Starting phenix.real_space_refine on Thu Feb 5 05:25:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnr_32046/02_2026/7vnr_32046_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnr_32046/02_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_32046/02_2026/7vnr_32046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnr_32046/02_2026/7vnr_32046.map" model { file = "/net/cci-nas-00/data/ceres_data/7vnr_32046/02_2026/7vnr_32046_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnr_32046/02_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-2.0-5952/lib/python3.9/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, 22 Unusual residues: {' K': 3, '7YV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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: 3.84, per 1000 atoms: 0.25 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: 1.43 Conformation dependent library (CDL) restraints added in 641.8 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: 0.50 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: 2.75 Time building geometry restraints manager: 1.84 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.930 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5226 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 covalent geometry : bond 0.01099 (15664) covalent geometry : angle 1.00786 (21144) hydrogen bonds : bond 0.15685 ( 1112) hydrogen bonds : angle 5.85537 ( 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 : 0.582 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: 0.7869 time to fit residues: 436.1971 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 : 0.662 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 F 111 ASN H 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.222001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131904 restraints weight = 27755.389| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 6.07 r_work: 0.3198 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15664 Z= 0.194 Angle : 0.855 13.601 21144 Z= 0.430 Chirality : 0.043 0.169 2340 Planarity : 0.006 0.093 2664 Dihedral : 6.049 59.700 2194 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.83 % Favored : 94.90 % Rotamer: Outliers : 4.54 % Allowed : 18.91 % Favored : 76.55 % 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: 0.97 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 207 TYR 0.028 0.001 TYR C 565 PHE 0.025 0.002 PHE D 16 TRP 0.023 0.002 TRP G 350 HIS 0.005 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00426 (15664) covalent geometry : angle 0.85468 (21144) hydrogen bonds : bond 0.05197 ( 1112) hydrogen bonds : angle 4.97359 ( 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 400 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 327 time to evaluate : 0.615 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 565 TYR cc_start: 0.8252 (t80) cc_final: 0.7724 (t80) REVERT: A 575 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7409 (ptp-170) REVERT: C 139 MET cc_start: 0.7191 (tmm) cc_final: 0.6545 (ttm) REVERT: C 344 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7677 (p0) REVERT: C 547 ARG cc_start: 0.9169 (tpp-160) cc_final: 0.8900 (tpm-80) REVERT: C 572 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8500 (tpp) REVERT: C 573 LEU cc_start: 0.8402 (mp) cc_final: 0.7966 (tp) REVERT: E 139 MET cc_start: 0.7170 (tmm) cc_final: 0.6463 (ttm) REVERT: G 139 MET cc_start: 0.6681 (tmm) cc_final: 0.5933 (mmm) REVERT: G 547 ARG cc_start: 0.9213 (tpp-160) cc_final: 0.8836 (tpm-80) REVERT: G 563 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9103 (pp20) REVERT: B 76 MET cc_start: 0.5279 (pmt) cc_final: 0.5057 (pmm) REVERT: B 145 MET cc_start: 0.6666 (mmm) cc_final: 0.6388 (mmm) REVERT: D 68 PHE cc_start: 0.7905 (t80) cc_final: 0.7452 (t80) REVERT: D 69 LEU cc_start: 0.9207 (pp) cc_final: 0.8997 (mp) REVERT: D 71 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7920 (mpt) REVERT: D 76 MET cc_start: 0.5119 (OUTLIER) cc_final: 0.4536 (pmm) REVERT: D 87 GLU cc_start: 0.9424 (tp30) cc_final: 0.9121 (tp30) REVERT: F 53 ASN cc_start: 0.8497 (t0) cc_final: 0.8204 (p0) REVERT: F 68 PHE cc_start: 0.8286 (t80) cc_final: 0.8043 (t80) REVERT: F 71 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8082 (mpt) REVERT: F 76 MET cc_start: 0.4996 (mtt) cc_final: 0.4226 (pmm) REVERT: F 112 LEU cc_start: 0.8351 (mm) cc_final: 0.8128 (tp) REVERT: H 68 PHE cc_start: 0.8004 (t80) cc_final: 0.7673 (t80) REVERT: H 71 MET cc_start: 0.8665 (mtt) cc_final: 0.8005 (mpt) REVERT: H 76 MET cc_start: 0.5297 (mtt) cc_final: 0.4987 (pmm) REVERT: H 87 GLU cc_start: 0.9354 (tp30) cc_final: 0.9059 (tp30) REVERT: H 116 LEU cc_start: 0.6655 (tp) cc_final: 0.6446 (tp) REVERT: H 121 VAL cc_start: 0.7685 (p) cc_final: 0.7391 (m) outliers start: 73 outliers final: 21 residues processed: 363 average time/residue: 0.6083 time to fit residues: 243.0250 Evaluate side-chains 288 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 346 ILE 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 332 GLN Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 569 HIS 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 76 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 79 THR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain H residue 19 PHE 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: 0.9980 chunk 183 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 329 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN C 334 HIS ** 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** H 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.214955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122612 restraints weight = 27793.702| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 4.29 r_work: 0.3051 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15664 Z= 0.217 Angle : 0.792 14.751 21144 Z= 0.398 Chirality : 0.044 0.241 2340 Planarity : 0.005 0.070 2664 Dihedral : 4.602 37.723 2168 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.72 % Favored : 95.06 % Rotamer: Outliers : 4.23 % Allowed : 20.83 % Favored : 74.94 % 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: 0.97 (0.19), residues: 1864 helix: 