : 0.435 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 306 LEU cc_start: 0.9266 (tt) cc_final: 0.9017 (tt) REVERT: C 139 MET cc_start: 0.7542 (tmm) cc_final: 0.6933 (mmm) REVERT: C 150 ARG cc_start: 0.6741 (ttp-170) cc_final: 0.6472 (mtt90) REVERT: C 306 LEU cc_start: 0.9266 (tt) cc_final: 0.9018 (tt) REVERT: C 344 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7673 (p0) REVERT: E 139 MET cc_start: 0.7499 (tmm) cc_final: 0.6794 (mmm) REVERT: E 306 LEU cc_start: 0.9263 (tt) cc_final: 0.9013 (tt) REVERT: E 346 ILE cc_start: 0.7488 (mp) cc_final: 0.7231 (mp) REVERT: G 139 MET cc_start: 0.7348 (tmm) cc_final: 0.6754 (ttm) REVERT: G 306 LEU cc_start: 0.9263 (tt) cc_final: 0.9033 (tt) REVERT: G 551 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8096 (tp30) REVERT: G 563 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9118 (pp20) REVERT: B 53 ASN cc_start: 0.8760 (t0) cc_final: 0.8457 (p0) REVERT: B 71 MET cc_start: 0.8566 (pp-130) cc_final: 0.8350 (pp-130) REVERT: B 100 ILE cc_start: 0.8618 (tp) cc_final: 0.8334 (pp) REVERT: B 124 MET cc_start: 0.8007 (ppp) cc_final: 0.7779 (ppp) REVERT: B 144 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5418 (ppp) REVERT: D 65 PHE cc_start: 0.9396 (p90) cc_final: 0.8885 (t80) REVERT: D 71 MET cc_start: 0.8632 (mtt) cc_final: 0.8004 (mpt) REVERT: D 87 GLU cc_start: 0.9421 (tp30) cc_final: 0.9147 (tp30) REVERT: D 116 LEU cc_start: 0.6375 (tp) cc_final: 0.5997 (tm) REVERT: D 124 MET cc_start: 0.7907 (ppp) cc_final: 0.7383 (ppp) REVERT: D 141 PHE cc_start: 0.8875 (t80) cc_final: 0.8520 (t80) REVERT: F 53 ASN cc_start: 0.8547 (t0) cc_final: 0.8247 (p0) REVERT: F 71 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8221 (mpt) REVERT: F 89 PHE cc_start: 0.8911 (m-80) cc_final: 0.8626 (m-80) REVERT: H 53 ASN cc_start: 0.8671 (t0) cc_final: 0.8437 (p0) REVERT: H 68 PHE cc_start: 0.7939 (t80) cc_final: 0.7615 (t80) REVERT: H 71 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7802 (pp-130) REVERT: H 79 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8138 (p) REVERT: H 100 ILE cc_start: 0.8557 (tp) cc_final: 0.8328 (pp) REVERT: H 116 LEU cc_start: 0.6353 (tp) cc_final: 0.6120 (tp) outliers start: 67 outliers final: 23 residues processed: 337 average time/residue: 0.5038 time to fit residues: 187.3856 Evaluate side-chains 303 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain G residue 578 SER Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain H residue 126 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 141 optimal weight: 8.9990 chunk 149 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 329 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN D 49 GLN D 111 ASN F 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.213427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117544 restraints weight = 28030.171| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.87 r_work: 0.3034 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15664 Z= 0.221 Angle : 0.803 12.598 21144 Z= 0.397 Chirality : 0.043 0.225 2340 Planarity : 0.005 0.067 2664 Dihedral : 4.139 15.895 2160 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.51 % Favored : 95.28 % Rotamer: Outliers : 3.98 % Allowed : 22.26 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1864 helix: 1.34 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -1.11 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 90 TYR 0.023 0.001 TYR C 565 PHE 0.038 0.002 PHE E 169 TRP 0.020 0.002 TRP G 350 HIS 0.008 0.001 HIS G 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (15664) covalent geometry : angle 0.80288 / 0.40 (21144) hydrogen bonds : bond 0.04702 / 3.14 ( 1112) hydrogen bonds : angle 4.90721 / 3.63 ( 3324) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 305 time to evaluate : 0.558 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: A 218 ASP cc_start: 0.8652 (m-30) cc_final: 0.8375 (m-30) REVERT: A 236 LYS cc_start: 0.8461 (mmpt) cc_final: 0.8211 (mttp) REVERT: A 547 ARG cc_start: 0.8765 (tpm170) cc_final: 0.8516 (tpm-80) REVERT: A 554 ARG cc_start: 0.8394 (mpt180) cc_final: 0.8161 (mmp-170) REVERT: A 559 LYS cc_start: 0.7042 (mmtt) cc_final: 0.6652 (mmtt) REVERT: A 560 ASP cc_start: 0.8163 (m-30) cc_final: 0.7840 (m-30) REVERT: C 139 MET cc_start: 0.7694 (tmm) cc_final: 0.7148 (ttm) REVERT: C 150 ARG cc_start: 0.6690 (ttp-170) cc_final: 0.6446 (mtt-85) REVERT: C 206 MET cc_start: 0.7157 (pp-130) cc_final: 0.6680 (mmp) REVERT: C 236 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8568 (mttp) REVERT: C 344 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7863 (p0) REVERT: C 547 ARG cc_start: 0.8993 (tpm-80) cc_final: 0.8652 (tpm-80) REVERT: C 551 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8446 (mm-30) REVERT: C 565 TYR cc_start: 0.8688 (t80) cc_final: 0.8461 (t80) REVERT: E 139 MET cc_start: 0.7596 (tmm) cc_final: 0.7005 (ttm) REVERT: E 346 