Starting phenix.real_space_refine on Wed Mar 4 07:42:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p5a_20254/03_2026/6p5a_20254.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p5a_20254/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6p5a_20254/03_2026/6p5a_20254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p5a_20254/03_2026/6p5a_20254.map" model { file = "/net/cci-nas-00/data/ceres_data/6p5a_20254/03_2026/6p5a_20254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p5a_20254/03_2026/6p5a_20254.cif" } 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-dev-5986/lib/python3.9/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: 2.94, per 1000 atoms: 0.25 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: 1.01 Conformation dependent library (CDL) restraints added in 487.9 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: 1.44 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: 2.33 Time building geometry restraints manager: 1.32 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=" C THR A 548 " pdb=" N PRO A 549 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.90e+00 bond pdb=" C THR G 548 " pdb=" N PRO G 549 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.85e+00 bond pdb=" C3' DT E -2 " pdb=" C2' DT E -2 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.08e+00 bond pdb=" C3' DT K -2 " pdb=" C2' DT K -2 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.05e+00 bond pdb=" O5' DA E -3 " pdb=" C5' DA E -3 " ideal model delta sigma weight residual 1.423 1.394 0.029 3.00e-02 1.11e+03 9.50e-01 ... (remaining 12449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 16522 1.09 - 2.19: 692 2.19 - 3.28: 152 3.28 - 4.38: 20 4.38 - 5.47: 12 Bond angle restraints: 17398 Sorted by residual: angle pdb=" C4' DA K -3 " pdb=" C3' DA K -3 " pdb=" C2' DA K -3 " ideal model delta sigma weight residual 102.40 107.10 -4.70 1.50e+00 4.44e-01 9.83e+00 angle pdb=" C4' DA E -3 " pdb=" C3' DA E -3 " pdb=" C2' DA E -3 " ideal model delta sigma weight residual 102.40 107.10 -4.70 1.50e+00 4.44e-01 9.80e+00 angle pdb=" C3' DA K -3 " pdb=" O3' DA K -3 " pdb=" P DT K -2 " ideal model delta sigma weight residual 120.20 116.46 3.74 1.50e+00 4.44e-01 6.21e+00 angle pdb=" C3' DA E -3 " pdb=" O3' DA E -3 " pdb=" P DT E -2 " ideal model delta sigma weight residual 120.20 116.46 3.74 1.50e+00 4.44e-01 6.21e+00 angle pdb=" C4 DT E -13 " pdb=" C5 DT E -13 " pdb=" C7 DT E -13 " ideal model delta sigma weight residual 122.40 118.97 3.43 1.50e+00 4.44e-01 5.23e+00 ... (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 - 0.048: 1645 0.048 - 0.095: 241 0.095 - 0.143: 55 0.143 - 0.191: 3 0.191 - 0.239: 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 -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.42e+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 -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO G 549 " pdb=" N PRO G 549 " pdb=" C PRO G 549 " pdb=" CB PRO G 549 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-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: 1.170 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.350 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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= 0.753 Angle : 0.526 5.475 17398 Z= 0.316 Chirality : 0.037 0.239 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 covalent geometry : bond 0.00263 (12454) covalent geometry : angle 0.52604 (17398) hydrogen bonds : bond 0.14780 ( 613) hydrogen bonds : angle 5.33899 ( 1645) Misc. bond : bond 0.58555 ( 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 : 0.385 Fit side-chains REVERT: A 273 ASP cc_start: 0.7712 (t70) cc_final: 0.7429 (t0) REVERT: A 476 MET cc_start: 0.8351 (tpp) cc_final: 0.7614 (tpt) REVERT: A 563 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.6931 (ptm160) REVERT: A 567 MET cc_start: 0.7410 (tpp) cc_final: 0.7168 (tpt) REVERT: B 700 LEU cc_start: 0.8528 (tt) cc_final: 0.7512 (mt) REVERT: G 239 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7741 (mm-30) REVERT: G 273 ASP cc_start: 0.7731 (t70) cc_final: 0.7445 (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: 0.6935 (ptm160) REVERT: G 567 MET cc_start: 0.7427 (tpp) cc_final: 0.7150 (tpt) REVERT: H 700 LEU cc_start: 0.8525 (tt) cc_final: 0.7504 (mt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1339 time to fit residues: 41.7284 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 : 0.368 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.0970 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 399 GLN A 546 HIS B 669 GLN B 684 ASN B 685 ASN B 686 ASN G 150 ASN G 546 HIS H 669 GLN H 684 ASN H 685 ASN H 686 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118069 restraints weight = 14759.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121902 restraints weight = 8850.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124517 restraints weight = 6282.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126314 restraints weight = 4953.