Starting phenix.real_space_refine on Fri Sep 11 22:10:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p5a_20254/09_2026/6p5a_20254.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p5a_20254/09_2026/6p5a_20254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6p5a_20254/09_2026/6p5a_20254.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p5a_20254/09_2026/6p5a_20254.cif" model { file = "/net/cci-nas-00/data/ceres_data/6p5a_20254/09_2026/6p5a_20254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p5a_20254/09_2026/6p5a_20254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p5a_20254/09_2026/6p5a_20254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p5a_20254/09_2026/6p5a_20254.map" } resolution = 3.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 142 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7150 2.51 5 N 2076 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11948 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3568 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 428} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "G" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3568 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 428} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "J" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.83, per 1000 atoms: 0.24 Number of scatterers: 11948 At special positions: 0 Unit cell: (126.44, 110.2, 106.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 142 15.00 Mg 4 11.99 O 2540 8.00 N 2076 7.00 C 7150 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 478.4 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 58.7% alpha, 8.2% beta 54 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.673A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.790A pdb=" N HIS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.808A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.567A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.558A pdb=" N SER A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.949A pdb=" N ILE A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.820A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.376A pdb=" N ASP A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 515 Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.974A pdb=" N ASN A 526 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 548 through 563 removed outlier: 3.515A pdb=" N ARG A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 568 removed outlier: 3.792A pdb=" N MET A 567 " --> pdb=" O ASN A 564 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 568 " --> pdb=" O THR A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 564 through 568' Processing helix chain 'B' and resid 620 through 639 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.711A pdb=" N SER B 657 " --> pdb=" O VAL B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 708 through 734 removed outlier: 3.626A pdb=" N LYS B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 140 removed outlier: 3.673A pdb=" N GLU G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 149 Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'G' and resid 172 through 183 removed outlier: 3.791A pdb=" N HIS G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 197 Processing helix chain 'G' and resid 206 through 213 removed outlier: 3.807A pdb=" N ILE G 210 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET G 213 " --> pdb=" O VAL G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 294 Processing helix chain 'G' and resid 305 through 315 removed outlier: 3.568A pdb=" N LEU G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 354 removed outlier: 3.557A pdb=" N SER G 354 " --> pdb=" O HIS G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 376 Processing helix chain 'G' and resid 387 through 392 removed outlier: 3.950A pdb=" N ILE G 391 " --> pdb=" O ASN G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 408 removed outlier: 3.820A pdb=" N ALA G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 422 Processing helix chain 'G' and resid 428 through 446 Processing helix chain 'G' and resid 465 through 480 removed outlier: 4.377A pdb=" N ASP G 471 " --> pdb=" O ASP G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 491 through 515 Processing helix chain 'G' and resid 521 through 526 removed outlier: 3.974A pdb=" N ASN G 526 " --> pdb=" O SER G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 540 Processing helix chain 'G' and resid 548 through 563 removed outlier: 3.514A pdb=" N ARG G 563 " --> pdb=" O TYR G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 568 removed outlier: 3.792A pdb=" N MET G 567 " --> pdb=" O ASN G 564 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU G 568 " --> pdb=" O THR G 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 