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7501 (mp) REVERT: E 546 LYS cc_start: 0.9203 (pptt) cc_final: 0.8850 (pptt) REVERT: E 547 ARG cc_start: 0.9119 (tpm-80) cc_final: 0.8686 (tpp80) REVERT: E 563 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8759 (mt-10) REVERT: E 565 TYR cc_start: 0.8615 (t80) cc_final: 0.8045 (t80) REVERT: E 572 MET cc_start: 0.9124 (mmt) cc_final: 0.8868 (tpp) REVERT: E 573 LEU cc_start: 0.9401 (pp) cc_final: 0.8922 (tp) REVERT: G 139 MET cc_start: 0.7683 (tmm) cc_final: 0.7030 (mmm) REVERT: G 225 LYS cc_start: 0.9041 (mttt) cc_final: 0.8494 (mmmt) REVERT: G 236 LYS cc_start: 0.8448 (mmpt) cc_final: 0.8213 (mttp) REVERT: G 554 ARG cc_start: 0.8438 (mmt180) cc_final: 0.8217 (mmm160) REVERT: G 563 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9207 (pp20) REVERT: B 53 ASN cc_start: 0.8800 (t0) cc_final: 0.8445 (p0) REVERT: B 100 ILE cc_start: 0.8637 (tp) cc_final: 0.8349 (pp) REVERT: B 116 LEU cc_start: 0.6706 (tp) cc_final: 0.6390 (tp) REVERT: B 144 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5907 (ppp) REVERT: D 71 MET cc_start: 0.8694 (mtt) cc_final: 0.8092 (mpt) REVERT: D 87 GLU cc_start: 0.9391 (tp30) cc_final: 0.9189 (tp30) REVERT: D 100 ILE cc_start: 0.8531 (tp) cc_final: 0.8321 (pp) REVERT: D 116 LEU cc_start: 0.6824 (tp) cc_final: 0.6230 (tm) REVERT: D 144 MET cc_start: 0.5721 (OUTLIER) cc_final: 0.5047 (ppp) REVERT: F 53 ASN cc_start: 0.8657 (t0) cc_final: 0.8299 (p0) REVERT: F 70 THR cc_start: 0.8134 (m) cc_final: 0.7601 (m) REVERT: F 71 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8082 (mpt) REVERT: F 89 PHE cc_start: 0.8934 (m-80) cc_final: 0.8610 (m-80) REVERT: H 47 GLU cc_start: 0.8677 (pt0) cc_final: 0.8464 (pm20) REVERT: H 53 ASN cc_start: 0.8771 (t0) cc_final: 0.8466 (p0) REVERT: H 68 PHE cc_start: 0.7947 (t80) cc_final: 0.7501 (t80) REVERT: H 71 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8154 (ptp) REVERT: H 116 LEU cc_start: 0.6937 (tp) cc_final: 0.6627 (tp) REVERT: H 144 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5502 (ppp) outliers start: 64 outliers final: 28 residues processed: 337 average time/residue: 0.5346 time to fit residues: 197.7401 Evaluate side-chains 306 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 578 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 50.0000 chunk 127 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 121 optimal weight: 0.0970 chunk 73 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 165 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 569 HIS ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN F 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.213143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123694 restraints weight = 28017.234| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 5.08 r_work: 0.3042 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15664 Z= 0.203 Angle : 0.812 15.990 21144 Z= 0.398 Chirality : 0.042 0.220 2340 Planarity : 0.005 0.064 2664 Dihedral : 4.146 17.193 2160 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.92 % Favored : 95.87 % Rotamer: Outliers : 5.16 % Allowed : 22.26 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1864 helix: 1.33 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -1.19 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 74 TYR 0.019 0.001 TYR G 565 PHE 0.026 0.002 PHE E 169 TRP 0.019 0.002 TRP G 350 HIS 0.018 0.001 HIS E 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (15664) covalent geometry : angle 0.81190 / 0.40 (21144) hydrogen bonds : bond 0.04522 / 3.03 ( 1112) hydrogen bonds : angle 4.89163 / 3.61 ( 3324) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 320 time to evaluate : 0.613 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 123 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7072 (mp0) REVERT: A 225 LYS cc_start: 0.9040 (mttt) cc_final: 0.8499 (mmmt) REVERT: A 236 LYS cc_start: 0.8645 (mmpt) cc_final: 0.8393 (mttp) REVERT: A 338 ARG cc_start: 0.8750 (pmt-80) cc_final: 0.8315 (pmm150) REVERT: A 346 ILE cc_start: 0.8201 (mp) cc_final: 0.7820 (mp) REVERT: A 559 LYS cc_start: 0.6866 (mmtt) cc_final: 0.6498 (tptp) REVERT: C 139 MET cc_start: 0.7640 (tmm) cc_final: 0.7074 (mmm) REVERT: C 150 ARG cc_start: 0.6669 (ttp-170) cc_final: 0.6413 (mtt-85) REVERT: C 225 LYS cc_start: 0.9038 (mttt) cc_final: 0.8497 (mmmt) REVERT: C 338 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.6323 (pmt-80) REVERT: C 547 ARG cc_start: 0.8945 (tpm-80) cc_final: 0.8395 (tpm-80) REVERT: C 551 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8430 (mm-30) REVERT: E 139 MET cc_start: 0.7591 (tmm) cc_final: 0.6983 (mmm) REVERT: E 551 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8419 (mm-30) REVERT: E 573 LEU cc_start: 0.9462 (pp) cc_final: 0.9172 (tp) REVERT: G 139 MET cc_start: 0.7630 (tmm) cc_final: 0.7050 (mmm) REVERT: G 206 MET cc_start: 0.7485 (pp-130) cc_final: 0.7130 (mmp) REVERT: G 217 MET cc_start: 0.7880 (ppp) cc_final: 0.7618 (pmm) REVERT: G 225 LYS cc_start: 0.9052 (mttt) cc_final: 0.8519 (mmmt) REVERT: G 236 LYS cc_start: 0.8648 (mmpt) cc_final: 0.8382 (mttp) REVERT: G 547 ARG cc_start: 0.8999 (tpm-80) cc_final: 0.8474 (tpp80) REVERT: G 563 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9217 (pp20) REVERT: G 565 TYR cc_start: 0.8459 (t80) cc_final: 0.8119 (t80) REVERT: B 53 ASN cc_start: 0.8761 (t0) cc_final: 0.8375 (p0) REVERT: B 62 THR cc_start: 0.4038 (p) cc_final: 0.3710 (p) REVERT: B 100 ILE cc_start: 0.8641 (tp) cc_final: 0.8380 (pp) REVERT: B 116 LEU cc_start: 0.6672 (tp) cc_final: 0.6447 (tp) REVERT: B 126 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7595 (ppp-140) REVERT: B 144 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.6266 (ppp) REVERT: D 62 THR cc_start: 0.2960 (p) cc_final: 0.2668 (p) REVERT: D 71 MET cc_start: 0.8776 (mtt) cc_final: 0.8191 (mpt) REVERT: D 87 GLU cc_start: 0.9369 (tp30) cc_final: 0.9110 (tp30) REVERT: D 100 ILE cc_start: 0.8555 (tp) cc_final: 0.8340 (pp) REVERT: D 116 LEU cc_start: 0.6619 (tp) cc_final: 0.6137 (tp) REVERT: D 144 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5386 (ppp) REVERT: F 53 ASN cc_start: 0.8705 (t0) cc_final: 0.8293 (p0) REVERT: F 71 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8263 (mpt) REVERT: H 53 ASN cc_start: 0.8744 (t0) cc_final: 0.8351 (p0) REVERT: H 68 PHE cc_start: 0.7839 (t80) cc_final: 0.7542 (t80) REVERT: H 71 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8113 (pp-130) REVERT: H 99 TYR cc_start: 0.8657 (m-80) cc_final: 0.8105 (m-80) REVERT: H 112 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8050 (tp) REVERT: H 116 LEU cc_start: 0.6628 (tp) cc_final: 0.6311 (tp) REVERT: H 126 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7230 (ppp-140) REVERT: H 144 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5619 (ppp) outliers start: 83 outliers final: 29 residues processed: 359 average time/residue: 0.4876 time to fit residues: 193.7172 Evaluate side-chains 311 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 552 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 149 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 83 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN D 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.214468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121700 restraints weight = 27929.830| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.89 r_work: 0.3140 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15664 Z= 0.163 Angle : 0.831 14.013 21144 Z= 0.405 Chirality : 0.042 0.214 2340 Planarity : 0.004 0.065 2664 Dihedral : 4.144 17.539 2160 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.40 % Favored : 95.39 % Rotamer: Outliers : 3.79 % Allowed : 26.12 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1864 helix: 1.41 (0.13), residues: 1432 sheet: None (None), residues: 0 loop : -1.06 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 90 TYR 0.014 0.001 TYR C 232 PHE 0.039 0.002 PHE B 68 TRP 0.021 0.002 TRP G 350 HIS 0.008 0.001 HIS G 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (15664) covalent geometry : angle 0.83094 / 0.41 (21144) hydrogen bonds : bond 0.04291 / 2.88 ( 1112) hydrogen bonds : angle 4.86685 / 3.59 ( 3324) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7106 (mm-30) REVERT: A 217 MET cc_start: 0.7534 (ppp) cc_final: 0.7295 (pmm) REVERT: A 225 LYS cc_start: 0.9054 (mttt) cc_final: 0.8528 (mmmt) REVERT: A 236 LYS cc_start: 0.8699 (mmpt) cc_final: 0.8452 (tppt) REVERT: A 247 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9148 (mp) REVERT: A 338 ARG cc_start: 0.8694 (pmt-80) cc_final: 0.8305 (pmm150) REVERT: A 547 ARG cc_start: 0.9215 (tpp80) cc_final: 0.8965 (tpp80) REVERT: C 123 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7178 (mm-30) REVERT: C 139 MET cc_start: 0.7568 (tmm) cc_final: 0.7027 (mmm) REVERT: C 150 ARG cc_start: 0.6790 (ttp-170) cc_final: 0.6506 (mtt-85) REVERT: C 225 LYS cc_start: 0.9046 (mttt) cc_final: 0.8521 (mmmt) REVERT: C 338 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.6303 (pmt-80) REVERT: C 547 ARG cc_start: 0.8978 (tpm-80) cc_final: 0.8693 (tpm-80) REVERT: E 139 MET cc_start: 0.7512 (tmm) cc_final: 0.7040 (ttm) REVERT: E 150 ARG cc_start: 0.6713 (ttp-170) cc_final: 0.6512 (mtt-85) REVERT: E 225 LYS cc_start: 0.9056 (mttt) cc_final: 0.8534 (mmmt) REVERT: E 247 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9147 (mp) REVERT: E 551 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8401 (tp30) REVERT: E 573 LEU cc_start: 0.9503 (pp) cc_final: 0.9250 (tp) REVERT: G 139 MET cc_start: 0.7576 (tmm) cc_final: 0.7070 (ttm) REVERT: G 150 ARG cc_start: 0.6757 (ttp-170) cc_final: 0.6541 (mtt-85) REVERT: G 206 MET cc_start: 0.7494 (pp-130) cc_final: 0.7094 (mmp) REVERT: G 217 MET cc_start: 0.7969 (ppp) cc_final: 0.7488 (pmm) REVERT: G 