1.30 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 90 TYR 0.025 0.001 TYR C 565 PHE 0.033 0.002 PHE E 169 TRP 0.017 0.002 TRP G 350 HIS 0.005 0.001 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00494 (15664) covalent geometry : angle 0.79223 (21144) hydrogen bonds : bond 0.04864 ( 1112) hydrogen bonds : angle 4.91556 ( 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 370 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 302 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 LEU cc_start: 0.9265 (tt) cc_final: 0.9038 (tt) REVERT: A 551 GLU cc_start: 0.8213 (tp30) cc_final: 0.7445 (tp30) REVERT: A 560 ASP cc_start: 0.8078 (m-30) cc_final: 0.7539 (m-30) REVERT: C 139 MET cc_start: 0.7592 (tmm) cc_final: 0.7021 (ttm) REVERT: C 306 LEU cc_start: 0.9268 (tt) cc_final: 0.9041 (tt) REVERT: C 344 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7741 (p0) REVERT: C 547 ARG cc_start: 0.9265 (tpp-160) cc_final: 0.8850 (tpm-80) REVERT: E 139 MET cc_start: 0.7598 (tmm) cc_final: 0.6940 (ttm) REVERT: E 236 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7989 (mttp) REVERT: E 306 LEU cc_start: 0.9271 (tt) cc_final: 0.9044 (tt) REVERT: E 547 ARG cc_start: 0.8946 (tpm-80) cc_final: 0.8204 (tpm-80) REVERT: E 551 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8483 (mm-30) REVERT: G 139 MET cc_start: 0.7435 (tmm) cc_final: 0.6748 (mmm) REVERT: G 236 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7983 (mttp) REVERT: G 563 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9202 (pp20) REVERT: G 565 TYR cc_start: 0.8497 (t80) cc_final: 0.8122 (t80) REVERT: B 32 LEU cc_start: 0.8421 (pp) cc_final: 0.7796 (pp) REVERT: B 53 ASN cc_start: 0.8758 (t0) cc_final: 0.8461 (p0) REVERT: B 71 MET cc_start: 0.8625 (pp-130) cc_final: 0.8373 (pp-130) REVERT: B 76 MET cc_start: 0.5941 (pmt) cc_final: 0.5622 (pmm) REVERT: B 100 ILE cc_start: 0.8675 (tp) cc_final: 0.8400 (pp) REVERT: B 116 LEU cc_start: 0.6410 (tp) cc_final: 0.6201 (tp) REVERT: B 144 MET cc_start: 0.5827 (OUTLIER) cc_final: 0.5500 (ppp) REVERT: D 65 PHE cc_start: 0.9396 (p90) cc_final: 0.8896 (t80) REVERT: D 71 MET cc_start: 0.8649 (mtt) cc_final: 0.8059 (mpt) REVERT: D 87 GLU cc_start: 0.9413 (tp30) cc_final: 0.9104 (tp30) REVERT: D 90 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8601 (ttp80) REVERT: D 116 LEU cc_start: 0.6834 (tp) cc_final: 0.6387 (tm) REVERT: F 53 ASN cc_start: 0.8618 (t0) cc_final: 0.8347 (p0) REVERT: F 70 THR cc_start: 0.8256 (m) cc_final: 0.7972 (m) REVERT: F 71 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8247 (mpt) REVERT: H 53 ASN cc_start: 0.8729 (t0) cc_final: 0.8453 (p0) REVERT: H 68 PHE cc_start: 0.8047 (t80) cc_final: 0.7676 (t80) REVERT: H 71 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7913 (pp-130) REVERT: H 87 GLU cc_start: 0.9357 (tp30) cc_final: 0.9129 (tp30) REVERT: H 116 LEU cc_start: 0.6751 (tp) cc_final: 0.6488 (tp) outliers start: 68 outliers final: 23 residues processed: 338 average time/residue: 0.6452 time to fit residues: 238.9211 Evaluate side-chains 296 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU 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 E residue 237 GLU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain G residue 578 SER 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 44 THR 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 71 MET Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain H residue 19 PHE 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 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: 7.9990 chunk 149 optimal weight: 0.0870 chunk 165 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 62 optimal weight: 20.0000 chunk 21 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN F 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.216421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128285 restraints weight = 28564.626| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 5.15 r_work: 0.3080 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5898 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= 0.162 Angle : 0.787 14.380 21144 Z= 0.384 Chirality : 0.041 0.193 2340 Planarity : 0.004 0.072 2664 Dihedral : 4.074 16.617 2160 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.45 % Favored : 95.33 % Rotamer: Outliers : 3.79 % Allowed : 21.70 % 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: 1.17 (0.19), residues: 1864 helix: 1.44 (0.13), residues: 1432 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 74 TYR 0.018 0.001 TYR G 565 PHE 0.035 0.002 PHE E 169 TRP 0.014 0.001 TRP E 350 HIS 0.007 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00354 (15664) covalent geometry : angle 0.78714 (21144) hydrogen bonds : bond 0.04419 ( 1112) hydrogen bonds : angle 4.81706 ( 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 377 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 316 time to evaluate : 0.614 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 346 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 560 ASP cc_start: 0.8080 (m-30) cc_final: 0.7783 (m-30) REVERT: C 139 MET cc_start: 0.7609 (tmm) cc_final: 0.6999 (mmm) REVERT: C 150 ARG cc_start: 0.6757 (ttp-170) cc_final: 0.6513 (mtt-85) REVERT: C 338 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.6129 (pmt-80) REVERT: C 344 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7764 (p0) REVERT: C 547 ARG cc_start: 0.9238 (tpp-160) cc_final: 0.8966 (tpm-80) REVERT: E 139 MET cc_start: 0.7544 (tmm) cc_final: 0.6961 (ttm) REVERT: E 150 ARG cc_start: 0.6689 (ttp-170) cc_final: 0.6465 (mtt-85) REVERT: E 236 LYS cc_start: 0.8341 (mmpt) cc_final: 0.8095 (mttp) REVERT: E 572 MET cc_start: 0.9102 (mmt) cc_final: 0.8864 (tpp) REVERT: E 573 LEU cc_start: 0.9408 (pp) cc_final: 0.8949 (tp) REVERT: G 139 MET cc_start: 0.7656 (tmm) cc_final: 0.7101 (ttm) REVERT: G 150 ARG cc_start: 0.6755 (ttp-170) cc_final: 0.6531 (mtt-85) REVERT: G 225 LYS cc_start: 0.9002 (mttt) cc_final: 0.8791 (mtmt) REVERT: G 236 LYS cc_start: 0.8329 (mmpt) cc_final: 0.8109 (mttp) REVERT: G 338 ARG cc_start: 0.8347 (pmt-80) cc_final: 0.7779 (pmt170) REVERT: G 547 ARG cc_start: 0.8936 (tpm-80) cc_final: 0.8606 (tpm-80) REVERT: G 563 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9154 (pp20) REVERT: B 32 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8704 (pp) REVERT: B 53 ASN cc_start: 0.8732 (t0) cc_final: 0.8439 (p0) REVERT: B 76 MET cc_start: 0.5958 (pmt) cc_final: 0.5592 (pmm) REVERT: B 100 ILE cc_start: 0.8624 (tp) cc_final: 0.8369 (pp) REVERT: B 116 LEU cc_start: 0.6561 (tp) cc_final: 0.6189 (tp) REVERT: B 144 MET cc_start: 0.6231 (ptp) cc_final: 0.6009 (ppp) REVERT: D 71 MET cc_start: 0.8681 (mtt) cc_final: 0.8041 (mpt) REVERT: D 87 GLU cc_start: 0.9420 (tp30) cc_final: 0.9078 (tp30) REVERT: D 90 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8542 (ttp80) REVERT: D 100 ILE cc_start: 0.8545 (tp) cc_final: 0.8334 (pp) REVERT: D 101 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7950 (p) REVERT: D 116 LEU cc_start: 0.6589 (tp) cc_final: 0.6051 (tm) REVERT: D 144 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5576 (ppp) REVERT: F 9 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5853 (pp) REVERT: F 53 ASN cc_start: 0.8662 (t0) cc_final: 0.8378 (p0) REVERT: F 68 PHE cc_start: 0.8035 (t80) cc_final: 0.7673 (t80) REVERT: F 71 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8185 (mpt) REVERT: F 109 MET cc_start: 0.6059 (tpp) cc_final: 0.5833 (tpp) REVERT: H 53 ASN cc_start: 0.8709 (t0) cc_final: 0.8429 (p0) REVERT: H 71 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8055 (mpt) REVERT: H 87 GLU cc_start: 0.9364 (tp30) cc_final: 0.9136 (tp30) REVERT: H 90 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8480 (ttp80) REVERT: H 100 ILE cc_start: 0.8625 (tp) cc_final: 0.8410 (pp) REVERT: H 116 LEU cc_start: 0.6657 (tp) cc_final: 0.6362 (tp) REVERT: H 126 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7261 (ppp-140) REVERT: H 144 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5523 (ppp) outliers start: 61 outliers final: 20 residues processed: 348 average time/residue: 0.6874 time to fit residues: 260.8867 Evaluate side-chains 311 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 346 ILE 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 344 ASN Chi-restraints excluded: chain C residue 573 LEU 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 G residue 247 LEU Chi-restraints excluded: chain G residue 578 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 32 LEU 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 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 125 ILE 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: 2.9990 chunk 33 optimal weight: 50.0000 chunk 127 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 165 optimal weight: 8.9990 chunk 133 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.212887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131973 restraints weight = 27995.485| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.95 r_work: 0.3060 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15664 Z= 0.218 Angle : 0.814 14.114 21144 Z= 0.403 Chirality : 0.043 0.211 2340 Planarity : 0.005 0.069 2664 Dihedral : 4.151 16.636 2160 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.72 % Favored : 95.06 % 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: 1.02 (0.19), residues: 1864 helix: 1.28 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.34 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 90 TYR 0.016 0.001 TYR C 565 PHE 0.026 0.002 PHE D 68 TRP 0.023 0.002 TRP E 350 HIS 0.009 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00499 (15664) covalent geometry : angle 0.81419 (21144) hydrogen bonds : bond 0.04758 ( 1112) hydrogen bonds : angle 4.89071 ( 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 396 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 313 time to evaluate : 0.601 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 306 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9060 (tt) REVERT: A 350 TRP cc_start: 0.7239 (OUTLIER) cc_final: 0.6872 (m100) REVERT: A 547 ARG cc_start: 0.8923 (tpm-80) cc_final: 0.8041 (tpm-80) REVERT: A 559 LYS cc_start: 0.6910 (mmtt) cc_final: 0.6419 (tptp) REVERT: A 560 ASP cc_start: 0.8235 (m-30) cc_final: 0.8004 (m-30) REVERT: A 565 TYR cc_start: 0.8625 (t80) cc_final: 0.8313 (t80) REVERT: C 139 MET cc_start: 0.7684 (tmm) cc_final: 0.7156 (mmm) REVERT: C 150 ARG cc_start: 0.6787 (ttp-170) cc_final: 0.6541 (mtt-85) REVERT: C 206 MET cc_start: 0.7411 (pp-130) cc_final: 0.7182 (mmp) REVERT: C 306 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9059 (tt) REVERT: C 338 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.6106 (pmt-80) REVERT: C 344 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7895 (p0) REVERT: C 560 ASP cc_start: 0.8418 (m-30) cc_final: 0.8168 (m-30) REVERT: E 139 MET cc_start: 0.7583 (tmm) cc_final: 0.7113 (ttm) REVERT: E 225 LYS cc_start: 0.9140 (mtmt) cc_final: 0.8492 (mmmt) REVERT: E 236 LYS cc_start: 0.8712 (mmpt) cc_final: 0.8440 (tppt) REVERT: E 306 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9066 (tt) REVERT: E 563 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8704 (mt-10) REVERT: G 139 MET cc_start: 0.7575 (tmm) cc_final: 0.7023 (mmm) REVERT: G 206 MET cc_start: 0.7448 (pp-130) cc_final: 0.7144 (mmp) REVERT: G 225 LYS cc_start: 0.9046 (mttt) cc_final: 0.8508 (mmmt) REVERT: G 236 LYS cc_start: 0.8719 (mmpt) cc_final: 0.8440 (mttp) REVERT: G 306 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9050 (tt) REVERT: G 563 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9227 (pp20) REVERT: B 53 ASN cc_start: 0.8774 (t0) cc_final: 0.8369 (p0) REVERT: B 62 THR cc_start: 0.4306 (p) cc_final: 0.3870 (p) REVERT: B 76 MET cc_start: 0.6298 (pmt) cc_final: 0.5890 (pmm) REVERT: B 100 ILE cc_start: 0.8572 (tp) cc_final: 0.8324 (pp) REVERT: B 105 LEU cc_start: 0.8641 (pp) cc_final: 0.8434 (pt) REVERT: B 116 LEU cc_start: 0.6568 (tp) cc_final: 0.6153 (tp) REVERT: D 62 THR cc_start: 0.3068 (p) cc_final: 0.2754 (p) REVERT: D 71 MET cc_start: 0.8844 (mtt) cc_final: 0.8225 (mpt) REVERT: D 87 GLU cc_start: 0.9370 (tp30) cc_final: 0.8816 (tp30) REVERT: D 90 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8397 (ttp80) REVERT: D 99 TYR cc_start: 0.8341 (m-80) cc_final: 