564 through 568' Processing helix chain 'H' and resid 620 through 639 Processing helix chain 'H' and resid 652 through 657 removed outlier: 3.711A pdb=" N SER H 657 " --> pdb=" O VAL H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 667 through 682 Processing helix chain 'H' and resid 693 through 702 Processing helix chain 'H' and resid 708 through 734 removed outlier: 3.626A pdb=" N LYS H 712 " --> pdb=" O ASP H 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 205 removed outlier: 6.491A pdb=" N ALA A 257 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 272 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN A 255 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE A 274 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR A 253 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS A 225 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 300 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 227 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER A 302 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 229 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N LEU A 296 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N PHE A 335 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 298 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE A 337 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 300 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.796A pdb=" N ILE A 246 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA4, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.491A pdb=" N ALA G 257 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE G 272 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN G 255 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE G 274 " --> pdb=" O TYR G 253 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR G 253 " --> pdb=" O PHE G 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS G 225 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE G 300 " --> pdb=" O CYS G 225 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU G 227 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER G 302 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE G 229 " --> pdb=" O SER G 302 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N LEU G 296 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N PHE G 335 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL G 298 " --> pdb=" O PHE G 335 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE G 337 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE G 300 " --> pdb=" O PHE G 337 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 239 through 241 removed outlier: 3.795A pdb=" N ILE G 246 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 356 through 358 475 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 256 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2863 1.34 - 1.45: 3084 1.45 - 1.57: 6177 1.57 - 1.69: 274 1.69 - 1.81: 56 Bond restraints: 12454 Sorted by residual: bond pdb=" C3' DT E -2 " pdb=" C2' DT E -2 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C3' DT K -2 " pdb=" C2' DT K -2 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.36e+01 bond pdb=" C3' DC E -23 " pdb=" C2' DC E -23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC K -23 " pdb=" C2' DC K -23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT C 6 " pdb=" C2' DT C 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 12449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 16077 1.09 - 2.19: 1013 2.19 - 3.28: 272 3.28 - 4.38: 26 4.38 - 5.47: 10 Bond angle restraints: 17398 Sorted by residual: angle pdb=" O5' DT E -2 " pdb=" C5' DT E -2 " pdb=" C4' DT E -2 " ideal model delta sigma weight residual 109.40 113.26 -3.86 8.00e-01 1.56e+00 2.33e+01 angle pdb=" O5' DT K -2 " pdb=" C5' DT K -2 " pdb=" C4' DT K -2 " ideal model delta sigma weight residual 109.40 113.23 -3.83 8.00e-01 1.56e+00 2.29e+01 angle pdb=" C4' DA K -3 " pdb=" C3' DA K -3 " pdb=" C2' DA K -3 " ideal model delta sigma weight residual 103.10 107.10 -4.00 9.00e-01 1.23e+00 1.98e+01 angle pdb=" C4' DA E -3 " pdb=" C3' DA E -3 " pdb=" C2' DA E -3 " ideal model delta sigma weight residual 103.10 107.10 -4.00 9.00e-01 1.23e+00 1.97e+01 angle pdb=" N3 DT J 4 " pdb=" C4 DT J 4 " pdb=" O4 DT J 4 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 ... (remaining 17393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.76: 6564 34.76 - 69.51: 518 69.51 - 104.27: 12 104.27 - 139.02: 4 139.02 - 173.78: 6 Dihedral angle restraints: 7104 sinusoidal: 3798 harmonic: 3306 Sorted by residual: dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -31.60 136.20 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C8 GTP G 602 " pdb=" C1' GTP G 602 " pdb=" N9 GTP G 602 " pdb=" O4' GTP G 602 " ideal model delta