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127559 restraints weight = 4187.701| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12456 Z= 0.138 Angle : 0.509 6.236 17398 Z= 0.288 Chirality : 0.036 0.128 1946 Planarity : 0.004 0.047 1730 Dihedral : 24.848 175.026 2698 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.19 % Allowed : 9.42 % Favored : 89.38 % 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: -0.20 (0.24), residues: 1112 helix: 0.81 (0.20), residues: 628 sheet: -0.96 (0.50), residues: 72 loop : -1.41 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 189 TYR 0.016 0.001 TYR A 559 PHE 0.011 0.001 PHE A 140 TRP 0.005 0.001 TRP G 266 HIS 0.002 0.000 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00302 (12454) covalent geometry : angle 0.50922 (17398) hydrogen bonds : bond 0.04134 ( 613) hydrogen bonds : angle 3.72330 ( 1645) Misc. bond : bond 0.00126 ( 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 167 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.376 Fit side-chains REVERT: A 310 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8573 (ttpp) REVERT: A 398 LYS cc_start: 0.8442 (pttt) cc_final: 0.7961 (ptpp) REVERT: A 476 MET cc_start: 0.8355 (tpp) cc_final: 0.7806 (tpt) REVERT: A 559 TYR cc_start: 0.8315 (t80) cc_final: 0.8082 (t80) REVERT: B 674 GLU cc_start: 0.7648 (tp30) cc_final: 0.7308 (tp30) REVERT: G 310 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8567 (ttpp) REVERT: G 476 MET cc_start: 0.8277 (tpp) cc_final: 0.7733 (tpt) REVERT: G 559 TYR cc_start: 0.8299 (t80) cc_final: 0.8077 (t80) REVERT: G 563 ARG cc_start: 0.7309 (ptm-80) cc_final: 0.7104 (ptm-80) REVERT: H 674 GLU cc_start: 0.7643 (tp30) cc_final: 0.7312 (tp30) outliers start: 12 outliers final: 4 residues processed: 163 average time/residue: 0.1185 time to fit residues: 27.3765 Evaluate side-chains 135 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain G residue 310 LYS Chi-restraints excluded: chain G residue 415 SER 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: 3.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3604 r_free = 0.3604 target = 0.141854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113937 restraints weight = 15085.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117462 restraints weight = 9268.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119931 restraints weight = 6706.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121569 restraints weight = 5358.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122831 restraints weight = 4585.662| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2580 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= 0.153 Angle : 0.518 6.633 17398 Z= 0.289 Chirality : 0.036 0.136 1946 Planarity : 0.004 0.050 1730 Dihedral : 24.619 175.035 2698 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.39 % Allowed : 10.52 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1112 helix: 1.40 (0.20), residues: 620 sheet: -0.60 (0.52), residues: 72 loop : -1.07 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 538 TYR 0.012 0.001 TYR G 559 PHE 0.011 0.001 PHE G 140 TRP 0.005 0.001 TRP G 312 HIS 0.003 0.001 HIS G 342 Details of bonding type rmsd covalent geometry : bond 0.00344 (12454) covalent geometry : angle 0.51759 (17398) hydrogen bonds : bond 0.04175 ( 613) hydrogen bonds : angle 3.56802 ( 1645) Misc. bond : bond 0.00183 ( 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 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.418 Fit side-chains REVERT: A 563 ARG cc_start: 0.7220 (ptm-80) cc_final: 0.6461 (ptp90) REVERT: B 696 GLU cc_start: 0.7959 (tp30) cc_final: 0.7727 (tm-30) REVERT: G 239 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7784 (mm-30) REVERT: G 563 ARG cc_start: 0.7382 (ptm-80) cc_final: 0.6869 (ptp90) REVERT: H 674 GLU cc_start: 0.7606 (tp30) cc_final: 0.7285 (tp30) outliers start: 14 outliers final: 6 residues processed: 138 average time/residue: 0.1120 time to fit residues: 22.4901 Evaluate side-chains 118 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 415 SER 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 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: 0.4980 chunk 62 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116877 restraints weight = 14933.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120485 restraints weight = 9126.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123017 restraints weight = 6573.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124767 restraints weight = 5227.