0.7986 (m-80) REVERT: D 100 ILE cc_start: 0.8545 (tp) cc_final: 0.8295 (pp) REVERT: D 101 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8169 (p) REVERT: D 116 LEU cc_start: 0.6617 (tp) cc_final: 0.6132 (tp) REVERT: D 144 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5334 (ppp) REVERT: F 36 MET cc_start: 0.8259 (ptt) cc_final: 0.8046 (pmm) REVERT: F 48 LEU cc_start: 0.8067 (tp) cc_final: 0.7562 (mm) REVERT: F 53 ASN cc_start: 0.8654 (t0) cc_final: 0.8337 (p0) REVERT: F 71 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8189 (mpt) REVERT: F 126 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.5510 (ppt170) REVERT: F 144 MET cc_start: 0.5419 (OUTLIER) cc_final: 0.4674 (ppp) REVERT: H 53 ASN cc_start: 0.8755 (t0) cc_final: 0.8382 (p0) REVERT: H 68 PHE cc_start: 0.8217 (t80) cc_final: 0.7877 (t80) REVERT: H 71 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8324 (ptp) REVERT: H 112 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7944 (tp) REVERT: H 116 LEU cc_start: 0.6740 (tp) cc_final: 0.6487 (tp) REVERT: H 144 MET cc_start: 0.5926 (OUTLIER) cc_final: 0.5162 (ppp) outliers start: 83 outliers final: 29 residues processed: 353 average time/residue: 0.5728 time to fit residues: 223.9119 Evaluate side-chains 319 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 275 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 51 MET 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 D residue 80 ASP Chi-restraints excluded: chain D residue 101 SER 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 32 LEU 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 126 ARG Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 32 LEU 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 115 LYS Chi-restraints excluded: chain H residue 125 ILE 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: 0.9980 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 50.0000 chunk 132 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN G 84 GLN ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.214326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120274 restraints weight = 27968.445| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.99 r_work: 0.3065 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15664 Z= 0.168 Angle : 0.822 14.227 21144 Z= 0.401 Chirality : 0.042 0.207 2340 Planarity : 0.004 0.070 2664 Dihedral : 4.114 15.989 2160 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.97 % Favored : 95.82 % Rotamer: Outliers : 3.86 % Allowed : 25.75 % Favored : 70.40 % 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: 1.22 (0.20), residues: 1864 helix: 1.40 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.17 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 74 TYR 0.016 0.001 TYR C 565 PHE 0.040 0.002 PHE B 68 TRP 0.037 0.002 TRP E 350 HIS 0.009 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00377 (15664) covalent geometry : angle 0.82183 (21144) hydrogen bonds : bond 0.04406 ( 1112) hydrogen bonds : angle 4.80847 ( 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 379 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 0.832 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 225 LYS cc_start: 0.8974 (mttt) cc_final: 0.8427 (mmmt) REVERT: A 338 ARG cc_start: 0.8784 (pmt-80) cc_final: 0.8414 (pmm150) REVERT: A 350 TRP cc_start: 0.7154 (OUTLIER) cc_final: 0.6885 (m100) REVERT: A 547 ARG cc_start: 0.8892 (tpm-80) cc_final: 0.8513 (tpm-80) REVERT: A 551 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8129 (mm-30) REVERT: C 139 MET cc_start: 0.7542 (tmm) cc_final: 0.7024 (mmm) REVERT: C 150 ARG cc_start: 0.6760 (ttp-170) cc_final: 0.6526 (mtp85) REVERT: C 206 MET cc_start: 0.7475 (pp-130) cc_final: 0.7087 (mmp) REVERT: C 217 MET cc_start: 0.7580 (ppp) cc_final: 0.7028 (pmm) REVERT: C 225 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8302 (mmmt) REVERT: C 547 ARG cc_start: 0.9223 (tpp80) cc_final: 0.8715 (tpp80) REVERT: C 560 ASP cc_start: 0.8263 (m-30) cc_final: 0.8023 (m-30) REVERT: E 139 MET cc_start: 0.7516 (tmm) cc_final: 0.7086 (ttm) REVERT: E 150 ARG cc_start: 0.6697 (ttp-170) cc_final: 0.6468 (mtt-85) REVERT: E 217 MET cc_start: 0.7765 (ppp) cc_final: 0.7208 (pmm) REVERT: E 225 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8355 (mmmt) REVERT: E 236 LYS cc_start: 0.8632 (mmpt) cc_final: 0.8366 (tppt) REVERT: E 563 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8770 (mt-10) REVERT: G 123 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7519 (mt-10) REVERT: G 139 MET cc_start: 0.7570 (tmm) cc_final: 0.6999 (mmm) REVERT: G 150 ARG cc_start: 0.6768 (ttp-170) cc_final: 0.6529 (mtt-85) REVERT: G 206 MET cc_start: 0.7454 (pp-130) cc_final: 0.7077 (mmp) REVERT: G 225 LYS cc_start: 0.8957 (mttt) cc_final: 0.8421 (mmmt) REVERT: G 236 LYS cc_start: 0.8557 (mmpt) cc_final: 0.8294 (tppt) REVERT: G 547 ARG cc_start: 0.8954 (tpm-80) cc_final: 0.8539 (tpm-80) REVERT: G 565 TYR cc_start: 0.8381 (t80) cc_final: 0.8139 (t80) REVERT: B 53 ASN cc_start: 0.8855 (t0) cc_final: 0.8440 (p0) REVERT: B 76 MET cc_start: 0.6330 (pmt) cc_final: 0.6034 (pmm) REVERT: B 116 LEU cc_start: 0.6423 (tp) cc_final: 0.6082 (tp) REVERT: B 144 MET cc_start: 0.6528 (ppp) cc_final: 0.6324 (ppp) REVERT: D 62 THR cc_start: 0.3380 (p) cc_final: 0.3167 (p) REVERT: D 71 MET cc_start: 0.8758 (mtt) cc_final: 0.8031 (mpt) REVERT: D 87 GLU cc_start: 0.9346 (tp30) cc_final: 0.8773 (tp30) REVERT: D 90 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8252 (ttp80) REVERT: D 99 TYR cc_start: 0.8407 (m-80) cc_final: 0.8123 (m-80) REVERT: D 100 ILE cc_start: 0.8564 (tp) cc_final: 0.8317 (pp) REVERT: D 101 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8094 (p) REVERT: D 116 LEU cc_start: 0.6816 (tp) cc_final: 0.6229 (tp) REVERT: D 144 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5529 (ppp) REVERT: F 53 ASN cc_start: 0.8681 (t0) cc_final: 0.8351 (p0) REVERT: F 71 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8194 (mpt) REVERT: F 126 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5599 (ppt170) REVERT: F 144 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.4765 (pp-130) REVERT: H 53 ASN cc_start: 0.8798 (t0) cc_final: 