Starting phenix.real_space_refine on Thu Sep 18 12:47:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnw_61629/09_2025/9jnw_61629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnw_61629/09_2025/9jnw_61629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jnw_61629/09_2025/9jnw_61629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnw_61629/09_2025/9jnw_61629.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jnw_61629/09_2025/9jnw_61629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnw_61629/09_2025/9jnw_61629.map" } resolution = 2.9 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= 0.009 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 296 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 9866 2.51 5 N 3124 2.21 5 O 3775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17087 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3002 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3025 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4971 Classifications: {'peptide': 604} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 580} Chain breaks: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.57, per 1000 atoms: 0.21 Number of scatterers: 17087 At special positions: 0 Unit cell: (102.837, 117.992, 158.045, 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 25 16.00 P 296 15.00 Mg 1 11.99 O 3775 8.00 N 3124 7.00 C 9866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 420.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 11 sheets defined 62.8% alpha, 3.5% beta 142 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.714A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.170A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.541A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.685A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.813A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.982A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.749A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.838A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 90 removed outlier: 3.992A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 116 Processing helix chain 'K' and resid 119 through 129 removed outlier: 3.620A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER K 125 " --> pdb=" O HIS K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 143 removed outlier: 3.649A pdb=" N ARG K 134 " --> pdb=" O ASP K 130 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.578A pdb=" N THR K 268 " --> pdb=" O ILE K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 302 through 309 removed outlier: 3.584A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.971A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 331 removed outlier: 4.103A pdb=" N ARG K 328 " --> pdb=" O GLU K 325 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN K 331 " --> pdb=" O ARG K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 340 Processing helix chain 'K' and resid 360 through 371 removed outlier: 4.058A pdb=" N LEU K 370 " --> pdb=" O LEU K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 385 removed outlier: 3.854A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 397 Processing helix chain 'K' and resid 405 through 409 removed outlier: 4.132A pdb=" N LEU K 409 " --> pdb=" O GLN K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 417 removed outlier: 4.016A pdb=" N VAL K 417 " --> pdb=" O LYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 467 through 478 Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 497 through 500 removed outlier: 3.541A pdb=" N ASN K 500 " --> pdb=" O LEU K 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 497 through 500' Processing helix chain 'K' and resid 501 through 518 Processing helix chain 'K' and resid 527 through 541 Processing helix chain 'K' and resid 553 through 565 Processing helix chain 'K' and resid 601 through 614 removed outlier: 3.653A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS K 613 " --> pdb=" O MET K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.896A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 728 removed outlier: 4.282A pdb=" N THR K 728 " --> pdb=" O ALA K 724 " (cutoff:3.500A) Processing helix chain 'K' and resid 730 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.076A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.997A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.503A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.807A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 248 through 251 removed outlier: 5.967A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.446A pdb=" N PHE K 274 " --> pdb=" O ILE K 300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 426 through 431 removed outlier: 4.159A pdb=" N ARG K 625 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU K 626 " --> pdb=" O LEU K 595 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL K 521 " --> pdb=" O PHE K 574 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU K 576 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE K 523 " --> pdb=" O LEU K 576 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 704 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2278 1.32 - 1.44: 6143 1.44 - 1.56: 8943 1.56 - 1.68: 589 1.68 - 1.81: 43 Bond restraints: 17996 Sorted by residual: bond pdb=" N LEU K 421 " pdb=" CA LEU K 421 " ideal model delta sigma weight residual 1.458 1.385 0.072 1.25e-02 6.40e+03 3.36e+01 bond pdb=" CA VAL K 417 " pdb=" CB VAL K 417 " ideal model delta sigma weight residual 