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125952 restraints weight = 4449.433| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12456 Z= 0.124 Angle : 0.489 6.478 17398 Z= 0.273 Chirality : 0.035 0.136 1946 Planarity : 0.003 0.042 1730 Dihedral : 24.443 176.075 2698 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.69 % Allowed : 12.70 % Favored : 86.61 % 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: 0.93 (0.25), residues: 1112 helix: 1.65 (0.21), residues: 628 sheet: -0.15 (0.62), residues: 58 loop : -0.83 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 540 TYR 0.020 0.001 TYR G 559 PHE 0.012 0.001 PHE G 140 TRP 0.003 0.001 TRP A 312 HIS 0.002 0.000 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00268 (12454) covalent geometry : angle 0.48910 (17398) hydrogen bonds : bond 0.03726 ( 613) hydrogen bonds : angle 3.38729 ( 1645) Misc. bond : bond 0.00130 ( 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 139 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.365 Fit side-chains REVERT: A 563 ARG cc_start: 0.7222 (ptm-80) cc_final: 0.6504 (ptp90) REVERT: B 696 GLU cc_start: 0.7947 (tp30) cc_final: 0.7695 (tm-30) REVERT: G 239 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7464 (mm-30) REVERT: G 563 ARG cc_start: 0.7283 (ptm-80) cc_final: 0.6696 (ptp90) outliers start: 7 outliers final: 3 residues processed: 135 average time/residue: 0.1080 time to fit residues: 21.4726 Evaluate side-chains 119 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 396 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 46 optimal weight: 0.0770 chunk 62 optimal weight: 0.0570 chunk 113 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120638 restraints weight = 14824.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124382 restraints weight = 9099.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126928 restraints weight = 6532.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128724 restraints weight = 5190.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129959 restraints weight = 4407.987| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12456 Z= 0.113 Angle : 0.484 6.412 17398 Z= 0.268 Chirality : 0.034 0.142 1946 Planarity : 0.003 0.037 1730 Dihedral : 24.337 176.208 2698 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.99 % Allowed : 13.59 % Favored : 85.42 % 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: 1.36 (0.25), residues: 1112 helix: 1.93 (0.21), residues: 632 sheet: 0.50 (0.64), residues: 58 loop : -0.62 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.016 0.001 TYR G 559 PHE 0.006 0.001 PHE A 493 TRP 0.002 0.000 TRP G 266 HIS 0.001 0.000 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00239 (12454) covalent geometry : angle 0.48434 (17398) hydrogen bonds : bond 0.03504 ( 613) hydrogen bonds : angle 3.20436 ( 1645) Misc. bond : bond 0.00105 ( 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 141 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.379 Fit side-chains REVERT: A 303 ASP cc_start: 0.8098 (t0) cc_final: 0.7269 (t0) REVERT: A 336 VAL cc_start: 0.9301 (t) cc_final: 0.8979 (m) REVERT: A 563 ARG cc_start: 0.7313 (ptm-80) cc_final: 0.6679 (ptp90) REVERT: G 239 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7506 (mm-30) REVERT: G 303 ASP cc_start: 0.8108 (t0) cc_final: 0.7279 (t0) REVERT: G 336 VAL cc_start: 0.9303 (t) cc_final: 0.8973 (m) REVERT: G 476 MET cc_start: 0.8267 (tpt) cc_final: 0.7818 (tpt) REVERT: G 563 ARG cc_start: 0.7233 (ptm-80) cc_final: 0.6887 (ptp90) outliers start: 10 outliers final: 6 residues processed: 136 average time/residue: 0.1025 time to fit residues: 20.5222 Evaluate side-chains 123 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 422 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114942 restraints weight = 15025.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118500 restraints weight = 9329.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120952 restraints weight = 6788.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122649 restraints weight = 5442.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123832 restraints weight = 4661.716| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12456 Z= 0.161 Angle : 0.517 6.785 17398 Z= 0.284 Chirality : 0.036 0.132 1946 Planarity : 0.003 0.035 1730 Dihedral : 24.600 174.474 2698 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.39 % Allowed : 15.18 % Favored : 83.43 % 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: 1.48 (0.25), residues: 1112 helix: 1.96 (0.21), residues: 622 sheet: 0.70 (0.59), residues: 68 loop : -0.44 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 146 TYR 0.021 0.001 TYR G 559 PHE 0.011 0.001 PHE A 493 TRP 0.006 0.001 TRP G 312 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00366 (12454) covalent geometry : angle 0.51739 (17398) hydrogen bonds : bond 0.04105 ( 613) hydrogen bonds : angle 3.36798 ( 1645) Misc. bond : bond 0.00132 ( 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 125 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.338 Fit side-chains REVERT: A 563 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.6751 (ptp90) REVERT: G 239 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7611 (mm-30) REVERT: G 563 ARG cc_start: 0.7430 (ptm-80) cc_final: 0.7107 (ptp90) outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 0.1220 time to fit residues: 20.8890 Evaluate side-chains 117 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE 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 A residue 422 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 422 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: 1.