sinusoidal sigma weight residual 104.59 -31.56 136.16 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C4' DT E -13 " pdb=" C3' DT E -13 " pdb=" O3' DT E -13 " pdb=" P DT E -12 " ideal model delta sinusoidal sigma weight residual -140.00 33.78 -173.78 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1670 0.062 - 0.124: 259 0.124 - 0.185: 15 0.185 - 0.247: 0 0.247 - 0.309: 2 Chirality restraints: 1946 Sorted by residual: chirality pdb=" C3' DA K -3 " pdb=" C4' DA K -3 " pdb=" O3' DA K -3 " pdb=" C2' DA K -3 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' DA E -3 " pdb=" C4' DA E -3 " pdb=" O3' DA E -3 " pdb=" C2' DA E -3 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' DC K -4 " pdb=" C4' DC K -4 " pdb=" O3' DC K -4 " pdb=" C2' DC K -4 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 1943 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN G 268 " -0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO G 269 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 269 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 269 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 268 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 269 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 172 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO G 173 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " 0.023 5.00e-02 4.00e+02 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 30 2.49 - 3.09: 7784 3.09 - 3.70: 18319 3.70 - 4.30: 27816 4.30 - 4.90: 43456 Nonbonded interactions: 97405 Sorted by model distance: nonbonded pdb=" OD1 ASN A 440 " pdb="MG MG A 602 " model vdw 1.890 2.170 nonbonded pdb=" OD1 ASN G 440 " pdb="MG MG G 603 " model vdw 1.907 2.170 nonbonded pdb=" O3' DA I 9 " pdb="MG MG G 601 " model vdw 2.077 2.170 nonbonded pdb=" O3' DA C 9 " pdb="MG MG A 603 " model vdw 2.078 2.170 nonbonded pdb=" OD2 ASP A 303 " pdb="MG MG A 603 " model vdw 2.135 2.170 ... (remaining 97400 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 128 through 569 or resid 603)) selection = (chain 'G' and (resid 128 through 569 or resid 603)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.150 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.220 Find NCS groups from input model: 0.220 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.008 0.587 12456 Z= 0.831 Angle : 0.614 5.475 17398 Z= 0.513 Chirality : 0.044 0.309 1946 Planarity : 0.004 0.052 1730 Dihedral : 20.140 173.780 4960 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.69 (0.22), residues: 1112 helix: -0.46 (0.18), residues: 622 sheet: -2.11 (0.47), residues: 60 loop : -1.85 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 569 TYR 0.008 0.001 TYR H 629 PHE 0.014 0.001 PHE A 272 TRP 0.005 0.001 TRP G 442 HIS 0.002 0.001 HIS G 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.37 (12454) covalent geometry : angle 0.61437 / 0.51 (17398) hydrogen bonds : bond 0.14780 / 9.71 ( 613) hydrogen bonds : angle 5.33899 / 3.74 ( 1645) Misc. bond : bond 0.58555 / 29.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.408 Fit side-chains REVERT: A 273 ASP cc_start: 0.7712 (t70) cc_final: 0.7431 (t0) REVERT: A 476 MET cc_start: 0.8351 (tpp) cc_final: 0.7613 (tpt) REVERT: A 563 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.6941 (ptm160) REVERT: A 567 MET cc_start: 0.7410 (tpp) cc_final: 0.7162 (tpt) REVERT: B 700 LEU cc_start: 0.8528 (tt) cc_final: 0.7510 (mt) REVERT: G 239 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7746 (mm-30) REVERT: G 273 ASP cc_start: 0.7731 (t70) cc_final: 0.7448 (t0) REVERT: G 476 MET cc_start: 0.8359 (tpp) cc_final: 0.7616 (tpt) REVERT: G 563 ARG cc_start: 0.7331 (ptm-80) cc_final: 0.6945 (ptm160) REVERT: G 567 MET cc_start: 0.7427 (tpp) cc_final: 0.7144 (tpt) REVERT: H 700 LEU cc_start: 0.8525 (tt) cc_final: 0.7502 (mt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1297 time to fit residues: 40.9790 Evaluate side-chains 134 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 169 HIS A 546 HIS B 669 GLN B 684 ASN B 685 ASN B 686 ASN G 150 ASN G 169 HIS G 546 HIS H 669 GLN H 684 ASN H 685 ASN H 686 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117891 restraints weight = 14839.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121729 restraints weight = 8844.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124377 restraints weight = 6248.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126199 restraints weight = 4914.