0.8433 (p0) REVERT: H 68 PHE cc_start: 0.8226 (t80) cc_final: 0.7806 (t80) REVERT: H 71 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8361 (ptp) REVERT: H 99 TYR cc_start: 0.8657 (m-80) cc_final: 0.8147 (m-80) REVERT: H 116 LEU cc_start: 0.6682 (tp) cc_final: 0.6405 (tp) REVERT: H 144 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5457 (ppp) outliers start: 62 outliers final: 17 residues processed: 349 average time/residue: 0.5852 time to fit residues: 224.1416 Evaluate side-chains 318 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 293 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 554 ARG Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain D residue 101 SER 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 80 ASP 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 101 SER 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: 10.0000 chunk 165 optimal weight: 30.0000 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN E 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.214516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.125275 restraints weight = 27772.716| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 5.11 r_work: 0.3040 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 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 = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15664 Z= 0.171 Angle : 0.842 14.896 21144 Z= 0.414 Chirality : 0.043 0.228 2340 Planarity : 0.004 0.064 2664 Dihedral : 4.142 16.076 2160 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.18 % Favored : 95.60 % Rotamer: Outliers : 3.48 % Allowed : 27.11 % Favored : 69.40 % 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: 1.23 (0.20), residues: 1864 helix: 1.46 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.31 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 90 TYR 0.014 0.001 TYR C 565 PHE 0.037 0.002 PHE B 68 TRP 0.038 0.001 TRP E 350 HIS 0.016 0.001 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00385 (15664) covalent geometry : angle 0.84250 (21144) hydrogen bonds : bond 0.04404 ( 1112) hydrogen bonds : angle 4.78751 ( 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 365 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 0.520 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 150 ARG cc_start: 0.6858 (ttp-170) cc_final: 0.6524 (mtt90) REVERT: A 225 LYS cc_start: 0.9006 (mttt) cc_final: 0.8499 (mmmt) REVERT: A 247 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9107 (mp) REVERT: A 338 ARG cc_start: 0.8812 (pmt-80) cc_final: 0.8457 (pmm150) REVERT: A 350 TRP cc_start: 0.7300 (OUTLIER) cc_final: 0.6902 (m100) REVERT: A 547 ARG cc_start: 0.9049 (tpm-80) cc_final: 0.8441 (tpm-80) REVERT: A 551 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8082 (mm-30) REVERT: C 139 MET cc_start: 0.7469 (tmm) cc_final: 0.7061 (ttm) REVERT: C 150 ARG cc_start: 0.6771 (ttp-170) cc_final: 0.6460 (mtt90) REVERT: C 206 MET cc_start: 0.7548 (pp-130) cc_final: 0.7090 (mmp) REVERT: C 547 ARG cc_start: 0.9041 (tpp80) cc_final: 0.8806 (tpp80) REVERT: C 551 GLU cc_start: 0.8593 (tp30) cc_final: 0.8139 (mm-30) REVERT: C 554 ARG cc_start: 0.8406 (mmt-90) cc_final: 0.8064 (mmp-170) REVERT: E 139 MET cc_start: 0.7418 (tmm) cc_final: 0.7009 (ttm) REVERT: E 150 ARG cc_start: 0.6769 (ttp-170) cc_final: 0.6545 (mtt-85) REVERT: E 217 MET cc_start: 0.7746 (ppp) cc_final: 0.7145 (pmm) REVERT: E 236 LYS cc_start: 0.8721 (mmpt) cc_final: 0.8482 (tppt) REVERT: E 563 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8790 (mt-10) REVERT: G 123 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7131 (mm-30) REVERT: G 139 MET cc_start: 0.7513 (tmm) cc_final: 0.7065 (ttm) REVERT: G 150 ARG cc_start: 0.6790 (ttp-170) cc_final: 0.6542 (mtt-85) REVERT: G 206 MET cc_start: 0.7516 (pp-130) cc_final: 0.7075 (mmp) REVERT: G 225 LYS cc_start: 0.8997 (mttt) cc_final: 0.8531 (mmmt) REVERT: G 236 LYS cc_start: 0.8697 (mmpt) cc_final: 0.8442 (tppt) REVERT: G 565 TYR cc_start: 0.8452 (t80) cc_final: 0.8251 (t80) REVERT: B 53 ASN cc_start: 0.8785 (t0) cc_final: 0.8390 (p0) REVERT: B 71 MET cc_start: 0.8771 (pp-130) cc_final: 0.8565 (ppp) REVERT: B 76 MET cc_start: 0.6466 (pmt) cc_final: 0.6098 (pmm) REVERT: B 116 LEU cc_start: 0.6485 (tp) cc_final: 0.6015 (tp) REVERT: B 124 MET cc_start: 0.7998 (ptt) cc_final: 0.7781 (ptt) REVERT: B 144 MET cc_start: 0.6687 (ppp) cc_final: 0.6428 (ppp) REVERT: D 68 PHE cc_start: 0.8024 (t80) cc_final: 0.7725 (t80) REVERT: D 71 MET cc_start: 0.8641 (mtt) cc_final: 0.7957 (mpt) REVERT: D 87 GLU cc_start: 0.9321 (tp30) cc_final: 0.8732 (tp30) REVERT: D 90 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8212 (ttp80) REVERT: D 99 TYR cc_start: 0.8518 (m-80) cc_final: 0.8257 (m-80) REVERT: D 100 ILE cc_start: 0.8576 (tp) cc_final: 0.8342 (pp) REVERT: D 101 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8144 (p) REVERT: D 116 LEU cc_start: 0.6803 (tp) cc_final: 0.6461 (tp) REVERT: D 144 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5605 (ppp) REVERT: F 53 ASN cc_start: 0.8658 (t0) cc_final: 0.8342 (p0) REVERT: F 71 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8147 (mpt) REVERT: F 100 ILE cc_start: 0.8838 (tp) cc_final: 0.8528 (pp) REVERT: F 126 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.5502 (ppt170) REVERT: F 144 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5152 (ppp) REVERT: H 53 ASN cc_start: 0.8753 (t0) cc_final: 0.8359 (p0) REVERT: H 68 PHE cc_start: 0.8108 (t80) cc_final: 0.7814 (t80) REVERT: H 71 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8234 (ptp) REVERT: H 99 TYR cc_start: 0.8533 (m-80) cc_final: 0.8052 (m-80) REVERT: H 116 LEU cc_start: 0.6655 (tp) cc_final: 0.6423 (tp) REVERT: H 144 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5384 (ppp) outliers start: 56 outliers final: 19 residues processed: 335 average time/residue: 0.6097 time to fit residues: 223.4192 Evaluate side-chains 316 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 288 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 533 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain D residue 101 SER 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 126 ARG Chi-restraints