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 ASN H 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111488 restraints weight = 15118.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114819 restraints weight = 9546.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117056 restraints weight = 7039.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118673 restraints weight = 5713.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119668 restraints weight = 4938.704| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12456 Z= 0.199 Angle : 0.560 7.403 17398 Z= 0.306 Chirality : 0.038 0.134 1946 Planarity : 0.003 0.040 1730 Dihedral : 24.939 174.546 2698 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.19 % Allowed : 14.98 % 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: 1.16 (0.25), residues: 1112 helix: 1.74 (0.20), residues: 618 sheet: 0.28 (0.55), residues: 78 loop : -0.59 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 555 TYR 0.019 0.001 TYR G 559 PHE 0.013 0.001 PHE G 324 TRP 0.008 0.001 TRP A 312 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00459 (12454) covalent geometry : angle 0.56050 (17398) hydrogen bonds : bond 0.04630 ( 613) hydrogen bonds : angle 3.59978 ( 1645) Misc. bond : bond 0.00170 ( 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 112 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.347 Fit side-chains REVERT: A 456 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5700 (mp) REVERT: A 476 MET cc_start: 0.8570 (tpt) cc_final: 0.8035 (tpt) REVERT: A 563 ARG cc_start: 0.7242 (ptm-80) cc_final: 0.6651 (ptp90) REVERT: G 239 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7660 (mm-30) REVERT: G 303 ASP cc_start: 0.8520 (t0) cc_final: 0.7746 (t0) REVERT: G 476 MET cc_start: 0.8577 (tpt) cc_final: 0.8044 (tpt) outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 0.1006 time to fit residues: 16.2338 Evaluate side-chains 105 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 680 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 99 optimal weight: 0.0270 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 62 optimal weight: 0.0010 chunk 11 optimal weight: 0.5980 chunk 67 optimal weight: 0.0970 overall best weight: 0.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN G 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119045 restraints weight = 14877.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122765 restraints weight = 9178.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125313 restraints weight = 6624.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127108 restraints weight = 5294.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128355 restraints weight = 4501.897| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12456 Z= 0.113 Angle : 0.497 7.305 17398 Z= 0.271 Chirality : 0.035 0.146 1946 Planarity : 0.003 0.038 1730 Dihedral : 24.399 177.592 2698 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.99 % Allowed : 15.58 % Favored : 83.43 % 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: 1.57 (0.26), residues: 1112 helix: 2.10 (0.21), residues: 620 sheet: 1.65 (0.68), residues: 44 loop : -0.56 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 540 TYR 0.018 0.001 TYR G 559 PHE 0.008 0.001 PHE A 157 TRP 0.004 0.001 TRP A 442 HIS 0.002 0.000 HIS G 342 Details of bonding type rmsd covalent geometry : bond 0.00237 (12454) covalent geometry : angle 0.49663 (17398) hydrogen bonds : bond 0.03541 ( 613) hydrogen bonds : angle 3.26338 ( 1645) Misc. bond : bond 0.00112 ( 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 123 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.426 Fit side-chains REVERT: A 303 ASP cc_start: 0.8370 (t0) cc_final: 0.7956 (t0) REVERT: A 336 VAL cc_start: 0.9307 (t) cc_final: 0.8968 (m) REVERT: A 456 ILE cc_start: 0.6037 (OUTLIER) cc_final: 0.5820 (mp) REVERT: A 476 MET cc_start: 0.8422 (tpt) cc_final: 0.8021 (tpt) REVERT: A 563 ARG cc_start: 0.7200 (ptm-80) cc_final: 0.6583 (ptp90) REVERT: G 239 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7447 (mm-30) REVERT: G 303 ASP cc_start: 0.8344 (t0) cc_final: 0.7925 (t0) REVERT: G 336 VAL cc_start: 0.9312 (t) cc_final: 0.8969 (m) REVERT: G 563 ARG cc_start: 0.7301 (ptm-80) cc_final: 0.6951 (ptp90) outliers start: 10 outliers final: 3 residues processed: 122 average time/residue: 0.1055 time to fit residues: 19.2196 Evaluate side-chains 114 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 422 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113008 restraints weight = 15081.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116760 restraints weight = 9236.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119400 restraints weight = 6643.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121123 restraints weight = 5267.