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127443 restraints weight = 4148.431| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12456 Z= 0.159 Angle : 0.594 6.145 17398 Z= 0.344 Chirality : 0.040 0.148 1946 Planarity : 0.004 0.050 1730 Dihedral : 24.749 171.506 2698 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.39 % Allowed : 9.13 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.40 (0.24), residues: 1112 helix: 0.65 (0.20), residues: 628 sheet: -0.82 (0.57), residues: 58 loop : -1.53 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 277 TYR 0.016 0.001 TYR A 559 PHE 0.010 0.001 PHE A 324 TRP 0.004 0.001 TRP A 312 HIS 0.002 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (12454) covalent geometry : angle 0.59428 / 0.34 (17398) hydrogen bonds : bond 0.05382 / 3.54 ( 613) hydrogen bonds : angle 4.01700 / 2.80 ( 1645) Misc. bond : bond 0.00501 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.395 Fit side-chains REVERT: A 370 GLU cc_start: 0.7594 (tt0) cc_final: 0.7234 (tt0) REVERT: A 398 LYS cc_start: 0.8404 (pttt) cc_final: 0.7890 (ptpp) REVERT: A 476 MET cc_start: 0.8337 (tpp) cc_final: 0.7727 (tpt) REVERT: A 563 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.6934 (ptm-80) REVERT: B 674 GLU cc_start: 0.7685 (tp30) cc_final: 0.7380 (tp30) REVERT: B 696 GLU cc_start: 0.7998 (tp30) cc_final: 0.7711 (tm-30) REVERT: G 370 GLU cc_start: 0.7625 (tt0) cc_final: 0.7282 (tt0) REVERT: G 398 LYS cc_start: 0.8421 (pttt) cc_final: 0.7874 (ptpp) REVERT: G 476 MET cc_start: 0.8342 (tpp) cc_final: 0.7711 (tpt) REVERT: G 559 TYR cc_start: 0.8252 (t80) cc_final: 0.8020 (t80) REVERT: H 674 GLU cc_start: 0.7675 (tp30) cc_final: 0.7379 (tp30) REVERT: H 696 GLU cc_start: 0.7999 (tp30) cc_final: 0.7715 (tm-30) outliers start: 14 outliers final: 2 residues processed: 152 average time/residue: 0.1028 time to fit residues: 22.6436 Evaluate side-chains 133 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain H residue 680 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116113 restraints weight = 15028.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119857 restraints weight = 8921.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122463 restraints weight = 6332.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124228 restraints weight = 4992.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125490 restraints weight = 4235.121| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12456 Z= 0.150 Angle : 0.559 9.093 17398 Z= 0.318 Chirality : 0.039 0.130 1946 Planarity : 0.004 0.051 1730 Dihedral : 25.130 172.234 2698 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.09 % Allowed : 11.41 % Favored : 87.50 % 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: 0.23 (0.24), residues: 1112 helix: 1.15 (0.20), residues: 628 sheet: -0.25 (0.56), residues: 58 loop : -1.29 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 563 TYR 0.018 0.001 TYR A 559 PHE 0.009 0.001 PHE G 493 TRP 0.004 0.001 TRP A 312 HIS 0.003 0.001 HIS G 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (12454) covalent geometry : angle 0.55928 / 0.32 (17398) hydrogen bonds : bond 0.04809 / 3.18 ( 613) hydrogen bonds : angle 3.77917 / 2.64 ( 1645) Misc. bond : bond 0.00400 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.459 Fit side-chains REVERT: A 563 ARG cc_start: 0.6987 (ptm-80) cc_final: 0.6642 (ptm160) REVERT: B 674 GLU cc_start: 0.7751 (tp30) cc_final: 0.7432 (tp30) REVERT: B 696 GLU cc_start: 0.8039 (tp30) cc_final: 0.7694 (tm-30) REVERT: G 239 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7706 (mm-30) REVERT: H 674 GLU cc_start: 0.7699 (tp30) cc_final: 0.7398 (tp30) REVERT: H 696 GLU cc_start: 0.8041 (tp30) cc_final: 0.7706 (tm-30) outliers start: 11 outliers final: 8 residues processed: 140 average time/residue: 0.1053 time to fit residues: 22.0995 Evaluate side-chains 130 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 680 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115319 restraints weight = 15043.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118815 restraints weight = 9215.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121271 restraints weight = 6641.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122953 restraints weight = 5293.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124187 restraints weight = 4503.827| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12456 Z= 0.143 Angle : 0.535 7.167 17398 Z= 0.308 Chirality : 0.038 0.135 1946 Planarity : 0.004 0.056 1730 Dihedral : 25.052 172.824 2698 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % 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: 0.53 (0.25), residues: 1112 helix: 1.39 (0.20), residues: 628 sheet: -0.18 (0.52), residues: 72 loop : -1.18 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 475 TYR 0.018 0.001 TYR G 559 PHE 0.010 0.001 PHE A 493 TRP 0.003 0.001 TRP G 312 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (12454) covalent geometry : angle 0.53535 / 0.31 (17398) hydrogen bonds : bond 0.04500 / 2.96 ( 613) hydrogen bonds : angle 3.67591 / 2.56 ( 1645) Misc. bond : bond 0.00007 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.394 