excluded: chain F residue 144 MET 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 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: 1.9990 chunk 162 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN E 329 GLN ** E 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.213351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.119360 restraints weight = 27989.815| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.77 r_work: 0.3117 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.7330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15664 Z= 0.189 Angle : 0.869 15.278 21144 Z= 0.427 Chirality : 0.044 0.341 2340 Planarity : 0.004 0.065 2664 Dihedral : 4.176 20.754 2160 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.35 % Favored : 95.44 % Rotamer: Outliers : 3.36 % Allowed : 28.61 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.08 (0.20), residues: 1864 helix: 1.36 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.37 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 74 TYR 0.015 0.001 TYR C 565 PHE 0.030 0.002 PHE B 68 TRP 0.028 0.001 TRP E 350 HIS 0.012 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00435 (15664) covalent geometry : angle 0.86879 (21144) hydrogen bonds : bond 0.04575 ( 1112) hydrogen bonds : angle 4.85550 ( 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 362 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 0.624 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 139 MET cc_start: 0.6794 (tmm) cc_final: 0.6090 (mpt) REVERT: A 150 ARG cc_start: 0.6904 (ttp-170) cc_final: 0.6542 (mtt90) REVERT: A 225 LYS cc_start: 0.9067 (mttt) cc_final: 0.8580 (mmmt) REVERT: A 338 ARG cc_start: 0.8758 (pmt-80) cc_final: 0.8422 (pmm150) REVERT: A 350 TRP cc_start: 0.7406 (OUTLIER) cc_final: 0.6740 (m100) REVERT: A 547 ARG cc_start: 0.9057 (tpm-80) cc_final: 0.8491 (tpm-80) REVERT: A 551 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8211 (mm-30) REVERT: A 554 ARG cc_start: 0.8461 (mpt180) cc_final: 0.8241 (mmp-170) REVERT: A 565 TYR cc_start: 0.8851 (t80) cc_final: 0.8218 (t80) REVERT: C 139 MET cc_start: 0.7450 (tmm) cc_final: 0.7031 (ttm) REVERT: C 150 ARG cc_start: 0.6776 (ttp-170) cc_final: 0.6449 (mtt90) REVERT: C 206 MET cc_start: 0.7616 (pp-130) cc_final: 0.7167 (mmp) REVERT: C 336 GLU cc_start: 0.8502 (pp20) cc_final: 0.8113 (pm20) REVERT: C 547 ARG cc_start: 0.9278 (tpp80) cc_final: 0.8722 (tpp80) REVERT: C 554 ARG cc_start: 0.8440 (mmt180) cc_final: 0.8187 (mmp-170) REVERT: E 139 MET cc_start: 0.7418 (tmm) cc_final: 0.6989 (ttm) REVERT: E 150 ARG cc_start: 0.6797 (ttp-170) cc_final: 0.6596 (mtp85) REVERT: E 217 MET cc_start: 0.7726 (ppp) cc_final: 0.7174 (pmm) REVERT: E 236 LYS cc_start: 0.8787 (mmpt) cc_final: 0.8521 (tppt) REVERT: E 338 ARG cc_start: 0.8005 (pmt-80) cc_final: 0.7654 (pmt-80) REVERT: E 551 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8563 (mm-30) REVERT: G 93 ARG cc_start: 0.8147 (tmt90) cc_final: 0.7734 (ptm-80) REVERT: G 123 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7160 (mm-30) REVERT: G 139 MET cc_start: 0.7506 (tmm) cc_final: 0.7054 (ttm) REVERT: G 150 ARG cc_start: 0.6800 (ttp-170) cc_final: 0.6458 (mtt90) REVERT: G 206 MET cc_start: 0.7533 (pp-130) cc_final: 0.7076 (mmp) REVERT: G 219 ARG cc_start: 0.6728 (tpm170) cc_final: 0.6451 (tpm170) REVERT: G 225 LYS cc_start: 0.9073 (mttt) cc_final: 0.8589 (mmmt) REVERT: G 236 LYS cc_start: 0.8760 (mmpt) cc_final: 0.8497 (tppt) REVERT: G 338 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.7293 (pmt-80) REVERT: G 344 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8025 (p0) REVERT: G 565 TYR cc_start: 0.8592 (t80) cc_final: 0.8364 (t80) REVERT: B 53 ASN cc_start: 0.8791 (t0) cc_final: 0.8371 (p0) REVERT: B 71 MET cc_start: 0.8591 (pp-130) cc_final: 0.8335 (ppp) REVERT: B 76 MET cc_start: 0.6472 (pmt) cc_final: 0.6091 (pmm) REVERT: B 116 LEU cc_start: 0.6663 (tp) cc_final: 0.6248 (tp) REVERT: B 124 MET cc_start: 0.8014 (ptt) cc_final: 0.7703 (ptt) REVERT: B 144 MET cc_start: 0.6801 (ppp) cc_final: 0.6548 (ppp) REVERT: D 71 MET cc_start: 0.8584 (mtt) cc_final: 0.7946 (mpt) REVERT: D 87 GLU cc_start: 0.9330 (tp30) cc_final: 0.8767 (tp30) REVERT: D 90 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8222 (ttp80) REVERT: D 99 TYR cc_start: 0.8597 (m-80) cc_final: 0.8353 (m-80) REVERT: D 101 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8217 (p) REVERT: D 116 LEU cc_start: 0.6830 (tp) cc_final: 0.6502 (tp) REVERT: D 144 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.5661 (ppp) REVERT: F 16 PHE cc_start: 0.7525 (t80) cc_final: 0.7306 (t80) REVERT: F 18 LEU cc_start: 0.8255 (mp) cc_final: 0.8035 (mm) REVERT: F 53 ASN cc_start: 0.8705 (t0) cc_final: 0.8370 (p0) REVERT: F 68 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7123 (t80) REVERT: F 71 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8127 (mpt) REVERT: F 126 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.5696 (ppt170) REVERT: F 141 PHE cc_start: 0.8579 (m-80) cc_final: 0.8310 (m-80) REVERT: F 144 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5743 (ppp) REVERT: H 53 ASN cc_start: 0.8733 (t0) cc_final: 0.8360 (p0) REVERT: H 65 PHE cc_start: 0.8996 (t80) cc_final: 0.8734 (t80) REVERT: H 68 PHE cc_start: 0.8142 (t80) cc_final: 0.7938 (t80) REVERT: H 71 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8364 (ptp) REVERT: H 99 TYR cc_start: 0.8569 (m-80) cc_final: 0.8273 (m-80) REVERT: H 116 LEU cc_start: 0.6864 (tp) cc_final: 0.6592 (tp) REVERT: H 144 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5418 (ppp) outliers start: 54 outliers final: 20 residues processed: 336 average time/residue: 0.6594 time to fit residues: 242.3268 Evaluate side-chains 310 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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 G residue 247 LEU Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 344 ASN 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 D residue 101 SER 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 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 126 ARG Chi-restraints excluded: chain F residue 136 VAL 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 