225 LYS cc_start: 0.9056 (mttt) cc_final: 0.8532 (mmmt) REVERT: G 236 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8415 (tppt) REVERT: G 340 MET cc_start: 0.9014 (mmm) cc_final: 0.8773 (mmm) REVERT: G 547 ARG cc_start: 0.9235 (tpm-80) cc_final: 0.8919 (tpp80) REVERT: G 550 LYS cc_start: 0.8670 (pptt) cc_final: 0.8012 (pptt) REVERT: G 551 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8570 (mm-30) REVERT: G 554 ARG cc_start: 0.8414 (mmt180) cc_final: 0.7681 (mmp-170) REVERT: B 53 ASN cc_start: 0.8737 (t0) cc_final: 0.8345 (p0) REVERT: B 62 THR cc_start: 0.4285 (p) cc_final: 0.3960 (p) REVERT: B 116 LEU cc_start: 0.6429 (tp) cc_final: 0.6169 (tp) REVERT: B 126 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7618 (ppp-140) REVERT: B 144 MET cc_start: 0.6822 (ptp) cc_final: 0.6505 (ppp) REVERT: D 62 THR cc_start: 0.3374 (p) cc_final: 0.3140 (p) REVERT: D 71 MET cc_start: 0.8781 (mtt) cc_final: 0.8192 (mpt) REVERT: D 87 GLU cc_start: 0.9369 (tp30) cc_final: 0.9123 (tp30) REVERT: D 90 ARG cc_start: 0.8700 (ttp80) cc_final: 0.8491 (ttp80) REVERT: D 99 TYR cc_start: 0.8464 (m-80) cc_final: 0.8159 (m-80) REVERT: D 116 LEU cc_start: 0.6663 (tp) cc_final: 0.6302 (tp) REVERT: D 144 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5290 (ppp) REVERT: F 53 ASN cc_start: 0.8802 (t0) cc_final: 0.8376 (p0) REVERT: F 71 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8130 (mpt) REVERT: H 53 ASN cc_start: 0.8754 (t0) cc_final: 0.8405 (p0) REVERT: H 71 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8316 (ptp) REVERT: H 99 TYR cc_start: 0.8484 (m-80) cc_final: 0.7976 (m-80) REVERT: H 112 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7966 (tp) REVERT: H 116 LEU cc_start: 0.6390 (tp) cc_final: 0.6073 (tp) REVERT: H 126 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7429 (ppp-140) REVERT: H 144 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.5923 (ppp) outliers start: 61 outliers final: 20 residues processed: 339 average time/residue: 0.5084 time to fit residues: 189.5073 Evaluate side-chains 319 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 533 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 127 optimal weight: 0.9990 chunk 165 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 GLN D 49 GLN H 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.214073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126302 restraints weight = 27384.396| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.38 r_work: 0.3024 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15664 Z= 0.170 Angle : 0.847 16.554 21144 Z= 0.414 Chirality : 0.043 0.228 2340 Planarity : 0.004 0.064 2664 Dihedral : 4.186 17.357 2160 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 4.17 % Allowed : 26.31 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1864 helix: 1.38 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -0.90 (0.34), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 74 TYR 0.012 0.001 TYR C 565 PHE 0.035 0.001 PHE B 68 TRP 0.042 0.001 TRP E 350 HIS 0.008 0.001 HIS G 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (15664) covalent geometry : angle 0.84690 / 0.41 (21144) hydrogen bonds : bond 0.04372 / 2.94 ( 1112) hydrogen bonds : angle 4.90443 / 3.64 ( 3324) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 303 time to evaluate : 0.386 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: A 123 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6951 (mp0) REVERT: A 150 ARG cc_start: 0.6847 (ttp-170) cc_final: 0.6567 (mtt-85) REVERT: A 225 LYS cc_start: 0.8993 (mttt) cc_final: 0.8496 (mmmt) REVERT: A 236 LYS cc_start: 0.8694 (mmpt) cc_final: 0.8444 (tppt) REVERT: A 338 ARG cc_start: 0.8708 (pmt-80) cc_final: 0.8293 (pmm150) REVERT: A 547 ARG cc_start: 0.9253 (tpp80) cc_final: 0.8713 (tpm-80) REVERT: A 550 LYS cc_start: 0.9250 (mtmm) cc_final: 0.8842 (mtmm) REVERT: A 551 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8153 (mm-30) REVERT: C 123 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7189 (mm-30) REVERT: C 139 MET cc_start: 0.7477 (tmm) cc_final: 0.6970 (mmm) REVERT: C 150 ARG cc_start: 0.6762 (ttp-170) cc_final: 0.6506 (mtt-85) REVERT: C 225 LYS cc_start: 0.8991 (mttt) cc_final: 0.8501 (mmmt) REVERT: C 338 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6365 (pmt-80) REVERT: C 551 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7979 (tp30) REVERT: E 139 MET cc_start: 0.7437 (tmm) cc_final: 0.7001 (ttm) REVERT: E 150 ARG cc_start: 0.6758 (ttp-170) cc_final: 0.6538 (mtt-85) REVERT: E 217 MET cc_start: 0.7728 (ppp) cc_final: 0.7159 (pmm) REVERT: E 225 LYS cc_start: 0.8999 (mttt) cc_final: 0.8535 (mmmt) REVERT: E 247 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9087 (mp) REVERT: E 547 ARG cc_start: 0.9289 (tpp80) cc_final: 0.8685 (tpp80) REVERT: E 551 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8427 (mm-30) REVERT: E 573 LEU cc_start: 