Fit side-chains REVERT: A 370 GLU cc_start: 0.7727 (tt0) cc_final: 0.7385 (tt0) REVERT: A 563 ARG cc_start: 0.6992 (ptm-80) cc_final: 0.6475 (ptm-80) REVERT: B 696 GLU cc_start: 0.8031 (tp30) cc_final: 0.7677 (tm-30) REVERT: G 239 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7693 (mm-30) REVERT: G 370 GLU cc_start: 0.7750 (tt0) cc_final: 0.7414 (tt0) REVERT: G 476 MET cc_start: 0.8103 (tpp) cc_final: 0.7579 (tpt) REVERT: G 559 TYR cc_start: 0.8259 (t80) cc_final: 0.8045 (t80) REVERT: H 696 GLU cc_start: 0.8031 (tp30) cc_final: 0.7690 (tm-30) outliers start: 12 outliers final: 10 residues processed: 131 average time/residue: 0.1068 time to fit residues: 20.7372 Evaluate side-chains 132 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 680 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113754 restraints weight = 15124.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117388 restraints weight = 9090.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119923 restraints weight = 6474.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121708 restraints weight = 5130.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122905 restraints weight = 4349.773| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12456 Z= 0.164 Angle : 0.554 6.813 17398 Z= 0.314 Chirality : 0.039 0.150 1946 Planarity : 0.004 0.064 1730 Dihedral : 25.050 172.460 2698 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.59 % Allowed : 12.80 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.74 (0.25), residues: 1112 helix: 1.50 (0.20), residues: 632 sheet: -0.04 (0.55), residues: 72 loop : -1.00 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 538 TYR 0.021 0.001 TYR A 559 PHE 0.011 0.001 PHE A 324 TRP 0.006 0.001 TRP A 312 HIS 0.004 0.001 HIS G 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (12454) covalent geometry : angle 0.55421 / 0.31 (17398) hydrogen bonds : bond 0.04645 / 3.06 ( 613) hydrogen bonds : angle 3.61162 / 2.51 ( 1645) Misc. bond : bond 0.00217 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.423 Fit side-chains REVERT: A 563 ARG cc_start: 0.7159 (ptm-80) cc_final: 0.6771 (ptp90) REVERT: B 696 GLU cc_start: 0.8009 (tp30) cc_final: 0.7729 (tm-30) REVERT: G 239 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7705 (mm-30) REVERT: G 370 GLU cc_start: 0.7693 (tt0) cc_final: 0.7280 (tt0) REVERT: G 476 MET cc_start: 0.8303 (tpp) cc_final: 0.7955 (tpt) REVERT: H 696 GLU cc_start: 0.8010 (tp30) cc_final: 0.7742 (tm-30) outliers start: 16 outliers final: 10 residues processed: 140 average time/residue: 0.1071 time to fit residues: 22.1860 Evaluate side-chains 133 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 680 LEU Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 HIS G 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114374 restraints weight = 15070.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118005 restraints weight = 9027.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120573 restraints weight = 6425.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122207 restraints weight = 5075.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123488 restraints weight = 4324.708| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12456 Z= 0.148 Angle : 0.537 6.490 17398 Z= 0.306 Chirality : 0.038 0.159 1946 Planarity : 0.004 0.058 1730 Dihedral : 24.954 172.847 2698 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.08 % Allowed : 12.60 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1112 helix: 1.59 (0.20), residues: 634 sheet: -0.04 (0.55), residues: 72 loop : -0.86 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 555 TYR 0.026 0.001 TYR G 559 PHE 0.011 0.001 PHE G 493 TRP 0.003 0.001 TRP A 312 HIS 0.003 0.001 HIS G 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (12454) covalent geometry : angle 0.53739 / 0.31 (17398) hydrogen bonds : bond 0.04340 / 2.85 ( 613) hydrogen bonds : angle 3.60351 / 2.52 ( 1645) Misc. bond : bond 0.00185 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.415 Fit side-chains REVERT: A 563 ARG cc_start: 0.7230 (ptm-80) cc_final: 0.6738 (ptp90) REVERT: B 696 GLU cc_start: 0.8015 (tp30) cc_final: 0.7753 (tm-30) REVERT: G 239 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7679 (mm-30) REVERT: G 245 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: G 370 GLU cc_start: 0.7713 (tt0) cc_final: 0.7380 (tt0) REVERT: G 476 MET cc_start: 0.8304 (tpp) cc_final: 0.8051 (tpt) REVERT: G 563 ARG cc_start: 0.7053 (ptm-80) cc_final: 0.6252 (ptp90) REVERT: H 696 GLU cc_start: 0.8012 (tp30) cc_final: 0.7753 (tm-30) outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 0.1064 time to fit residues: 21.8716 Evaluate side-chains 137 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 568 LEU Chi-restraints excluded: chain H residue 680 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115240 restraints weight = 14938.