115 LYS Chi-restraints excluded: chain H residue 125 ILE 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: 0.7980 chunk 124 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 147 optimal weight: 0.0270 chunk 92 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 GLN ** F 135 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 = 0.4768 r_free = 0.4768 target = 0.214128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.123391 restraints weight = 27424.237| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.70 r_work: 0.3167 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.7601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15664 Z= 0.166 Angle : 0.905 16.015 21144 Z= 0.440 Chirality : 0.044 0.319 2340 Planarity : 0.005 0.066 2664 Dihedral : 4.204 25.606 2160 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 2.80 % Allowed : 30.16 % Favored : 67.04 % 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 (0.20), residues: 1864 helix: 1.40 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -1.34 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 90 TYR 0.014 0.001 TYR C 565 PHE 0.041 0.001 PHE D 68 TRP 0.025 0.001 TRP E 350 HIS 0.012 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00371 (15664) covalent geometry : angle 0.90519 (21144) hydrogen bonds : bond 0.04330 ( 1112) hydrogen bonds : angle 4.79979 ( 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 352 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 0.609 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: A 123 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7108 (mm-30) REVERT: A 139 MET cc_start: 0.6781 (tmm) cc_final: 0.6264 (ttm) REVERT: A 150 ARG cc_start: 0.6996 (ttp-170) cc_final: 0.6582 (mtt90) REVERT: A 225 LYS cc_start: 0.9009 (mttt) cc_final: 0.8549 (mmmt) REVERT: A 336 GLU cc_start: 0.8097 (pp20) cc_final: 0.7567 (pm20) REVERT: A 338 ARG cc_start: 0.8732 (pmt-80) cc_final: 0.8337 (pmm150) REVERT: A 350 TRP cc_start: 0.7391 (OUTLIER) cc_final: 0.6667 (m100) REVERT: A 547 ARG cc_start: 0.9070 (tpm-80) cc_final: 0.8812 (tpm-80) REVERT: A 551 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8078 (tp30) REVERT: A 560 ASP cc_start: 0.8942 (p0) cc_final: 0.8686 (p0) REVERT: C 139 MET cc_start: 0.7391 (tmm) cc_final: 0.6888 (mmm) REVERT: C 150 ARG cc_start: 0.6798 (ttp-170) cc_final: 0.6592 (mtp85) REVERT: C 218 ASP cc_start: 0.8674 (m-30) cc_final: 0.8389 (m-30) REVERT: C 336 GLU cc_start: 0.8561 (pp20) cc_final: 0.8229 (pm20) REVERT: E 123 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7227 (mm-30) REVERT: E 139 MET cc_start: 0.7367 (tmm) cc_final: 0.6942 (ttm) REVERT: E 217 MET cc_start: 0.7614 (ppp) cc_final: 0.7080 (pmm) REVERT: E 236 LYS cc_start: 0.8801 (mmpt) cc_final: 0.8549 (tppt) REVERT: E 338 ARG cc_start: 0.8042 (pmt-80) cc_final: 0.7703 (pmt-80) REVERT: E 547 ARG cc_start: 0.9138 (tpp80) cc_final: 0.8854 (tpp80) REVERT: E 551 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8449 (mm-30) REVERT: G 93 ARG cc_start: 0.8156 (tmt90) cc_final: 0.7764 (ptm-80) REVERT: G 123 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7116 (mm-30) REVERT: G 139 MET cc_start: 0.7448 (tmm) cc_final: 0.6916 (mmm) REVERT: G 217 MET cc_start: 0.7506 (ppp) cc_final: 0.7304 (pmm) REVERT: G 219 ARG cc_start: 0.6681 (tpm170) cc_final: 0.6440 (tpm170) REVERT: G 225 LYS cc_start: 0.9013 (mttt) cc_final: 0.8559 (mmmt) REVERT: G 236 LYS cc_start: 0.8749 (mmpt) cc_final: 0.8483 (tppt) REVERT: B 53 ASN cc_start: 0.8807 (t0) cc_final: 0.8383 (p0) REVERT: B 76 MET cc_start: 0.6460 (pmt) cc_final: 0.6061 (pmm) REVERT: B 100 ILE cc_start: 0.8754 (tp) cc_final: 0.8494 (pp) REVERT: B 116 LEU cc_start: 0.6586 (tp) cc_final: 0.6156 (tp) REVERT: B 124 MET cc_start: 0.7986 (ptt) cc_final: 0.7669 (ptt) REVERT: B 144 MET cc_start: 0.6868 (ppp) cc_final: 0.6607 (ppp) REVERT: D 71 MET cc_start: 0.8575 (mtt) cc_final: 0.7963 (mpt) REVERT: D 87 GLU cc_start: 0.9321 (tp30) cc_final: 0.8755 (tp30) REVERT: D 90 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8193 (ttp80) REVERT: D 99 TYR cc_start: 0.8728 (m-80) cc_final: 0.8102 (m-80) REVERT: D 116 LEU cc_start: 0.6691 (tp) cc_final: 0.6395 (tp) REVERT: D 144 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5732 (ppp) REVERT: F 53 ASN cc_start: 0.8710 (t0) cc_final: 0.8391 (p0) REVERT: F 71 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8126 (mpt) REVERT: F 126 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.5676 (ppt170) REVERT: F 141 PHE cc_start: 0.8550 (m-80) cc_final: 0.8281 (m-80) REVERT: F 144 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6041 (ppp) REVERT: H 53 ASN cc_start: 0.8663 (t0) cc_final: 0.8279 (p0) REVERT: H 68 PHE cc_start: 0.8192 (t80) cc_final: 0.7830 (t80) REVERT: H 71 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8316 (ptp) REVERT: H 116 LEU cc_start: 0.6771 (tp) cc_final: 0.6515 (tp) REVERT: H 144 MET cc_start: 0.6056 (OUTLIER) cc_final: 0.5298 (ppp) outliers start: 45 outliers final: 17 residues processed: 330 average time/residue: 0.6345 time to fit residues: 228.2772 Evaluate side-chains 307 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain A residue 350 TRP 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 533 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 107 HIS 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 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 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 115 LYS 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: 2.9990 chunk 125 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 GLN ** F 135 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 = 0.4763 r_free = 0.4763 target = 0.213659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.122314 restraints weight = 27281.049| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.73 r_work: 0.3094 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.7808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15664 Z= 0.177 Angle : 0.951 17.049 21144 Z= 0.463 Chirality : 0.044 0.344 2340 Planarity : 0.005 0.081 2664 Dihedral : 4.307 30.956 2160 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.33 % Rotamer: Outliers : 