0.9526 (pp) cc_final: 0.9305 (tp) REVERT: G 123 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7215 (mm-30) REVERT: G 139 MET cc_start: 0.7510 (tmm) cc_final: 0.6973 (mmm) REVERT: G 150 ARG cc_start: 0.6782 (ttp-170) cc_final: 0.6539 (mtt-85) REVERT: G 206 MET cc_start: 0.7508 (pp-130) cc_final: 0.7095 (mmp) REVERT: G 225 LYS cc_start: 0.8997 (mttt) cc_final: 0.8532 (mmmt) REVERT: G 236 LYS cc_start: 0.8670 (mmpt) cc_final: 0.8411 (tppt) REVERT: G 340 MET cc_start: 0.8963 (mmm) cc_final: 0.8756 (mmm) REVERT: B 53 ASN cc_start: 0.8716 (t0) cc_final: 0.8302 (p0) REVERT: B 71 MET cc_start: 0.8724 (pp-130) cc_final: 0.8492 (ppp) REVERT: B 116 LEU cc_start: 0.6508 (tp) cc_final: 0.6262 (tp) REVERT: B 144 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6561 (ppp) REVERT: D 71 MET cc_start: 0.8645 (mtt) cc_final: 0.8036 (mpt) REVERT: D 87 GLU cc_start: 0.9340 (tp30) cc_final: 0.9099 (tp30) REVERT: D 99 TYR cc_start: 0.8629 (m-80) cc_final: 0.8141 (m-80) REVERT: D 116 LEU cc_start: 0.6757 (tp) cc_final: 0.6398 (tp) REVERT: D 144 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5443 (ppp) REVERT: F 9 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.5923 (pp) REVERT: F 12 PHE cc_start: 0.7299 (m-80) cc_final: 0.6649 (m-80) REVERT: F 13 LYS cc_start: 0.8414 (tppt) cc_final: 0.8115 (mttp) REVERT: F 14 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8495 (pp20) REVERT: F 53 ASN cc_start: 0.8823 (t0) cc_final: 0.8400 (p0) REVERT: F 71 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8193 (mpt) REVERT: F 72 MET cc_start: 0.8033 (mtp) cc_final: 0.7823 (mpt) REVERT: F 100 ILE cc_start: 0.8901 (tp) cc_final: 0.8609 (pp) REVERT: F 126 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.5777 (ppt170) REVERT: F 144 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.5046 (ppp) REVERT: H 53 ASN cc_start: 0.8788 (t0) cc_final: 0.8385 (p0) REVERT: H 71 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8296 (ptp) REVERT: H 99 TYR cc_start: 0.8541 (m-80) cc_final: 0.8027 (m-80) REVERT: H 112 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7956 (tp) REVERT: H 116 LEU cc_start: 0.6358 (tp) cc_final: 0.6079 (tp) REVERT: H 144 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5972 (ppp) outliers start: 67 outliers final: 21 residues processed: 331 average time/residue: 0.5408 time to fit residues: 196.1705 Evaluate side-chains 320 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 533 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 53 optimal weight: 0.0000 chunk 162 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN G 84 GLN H 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.212038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.120235 restraints weight = 27782.101| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.23 r_work: 0.3023 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15664 Z= 0.215 Angle : 0.878 18.087 21144 Z= 0.432 Chirality : 0.044 0.247 2340 Planarity : 0.005 0.065 2664 Dihedral : 4.242 17.173 2160 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.28 % Rotamer: Outliers : 3.42 % Allowed : 27.99 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1864 helix: 1.29 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -0.90 (0.34), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 90 TYR 0.013 0.001 TYR C 565 PHE 0.030 0.002 PHE B 68 TRP 0.043 0.002 TRP E 350 HIS 0.006 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (15664) covalent geometry : angle 0.87797 / 0.43 (21144) hydrogen bonds : bond 0.04539 / 3.03 ( 1112) hydrogen bonds : angle 4.93499 / 3.64 ( 3324) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.423 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: A 123 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6930 (mp0) REVERT: A 225 LYS cc_start: 0.9001 (mttt) cc_final: 0.8509 (mmmt) REVERT: A 236 LYS cc_start: 0.8721 (mmpt) cc_final: 0.8441 (tppt) REVERT: A 338 ARG cc_start: 0.8767 (pmt-80) cc_final: 0.8321 (pmm150) REVERT: A 547 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8758 (tpm-80) REVERT: A 550 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8783 (mtmm) REVERT: A 551 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8254 (mm-30) REVERT: A 565 TYR cc_start: 0.8702 (t80) cc_final: 0.8203 (t80) REVERT: C 123 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7159 (mm-30) REVERT: C 139 MET cc_start: 0.7441 (tmm) cc_final: 0.6958 (mmm) REVERT: C 150 ARG cc_start: 0.6711 (ttp-170) cc_final: 0.6467 (mtp85) REVERT: C 225 LYS cc_start: 0.8995 (mttt) cc_final: 0.8492 (mmmt) REVERT: C 338 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.6259 (pmt-80) REVERT: C 547 ARG cc_start: 0.8774 (tpm-80) cc_final: 0.8334 (tpm-80) REVERT: C 551 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8374 (mm-30) REVERT: C 560 ASP cc_start: 0.8370 (m-30) cc_final: 0.8108 (m-30) REVERT: E 139 MET cc_start: 0.7471 (tmm) cc_final: 0.7085 (ttm) REVERT: E 150 ARG cc_start: 0.6729 (ttp-170) cc_final: 0.6490 (mtt-85) REVERT: E 217 MET cc_start: 0.7739 (ppp) cc_final: 0.7189 (pmm) REVERT: E 219 ARG cc_start: 0.6670 (tpm170) cc_final: 0.6375 (tpm170) REVERT: E 225 LYS cc_start: 0.9017 (mttt) cc_final: 0.8509 (mmmt) REVERT: E 546 LYS cc_start: 0.9228 (pptt) cc_final: 0.8771 (pttt) REVERT: E 547 ARG cc_start: 0.9361 (tpp80) cc_final: 0.8751 (tpp80) REVERT: E 551 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8489 (mm-30) REVERT: G 123 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7165 (mm-30) REVERT: G 139 MET cc_start: 0.7464 (tmm) cc_final: 0.7026 (ttm) REVERT: G 150 ARG cc_start: 0.6776 (ttp-170) cc_final: 0.6519 (mtt-85) REVERT: G 206 MET cc_start: 0.7515 (pp-130) cc_final: 0.7148 (mmp) REVERT: G 217 MET cc_start: 0.7648 (ppp) cc_final: 0.6955 (pmm) REVERT: G 225 LYS cc_start: 0.9020 (mttt) cc_final: 0.8514 (mmmt) REVERT: G 236 LYS cc_start: 0.8715 (mmpt) cc_final: 0.8455 (tppt) REVERT: G 559 LYS cc_start: 0.7359 (mmtt) cc_final: 0.7122 (mmtt) REVERT: G 572 MET cc_start: 0.9373 (mmt) cc_final: 0.9036 (tpp) REVERT: B 53 ASN cc_start: 0.8743 (t0) cc_final: 0.8509 (m-40) REVERT: B 116 LEU cc_start: 0.6753 (tp) cc_final: 0.6476 (tp) REVERT: B 144 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6681 (ppp) REVERT: D 71 MET cc_start: 0.8631 (mtt) cc_final: 0.8009 (mpt) REVERT: D 90 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8394 (tmm160) REVERT: D 99 TYR cc_start: 0.8603 (m-80) cc_final: 0.8301 (m-80) REVERT: D 116 LEU cc_start: 0.6881 (tp) cc_final: 0.6546 (tp) REVERT: D 144 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5520 (ppp) REVERT: F 13 LYS cc_start: 0.8485 (tppt) cc_final: 0.8222 (mppt) REVERT: F 14 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8590 (pp20) REVERT: F 53 ASN cc_start: 0.8881 (t0) cc_final: 0.8458 (p0) REVERT: F 71 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8147 (mpt) REVERT: F 72 MET cc_start: 0.8101 (mtp) cc_final: 0.7803 (mpt) REVERT: F 76 MET cc_start: 0.5622 (pmm) cc_final: 0.4441 (ptp) REVERT: F 100 ILE cc_start: 0.8861 (tp) cc_final: 0.8574 (pp) REVERT: F 126 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.5594 (ppt170) REVERT: F 144 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5307 (ppp) REVERT: H 53 ASN cc_start: 0.8860 (t0) cc_final: 0.8466 (p0) REVERT: H 71 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8449 (ptp) REVERT: H 99 TYR cc_start: 0.8593 (m-80) cc_final: 0.8151 (m-80) REVERT: H 116 LEU cc_start: 0.6512 (tp) cc_final: 0.6245 (tp) REVERT: H 144 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6132 (ppp) outliers start: 55 outliers final: 25 residues processed: 319 average time/residue: 0.5471 time to fit residues: 191.4408 Evaluate side-chains 313 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 280 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 533 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 119 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.213460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.120978 restraints weight = 27767.423| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.86 r_work: 0.3089 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.7506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15664 Z= 0.175 Angle : 0.904 16.691 21144 Z= 0.441 Chirality : 0.043 0.238 2340 Planarity : 0.005 0.071 2664 Dihedral : 4.234 17.574 2160 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 3.11 % Allowed : 28.92 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1864 helix: 1.36 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -0.96 (0.34), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 90 TYR 0.021 0.001 TYR C 565 PHE 0.034 0.001 PHE H 68 TRP 0.049 0.001 TRP E 350 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (15664) covalent geometry : angle 0.90359 / 0.44 (21144) hydrogen bonds : bond 0.04384 / 2.93 ( 1112) hydrogen bonds : angle 4.89740 / 3.61 ( 3324) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 299 time to evaluate : 0.460 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: A 123 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6899 (mp0) REVERT: A 139 MET cc_start: 0.6816 (tmm) cc_final: 0.6309 (ttm) REVERT: A 150 ARG cc_start: 0.6879 (ttp-170) cc_final: 0.6528 (mtt90) REVERT: A 218 ASP cc_start: 0.8680 (m-30) cc_final: 0.8428 (m-30) REVERT: A 225 LYS cc_start: 0.9082 (mttt) cc_final: 0.8604 (mmmt) REVERT: A 236 LYS cc_start: 0.8808 (mmpt) cc_final: 0.8563 (tppt) REVERT: A 338 ARG cc_start: 0.8741 (pmt-80) cc_final: 0.8353 (pmm150) REVERT: A 547 ARG cc_start: 0.9362 (tpp80) cc_final: 0.9117 (tpp80) REVERT: C 123 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7195 (mm-30) REVERT: C 139 MET cc_start: 0.7423 (tmm) cc_final: 0.6939 (mmm) REVERT: C 150 ARG cc_start: 0.6753 (ttp-170) cc_final: 0.6402 (mtt90) REVERT: C 206 MET cc_start: 0.7614 (pp-130) cc_final: 0.7074 (mmp) REVERT: C 225 LYS cc_start: 0.9065 (mttt) cc_final: 0.8591 (mmmt) REVERT: C 336 GLU cc_start: 0.8557 (pp20) cc_final: 0.7924 (pm20) REVERT: C 338 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.6326 (pmt-80) REVERT: C 547 ARG cc_start: 0.8821 (tpm-80) cc_final: 0.8415 (tpm-80) REVERT: C 551 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8379 (mm-30) REVERT: C 563 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9230 (pp20) REVERT: E 123 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7244 (mm-30) REVERT: E 139 MET cc_start: 0.7409 (tmm) cc_final: 0.7043 (tpt) REVERT: E 150 ARG cc_start: 0.6752 (ttp-170) cc_final: 0.6543 (mtt-85) REVERT: E 217 MET cc_start: 0.7588 (ppp) cc_final: 0.7161 (pmm) REVERT: E 219 ARG cc_start: 0.6729 (tpm170) cc_final: 0.6462 (tpm170) REVERT: E 225 LYS cc_start: 0.9063 (mttt) cc_final: 0.8586 (mmmt) REVERT: E 551 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8490 (tp30) REVERT: E 565 TYR cc_start: 0.8105 (t80) cc_final: 0.7843 (t80) REVERT: G 123 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7101 (mp0) REVERT: G 139 MET cc_start: 0.7469 (tmm) cc_final: 0.6948 (mmm) REVERT: G 150 ARG cc_start: 0.6794 (ttp-170) cc_final: 0.6556 (mtt-85) REVERT: G 206 MET cc_start: 0.7599 (pp-130) cc_final: 0.7213 (mmp) REVERT: G 217 MET cc_start: 0.7656 (ppp) cc_final: 0.7047 (pmm) REVERT: G 219 ARG cc_start: 0.6705 (tpm170) cc_final: 0.6457 (tpm170) REVERT: G 225 LYS cc_start: 0.9083 (mttt) cc_final: 0.8596 (mmmt) REVERT: G 236 LYS cc_start: 0.8783 (mmpt) cc_final: 0.8518 (tppt) REVERT: G 350 TRP cc_start: 0.7244 (OUTLIER) cc_final: 0.6699 (m100) REVERT: G 546 LYS cc_start: 0.9281 (pptt) cc_final: 0.8818 (pttt) REVERT: B 100 ILE cc_start: 0.8810 (tp) cc_final: 0.8599 (pp) REVERT: B 116 LEU cc_start: 0.6664 (tp) cc_final: 0.6383 (tp) REVERT: B 144 MET cc_start: 0.7059 (ptp) cc_final: 0.6776 (ppp) REVERT: D 55 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8317 (p) REVERT: D 71 MET cc_start: 0.8598 (mtt) cc_final: 0.8018 (mpt) REVERT: D 99 TYR cc_start: 0.8596 (m-80) cc_final: 0.8285 (m-80) REVERT: D 116 LEU cc_start: 0.6783 (tp) cc_final: 0.6495 (tp) REVERT: D 144 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5656 (ppp) REVERT: F 14 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8558 (pp20) REVERT: F 53 ASN cc_start: 0.8871 (t0) cc_final: 0.8455 (p0) REVERT: F 71 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8042 (pp-130) REVERT: F 72 MET cc_start: 0.8229 (mtp) cc_final: 0.6920 (mtt) REVERT: F 76 MET cc_start: 0.5827 (pmm) cc_final: 0.4656 (ptp) REVERT: F 100 ILE cc_start: 0.8828 (tp) cc_final: 0.8543 (pp) REVERT: F 126 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.5539 (ppt170) REVERT: F 144 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5021 (pp-130) REVERT: H 53 ASN cc_start: 0.8876 (t0) cc_final: 0.8468 (p0) REVERT: H 68 PHE cc_start: 0.8339 (t80) cc_final: 0.7596 (t80) REVERT: H 71 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8287 (ptp) REVERT: H 99 TYR cc_start: 0.8635 (m-80) cc_final: 0.8080 (m-80) REVERT: H 116 LEU cc_start: 0.6441 (tp) cc_final: 0.6166 (tp) REVERT: H 144 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6106 (ppp) outliers start: 50 outliers final: 21 residues processed: 317 average time/residue: 0.5238 time to fit residues: 182.0474 Evaluate side-chains 304 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 533 VAL Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 11 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 62 optimal weight: 0.0070 chunk 83 optimal weight: 0.7980 chunk 131 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 HIS B 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.215184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131118 restraints weight = 28030.745| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.78 r_work: 0.3146 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.7781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15664 Z= 0.165 Angle : 0.942 18.154 21144 Z= 0.455 Chirality : 0.044 0.305 2340 Planarity : 0.005 0.076 2664 Dihedral : 4.271 22.582 2160 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.17 % Rotamer: Outliers : 2.49 % Allowed : 29.98 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1864 helix: 1.32 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -1.08 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 90 TYR 0.016 0.001 TYR C 565 PHE 0.047 0.001 PHE H 68 TRP 0.045 0.001 TRP E 350 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15664) covalent geometry : angle 0.94222 / 0.46 (21144) hydrogen bonds : bond 0.04305 / 2.89 ( 1112) hydrogen bonds : angle 4.87972 / 3.59 ( 3324) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 0.449 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: A 123 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7024 (mm-30) REVERT: A 139 MET cc_start: 0.6817 (tmm) cc_final: 