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118856 restraints weight = 9082.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121235 restraints weight = 6506.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123009 restraints weight = 5196.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124066 restraints weight = 4425.950| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12456 Z= 0.126 Angle : 0.532 6.879 17398 Z= 0.304 Chirality : 0.038 0.143 1946 Planarity : 0.003 0.052 1730 Dihedral : 24.845 173.202 2698 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.59 % Allowed : 13.89 % Favored : 84.52 % 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: 1.09 (0.26), residues: 1112 helix: 1.73 (0.20), residues: 634 sheet: 0.16 (0.55), residues: 72 loop : -0.76 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 555 TYR 0.018 0.001 TYR A 559 PHE 0.009 0.001 PHE G 493 TRP 0.002 0.000 TRP A 312 HIS 0.002 0.001 HIS G 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (12454) covalent geometry : angle 0.53167 / 0.30 (17398) hydrogen bonds : bond 0.04056 / 2.66 ( 613) hydrogen bonds : angle 3.51695 / 2.46 ( 1645) Misc. bond : bond 0.00160 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.416 Fit side-chains REVERT: A 563 ARG cc_start: 0.7385 (ptm-80) cc_final: 0.6694 (ptp90) REVERT: B 696 GLU cc_start: 0.7984 (tp30) cc_final: 0.7768 (tm-30) REVERT: G 239 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7646 (mm-30) REVERT: G 245 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: G 370 GLU cc_start: 0.7702 (tt0) cc_final: 0.7361 (tt0) REVERT: G 476 MET cc_start: 0.8251 (tpp) cc_final: 0.7996 (tpt) REVERT: G 563 ARG cc_start: 0.7181 (ptm-80) cc_final: 0.6458 (ptp90) REVERT: H 696 GLU cc_start: 0.7993 (tp30) cc_final: 0.7780 (tm-30) outliers start: 16 outliers final: 10 residues processed: 129 average time/residue: 0.1079 time to fit residues: 20.5549 Evaluate side-chains 133 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 680 LEU Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114969 restraints weight = 15007.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118518 restraints weight = 9250.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120935 restraints weight = 6660.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122633 restraints weight = 5325.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123715 restraints weight = 4545.507| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12456 Z= 0.134 Angle : 0.529 7.272 17398 Z= 0.301 Chirality : 0.038 0.133 1946 Planarity : 0.003 0.049 1730 Dihedral : 24.817 172.581 2698 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.39 % Allowed : 14.38 % Favored : 84.23 % 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: 1.18 (0.26), residues: 1112 helix: 1.77 (0.21), residues: 636 sheet: 0.16 (0.55), residues: 72 loop : -0.68 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 540 TYR 0.018 0.001 TYR G 559 PHE 0.009 0.001 PHE G 324 TRP 0.004 0.001 TRP A 312 HIS 0.003 0.000 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (12454) covalent geometry : angle 0.52926 / 0.30 (17398) hydrogen bonds : bond 0.04123 / 2.70 ( 613) hydrogen bonds : angle 3.48504 / 2.43 ( 1645) Misc. bond : bond 0.00165 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.404 Fit side-chains REVERT: A 563 ARG cc_start: 0.7362 (ptm-80) cc_final: 0.6726 (ptp90) REVERT: B 696 GLU cc_start: 0.7979 (tp30) cc_final: 0.7765 (tm-30) REVERT: G 245 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: G 370 GLU cc_start: 0.7732 (tt0) cc_final: 0.7417 (tt0) REVERT: G 563 ARG cc_start: 0.7198 (ptm-80) cc_final: 0.6522 (ptp90) REVERT: H 696 GLU cc_start: 0.7989 (tp30) cc_final: 0.7782 (tm-30) outliers start: 14 outliers final: 11 residues processed: 133 average time/residue: 0.1089 time to fit residues: 21.4745 Evaluate side-chains 133 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 680 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 0.0370 chunk 100 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112409 restraints weight = 15062.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115994 restraints weight = 9254.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118495 restraints weight = 6666.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120114 restraints weight = 5317.