2.61 % Allowed : 30.85 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.40 (0.13), residues: 1432 sheet: None (None), residues: 0 loop : -1.41 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 74 TYR 0.016 0.001 TYR C 565 PHE 0.043 0.002 PHE D 68 TRP 0.020 0.001 TRP E 350 HIS 0.012 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00402 (15664) covalent geometry : angle 0.95071 (21144) hydrogen bonds : bond 0.04477 ( 1112) hydrogen bonds : angle 4.83514 ( 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 336 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 0.426 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: 0.7436 (mt-10) cc_final: 0.7062 (mm-30) REVERT: A 139 MET cc_start: 0.6787 (tmm) cc_final: 0.6322 (ttm) REVERT: A 150 ARG cc_start: 0.6990 (ttp-170) cc_final: 0.6578 (mtt90) REVERT: A 217 MET cc_start: 0.7690 (ppp) cc_final: 0.7374 (pmm) REVERT: A 225 LYS cc_start: 0.9009 (mttt) cc_final: 0.8538 (mmmt) REVERT: A 336 GLU cc_start: 0.8189 (pp20) cc_final: 0.7534 (pm20) REVERT: A 338 ARG cc_start: 0.8735 (pmt-80) cc_final: 0.8349 (pmm150) REVERT: A 344 ASN cc_start: 0.8845 (t0) cc_final: 0.8638 (p0) REVERT: A 350 TRP cc_start: 0.7464 (OUTLIER) cc_final: 0.6653 (m100) REVERT: C 139 MET cc_start: 0.7444 (tmm) cc_final: 0.7010 (ttm) REVERT: C 218 ASP cc_start: 0.8641 (m-30) cc_final: 0.8316 (m-30) REVERT: C 336 GLU cc_start: 0.8605 (pp20) cc_final: 0.8278 (pm20) REVERT: E 123 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7232 (mm-30) REVERT: E 139 MET cc_start: 0.7433 (tmm) cc_final: 0.6995 (ttm) REVERT: E 217 MET cc_start: 0.7643 (ppp) cc_final: 0.7090 (pmm) REVERT: E 236 LYS cc_start: 0.8787 (mmpt) cc_final: 0.8554 (tppt) REVERT: E 338 ARG cc_start: 0.8087 (pmt-80) cc_final: 0.7717 (pmt-80) REVERT: E 546 LYS cc_start: 0.9275 (pptt) cc_final: 0.9051 (pptt) REVERT: E 547 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8873 (tpp80) REVERT: G 123 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7062 (mm-30) REVERT: G 139 MET cc_start: 0.7522 (tmm) cc_final: 0.7007 (ttm) REVERT: G 219 ARG cc_start: 0.6740 (tpm170) cc_final: 0.6518 (tpm170) REVERT: G 225 LYS cc_start: 0.9007 (mttt) cc_final: 0.8542 (mmmt) REVERT: G 236 LYS cc_start: 0.8831 (mmpt) cc_final: 0.8589 (mptt) REVERT: G 336 GLU cc_start: 0.8741 (pp20) cc_final: 0.8346 (pm20) REVERT: G 338 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7262 (pmt-80) REVERT: G 546 LYS cc_start: 0.9316 (pptt) cc_final: 0.8986 (pttt) REVERT: G 554 ARG cc_start: 0.8412 (mmt180) cc_final: 0.7940 (mmp-170) REVERT: B 36 MET cc_start: 0.8384 (ptt) cc_final: 0.8153 (pmm) REVERT: B 62 THR cc_start: 0.5646 (p) cc_final: 0.5421 (p) REVERT: B 76 MET cc_start: 0.6484 (pmt) cc_final: 0.6112 (pmm) REVERT: B 115 LYS cc_start: 0.8887 (mttm) cc_final: 0.8653 (mmmm) REVERT: B 116 LEU cc_start: 0.6668 (tp) cc_final: 0.6298 (tp) REVERT: B 124 MET cc_start: 0.8026 (ptt) cc_final: 0.7709 (ptm) REVERT: B 144 MET cc_start: 0.6899 (ppp) cc_final: 0.6642 (ppp) REVERT: D 71 MET cc_start: 0.8605 (mtt) cc_final: 0.7990 (mpt) REVERT: D 87 GLU cc_start: 0.9317 (tp30) cc_final: 0.8773 (tp30) REVERT: D 90 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8221 (ttp80) REVERT: D 99 TYR cc_start: 0.8607 (m-80) cc_final: 0.8099 (m-80) REVERT: D 116 LEU cc_start: 0.6801 (tp) cc_final: 0.6518 (tp) REVERT: D 144 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5785 (ppp) REVERT: F 13 LYS cc_start: 0.8443 (tppt) cc_final: 0.7986 (mmtm) REVERT: F 53 ASN cc_start: 0.8749 (t0) cc_final: 0.8430 (p0) REVERT: F 71 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8141 (mpt) REVERT: F 126 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.5773 (ppt170) REVERT: F 141 PHE cc_start: 0.8539 (m-80) cc_final: 0.8246 (m-80) REVERT: F 144 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6023 (pp-130) REVERT: H 14 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8663 (pp20) REVERT: H 53 ASN cc_start: 0.8677 (t0) cc_final: 0.8256 (p0) REVERT: H 71 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8298 (ptp) REVERT: H 72 MET cc_start: 0.8207 (mtp) cc_final: 0.7961 (mpp) REVERT: H 99 TYR cc_start: 0.8518 (m-80) cc_final: 0.8079 (m-80) REVERT: H 116 LEU cc_start: 0.6878 (tp) cc_final: 0.6622 (tp) REVERT: H 144 MET cc_start: 0.5960 (OUTLIER) cc_final: 0.5204 (ppp) outliers start: 42 outliers final: 16 residues processed: 313 average time/residue: 0.6091 time to fit residues: 208.5969 Evaluate side-chains 316 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain A residue 350 TRP 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 533 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain G residue 338 ARG 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 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 115 LYS 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: 9.9990 chunk 166 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 0.0870 overall best weight: 1.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 GLN E 329 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.212470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120480 restraints weight = 27110.042| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.97 r_work: 0.3063 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.7965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15664 Z= 0.195 Angle : 0.963 17.030 21144 Z= 0.468 Chirality : 0.045 0.311 2340 Planarity : 0.005 0.068 2664 Dihedral : 4.340 25.235 2160 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.17 % Rotamer: Outliers : 2.30 % Allowed : 31.65 % Favored : 66.04 % 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: 0.90 (0.19), residues: 1864 helix: 1.23 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.52 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 93 TYR 0.015 0.001 TYR C 565 PHE 0.047 0.002 PHE D 68 TRP 0.017 0.001 TRP E 350 HIS 0.012 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00450 (15664) covalent geometry : angle 0.96288 (21144) hydrogen bonds : bond 0.04598 ( 1112) hydrogen bonds : angle 4.90056 ( 3324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10031.83 seconds wall clock time: 170 minutes 44.61 seconds (10244.61 seconds total)