0.6380 (ttm) REVERT: A 150 ARG cc_start: 0.6972 (ttp-170) cc_final: 0.6573 (mtt90) REVERT: A 218 ASP cc_start: 0.8664 (m-30) cc_final: 0.8331 (p0) REVERT: A 225 LYS cc_start: 0.8980 (mttt) cc_final: 0.8534 (mmmt) REVERT: A 236 LYS cc_start: 0.8735 (mmpt) cc_final: 0.8505 (tppt) REVERT: A 338 ARG cc_start: 0.8727 (pmt-80) cc_final: 0.8326 (pmm150) REVERT: A 550 LYS cc_start: 0.9247 (mtmm) cc_final: 0.8703 (pttt) REVERT: C 123 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7148 (mm-30) REVERT: C 139 MET cc_start: 0.7384 (tmm) cc_final: 0.7102 (tpt) REVERT: C 206 MET cc_start: 0.7501 (pp-130) cc_final: 0.6992 (mmp) REVERT: C 225 LYS cc_start: 0.8963 (mttt) cc_final: 0.8511 (mmmt) REVERT: C 336 GLU cc_start: 0.8609 (pp20) cc_final: 0.8045 (pm20) REVERT: C 338 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.6306 (pmt-80) REVERT: C 551 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8203 (tp30) REVERT: E 123 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7217 (mm-30) REVERT: E 139 MET cc_start: 0.7321 (tmm) cc_final: 0.6950 (ttm) REVERT: E 150 ARG cc_start: 0.6840 (ttp-170) cc_final: 0.6575 (mtt90) REVERT: E 217 MET cc_start: 0.7646 (ppp) cc_final: 0.7172 (pmm) REVERT: E 225 LYS cc_start: 0.8978 (mttt) cc_final: 0.8524 (mmmt) REVERT: E 565 TYR cc_start: 0.8060 (t80) cc_final: 0.7774 (t80) REVERT: G 123 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7092 (mp0) REVERT: G 139 MET cc_start: 0.7393 (tmm) cc_final: 0.6989 (ttm) REVERT: G 150 ARG cc_start: 0.6906 (ttp-170) cc_final: 0.6683 (mtp85) REVERT: G 217 MET cc_start: 0.7766 (ppp) cc_final: 0.7549 (pmm) REVERT: G 225 LYS cc_start: 0.8985 (mttt) cc_final: 0.8512 (mmmt) REVERT: G 236 LYS cc_start: 0.8733 (mmpt) cc_final: 0.8492 (tppt) REVERT: G 350 TRP cc_start: 0.7096 (OUTLIER) cc_final: 0.6541 (m100) REVERT: G 546 LYS cc_start: 0.9287 (pptt) cc_final: 0.8819 (pttt) REVERT: B 71 MET cc_start: 0.8569 (tpp) cc_final: 0.7986 (pp-130) REVERT: B 84 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8332 (mt-10) REVERT: B 100 ILE cc_start: 0.8745 (tp) cc_final: 0.8517 (pp) REVERT: B 116 LEU cc_start: 0.6329 (tp) cc_final: 0.6055 (tp) REVERT: B 144 MET cc_start: 0.7065 (ptp) cc_final: 0.6797 (ppp) REVERT: D 55 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8374 (p) REVERT: D 71 MET cc_start: 0.8428 (mtt) cc_final: 0.7966 (mpt) REVERT: D 99 TYR cc_start: 0.8513 (m-80) cc_final: 0.8117 (m-80) REVERT: D 116 LEU cc_start: 0.6526 (tp) cc_final: 0.6223 (tp) REVERT: D 144 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5674 (ppp) REVERT: F 37 ARG cc_start: 0.8946 (mpt-90) cc_final: 0.8662 (mmt90) REVERT: F 53 ASN cc_start: 0.8850 (t0) cc_final: 0.8426 (p0) REVERT: F 71 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8178 (mpt) REVERT: F 72 MET cc_start: 0.8320 (mtp) cc_final: 0.7912 (mpt) REVERT: F 126 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.5572 (ppt170) REVERT: F 144 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5101 (pp-130) REVERT: H 53 ASN cc_start: 0.8862 (t0) cc_final: 0.8449 (p0) REVERT: H 71 MET cc_start: 0.8766 (mtt) cc_final: 0.8333 (ptp) REVERT: H 76 MET cc_start: 0.3583 (mpt) cc_final: 0.3174 (mmt) REVERT: H 116 LEU cc_start: 0.6232 (tp) cc_final: 0.5961 (tp) REVERT: H 144 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6116 (ppp) outliers start: 40 outliers final: 17 residues processed: 311 average time/residue: 0.5518 time to fit residues: 188.3456 Evaluate side-chains 305 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 533 VAL Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 33 optimal weight: 50.0000 chunk 152 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 210 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 GLN ** G 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.209613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.120378 restraints weight = 27469.575| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 5.05 r_work: 0.2931 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.7968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 15664 Z= 0.330 Angle : 1.005 15.615 21144 Z= 0.497 Chirality : 0.049 0.314 2340 Planarity : 0.006 0.078 2664 Dihedral : 4.606 28.516 2160 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % Rotamer: Outliers : 2.80 % Allowed : 30.10 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1864 helix: 0.93 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.28 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 74 TYR 0.024 0.002 TYR C 565 PHE 0.044 0.002 PHE H 68 TRP 0.031 0.002 TRP E 350 HIS 0.012 0.001 HIS G 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.33 (15664) covalent geometry : angle 1.00452 / 0.50 (21144) hydrogen bonds : bond 0.05143 / 3.41 ( 1112) hydrogen bonds : angle 5.21918 / 3.85 ( 3324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7950.58 seconds wall clock time: 135 minutes 19.08 seconds (8119.08 seconds total)