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121286 restraints weight = 4553.470| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12456 Z= 0.140 Angle : 0.536 7.941 17398 Z= 0.304 Chirality : 0.038 0.133 1946 Planarity : 0.003 0.047 1730 Dihedral : 24.812 172.186 2698 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.79 % Allowed : 14.68 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1112 helix: 1.78 (0.20), residues: 634 sheet: 0.10 (0.55), residues: 72 loop : -0.66 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 146 TYR 0.017 0.001 TYR A 559 PHE 0.010 0.001 PHE A 493 TRP 0.004 0.001 TRP G 312 HIS 0.003 0.000 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (12454) covalent geometry : angle 0.53649 / 0.30 (17398) hydrogen bonds : bond 0.04139 / 2.72 ( 613) hydrogen bonds : angle 3.47978 / 2.43 ( 1645) Misc. bond : bond 0.00164 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.437 Fit side-chains REVERT: A 563 ARG cc_start: 0.7390 (ptm-80) cc_final: 0.6798 (ptp90) REVERT: A 566 GLU cc_start: 0.7965 (tp30) cc_final: 0.7718 (tp30) REVERT: B 696 GLU cc_start: 0.7986 (tp30) cc_final: 0.7767 (tm-30) REVERT: G 245 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: G 370 GLU cc_start: 0.7768 (tt0) cc_final: 0.7463 (tt0) REVERT: G 476 MET cc_start: 0.8126 (tpp) cc_final: 0.7564 (tpt) REVERT: G 563 ARG cc_start: 0.7190 (ptm-80) cc_final: 0.6523 (ptp90) REVERT: H 696 GLU cc_start: 0.7998 (tp30) cc_final: 0.7779 (tm-30) outliers start: 18 outliers final: 13 residues processed: 142 average time/residue: 0.1135 time to fit residues: 23.3992 Evaluate side-chains 135 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 680 LEU Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114586 restraints weight = 15089.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118100 restraints weight = 9347.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120543 restraints weight = 6776.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122197 restraints weight = 5415.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123228 restraints weight = 4635.032| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12456 Z= 0.145 Angle : 0.549 7.640 17398 Z= 0.308 Chirality : 0.038 0.131 1946 Planarity : 0.003 0.042 1730 Dihedral : 24.810 171.973 2698 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.79 % Allowed : 14.58 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 1112 helix: 1.72 (0.20), residues: 638 sheet: 0.18 (0.55), residues: 72 loop : -0.63 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 146 TYR 0.017 0.001 TYR G 559 PHE 0.009 0.001 PHE A 324 TRP 0.004 0.001 TRP G 312 HIS 0.003 0.000 HIS G 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (12454) covalent geometry : angle 0.54867 / 0.31 (17398) hydrogen bonds : bond 0.04144 / 2.72 ( 613) hydrogen bonds : angle 3.47073 / 2.43 ( 1645) Misc. bond : bond 0.00162 / 0.08 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.438 Fit side-chains REVERT: A 245 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: A 563 ARG cc_start: 0.7364 (ptm-80) cc_final: 0.6751 (ptp90) REVERT: A 566 GLU cc_start: 0.7909 (tp30) cc_final: 0.7673 (tp30) REVERT: B 696 GLU cc_start: 0.7952 (tp30) cc_final: 0.7745 (tm-30) REVERT: G 245 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: G 370 GLU cc_start: 0.7804 (tt0) cc_final: 0.7470 (tt0) REVERT: G 476 MET cc_start: 0.8153 (tpp) cc_final: 0.7758 (tpt) REVERT: G 563 ARG cc_start: 0.7198 (ptm-80) cc_final: 0.6496 (ptp90) REVERT: H 696 GLU cc_start: 0.7923 (tp30) cc_final: 0.7711 (tm-30) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.1142 time to fit residues: 21.4153 Evaluate side-chains 136 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 680 LEU Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 9.9990 chunk 53 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115640 restraints weight = 14914.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119351 restraints weight = 9039.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121930 restraints weight = 6469.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123684 restraints weight = 5127.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124785 restraints weight = 4351.168| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12456 Z= 0.137 Angle : 0.542 7.725 17398 Z= 0.305 Chirality : 0.038 0.135 1946 Planarity : 0.003 0.041 1730 Dihedral : 24.783 172.037 2698 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.69 % Allowed : 14.48 % Favored : 83.83 % 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: 1.21 (0.26), residues: 1112 helix: 1.75 (0.20), residues: 638 sheet: 0.23 (0.55), residues: 72 loop : -0.60 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 146 TYR 0.017 0.001 TYR G 559 PHE 0.009 0.001 PHE A 493 TRP 0.004 0.001 TRP G 312 HIS 0.003 0.000 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (12454) covalent geometry : angle 0.54204 / 0.30 (17398) hydrogen bonds : bond 0.04084 / 2.68 ( 613) hydrogen bonds : angle 3.43878 / 2.41 ( 1645) Misc. bond : bond 0.00152 / 0.08 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.77 seconds wall clock time: 33 minutes 18.74 seconds (1998.74 seconds total)