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122393 restraints weight = 4502.574| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3548 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 : 0.521 7.732 17398 Z= 0.283 Chirality : 0.036 0.133 1946 Planarity : 0.003 0.036 1730 Dihedral : 24.633 175.117 2698 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.79 % Allowed : 16.47 % Favored : 82.74 % 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: 1.59 (0.26), residues: 1112 helix: 2.00 (0.20), residues: 624 sheet: 0.92 (0.62), residues: 68 loop : -0.35 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 540 TYR 0.017 0.001 TYR G 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 covalent geometry : bond 0.00339 (12454) covalent geometry : angle 0.52079 (17398) hydrogen bonds : bond 0.04061 ( 613) hydrogen bonds : angle 3.36299 ( 1645) Misc. bond : bond 0.00137 ( 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 114 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.397 Fit side-chains REVERT: A 303 ASP cc_start: 0.8465 (t0) cc_final: 0.7653 (t0) REVERT: A 456 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5835 (mp) REVERT: A 476 MET cc_start: 0.8485 (tpt) cc_final: 0.7972 (tpt) REVERT: B 627 MET cc_start: 0.7208 (ttt) cc_final: 0.6885 (ttt) REVERT: G 239 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7534 (mm-30) REVERT: G 303 ASP cc_start: 0.8454 (t0) cc_final: 0.7635 (t0) REVERT: G 563 ARG cc_start: 0.7364 (ptm-80) cc_final: 0.7047 (ptp90) outliers start: 8 outliers final: 5 residues processed: 113 average time/residue: 0.1070 time to fit residues: 17.8025 Evaluate side-chains 110 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 422 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 0.0970 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118656 restraints weight = 14931.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122323 restraints weight = 9288.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124806 restraints weight = 6734.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126660 restraints weight = 5386.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127906 restraints weight = 4580.637| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12456 Z= 0.117 Angle : 0.502 7.782 17398 Z= 0.272 Chirality : 0.035 0.141 1946 Planarity : 0.003 0.035 1730 Dihedral : 24.491 176.527 2698 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.69 % Allowed : 16.47 % Favored : 82.84 % 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: 1.67 (0.25), residues: 1112 helix: 2.11 (0.20), residues: 624 sheet: 1.29 (0.68), residues: 54 loop : -0.38 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 540 TYR 0.017 0.001 TYR G 559 PHE 0.008 0.001 PHE A 493 TRP 0.002 0.001 TRP G 312 HIS 0.002 0.000 HIS G 342 Details of bonding type rmsd covalent geometry : bond 0.00252 (12454) covalent geometry : angle 0.50194 (17398) hydrogen bonds : bond 0.03665 ( 613) hydrogen bonds : angle 3.26989 ( 1645) Misc. bond : bond 0.00119 ( 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 120 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.281 Fit side-chains REVERT: A 303 ASP cc_start: 0.8408 (t0) cc_final: 0.7637 (t0) REVERT: A 476 MET cc_start: 0.8376 (tpt) cc_final: 0.7885 (tpt) REVERT: A 559 TYR cc_start: 0.8471 (t80) cc_final: 0.8251 (t80) REVERT: B 627 MET cc_start: 0.7112 (ttt) cc_final: 0.6777 (ttt) REVERT: G 239 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7468 (mm-30) REVERT: G 303 ASP cc_start: 0.8395 (t0) cc_final: 0.7619 (t0) REVERT: G 336 VAL cc_start: 0.9309 (t) cc_final: 0.8936 (m) REVERT: G 476 MET cc_start: 0.8393 (tpt) cc_final: 0.7924 (tpt) REVERT: G 563 ARG cc_start: 0.7317 (ptm-80) cc_final: 0.7105 (ptp90) REVERT: H 627 MET cc_start: 0.7103 (ttt) cc_final: 0.6748 (ttt) outliers start: 7 outliers final: 6 residues processed: 118 average time/residue: 0.1140 time to fit residues: 19.4943 Evaluate side-chains 116 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 422 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116197 restraints weight = 14941.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119702 restraints weight = 9348.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122134 restraints weight = 6829.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123849 restraints weight = 5503.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125026 restraints weight = 4715.357| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3653 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= 0.146 Angle : 0.523 7.870 17398 Z= 0.282 Chirality : 0.036 0.134 1946 Planarity : 0.003 0.032 1730 Dihedral : 24.654 175.422 2698 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.89 % Allowed : 15.87 % Favored : 83.23 % 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: 1.61 (0.25), residues: 1112 helix: 2.03 (0.20), residues: 624 sheet: 0.91 (0.61), residues: 68 loop : -0.36 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 540 TYR 0.019 0.001 TYR G 559 PHE 0.010 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 covalent geometry : bond 0.00329 (12454) covalent geometry : angle 0.52253 (17398) hydrogen bonds : bond 0.04039 ( 613) hydrogen bonds : angle 3.34313 ( 1645) Misc. bond : bond 0.00131 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.64 seconds wall clock time: 31 minutes 30.01 seconds (1890.01 seconds total)