1.540 1.478 0.062 1.36e-02 5.41e+03 2.10e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.32e-02 5.74e+03 2.08e+01 bond pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.35e-02 5.49e+03 1.38e+01 bond pdb=" CA SER K 420 " pdb=" C SER K 420 " ideal model delta sigma weight residual 1.523 1.477 0.047 1.34e-02 5.57e+03 1.21e+01 ... (remaining 17991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 25146 2.42 - 4.84: 380 4.84 - 7.25: 33 7.25 - 9.67: 5 9.67 - 12.09: 3 Bond angle restraints: 25567 Sorted by residual: angle pdb=" N LEU K 422 " pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 110.20 98.11 12.09 1.44e+00 4.82e-01 7.05e+01 angle pdb=" N LEU K 421 " pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 109.59 99.32 10.27 1.47e+00 4.63e-01 4.88e+01 angle pdb=" N THR A 80 " pdb=" CA THR A 80 " pdb=" C THR A 80 " ideal model delta sigma weight residual 110.80 100.82 9.98 2.13e+00 2.20e-01 2.20e+01 angle pdb=" N VAL K 417 " pdb=" CA VAL K 417 " pdb=" C VAL K 417 " ideal model delta sigma weight residual 109.34 99.88 9.46 2.08e+00 2.31e-01 2.07e+01 angle pdb=" C VAL K 417 " pdb=" CA VAL K 417 " pdb=" CB VAL K 417 " ideal model delta sigma weight residual 111.29 104.26 7.03 1.64e+00 3.72e-01 1.84e+01 ... (remaining 25562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 8661 35.90 - 71.80: 1428 71.80 - 107.70: 32 107.70 - 143.59: 13 143.59 - 179.49: 7 Dihedral angle restraints: 10141 sinusoidal: 6130 harmonic: 4011 Sorted by residual: dihedral pdb=" O2A ADP K1202 " pdb=" O3A ADP K1202 " pdb=" PA ADP K1202 " pdb=" PB ADP K1202 " ideal model delta sinusoidal sigma weight residual -60.00 119.49 -179.49 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " pdb=" O2A ADP K1202 " ideal model delta sinusoidal sigma weight residual -60.00 87.38 -147.38 1 2.00e+01 2.50e-03 4.42e+01 dihedral pdb=" CA LYS K 768 " pdb=" C LYS K 768 " pdb=" N ARG K 769 " pdb=" CA ARG K 769 " ideal model delta harmonic sigma weight residual -180.00 -146.76 -33.24 0 5.00e+00 4.00e-02 4.42e+01 ... (remaining 10138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2409 0.059 - 0.117: 431 0.117 - 0.175: 44 0.175 - 0.234: 3 0.234 - 0.292: 1 Chirality restraints: 2888 Sorted by residual: chirality pdb=" CB VAL K 417 " pdb=" CA VAL K 417 " pdb=" CG1 VAL K 417 " pdb=" CG2 VAL K 417 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA VAL K 417 " pdb=" N VAL K 417 " pdb=" C VAL K 417 " pdb=" CB VAL K 417 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA THR K 419 " pdb=" N THR K 419 " pdb=" C THR K 419 " pdb=" CB THR K 419 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.19e-01 ... (remaining 2885 not shown) Planarity restraints: 2228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 416 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C ASP K 416 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP K 416 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL K 417 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 72 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO K 73 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO K 73 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 73 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 320 " 0.012 2.00e-02 2.50e+03 1.27e-02 3.21e+00 pdb=" CG TYR K 320 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR K 320 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR K 320 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR K 320 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR K 320 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR K 320 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR K 320 " 0.001 2.00e-02 2.50e+03 ... (remaining 2225 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 160 2.55 - 3.14: 13520 3.14 - 3.73: 29650 3.73 - 4.31: 41193 4.31 - 4.90: 61175 Nonbonded interactions: 145698 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 1.968 2.170 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 1.982 3.040 nonbonded pdb=" O2 DC I 92 " pdb=" N2 DG J 56 " model vdw 2.047 2.496 nonbonded pdb=" OG SER K 434 " pdb=" OE1 GLN K 437 " model vdw 2.121 3.040 nonbonded pdb=" NZ LYS B 59 " pdb=" OE2 GLU B 63 " model vdw 2.131 3.120 ... (remaining 145693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 15 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'I' and (resid 1 through 2 or resid 4 through 55 or resid 57 through 64 o \ r resid 67 or resid 69 through 74 or resid 76 through 77 or resid 79 or resid 83 \ through 88 or resid 90 through 91 or resid 93 through 147)) selection = (chain 'J' and (resid 2 through 55 or resid 57 through 61 or resid 63 through 65 \ or resid 68 or resid 71 through 72 or resid 74 through 79 or resid 81 or resid \ 84 through 91 or resid 93 through 147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.490 Find NCS groups from input model: 0.120 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 0.072 17996 Z= 0.357 Angle : 0.782 12.089 25567 Z= 0.448 Chirality : 0.044 0.292 2888 Planarity : 0.004 0.045 2228 Dihedral : 26.521 179.492 7541 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.21 % Favored : 92.50 % Rotamer: Outliers : 0.08 % Allowed : 0.68 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -0.18 (0.24), residues: 1346 helix: 1.15 (0.19), residues: 803 sheet: -2.83 (0.76), residues: 55 loop : -1.99 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 645 TYR 0.029 0.002 TYR K 320 PHE 0.023 0.002 PHE K 385 TRP 0.019 0.002 TRP K 267 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00790 (17996) covalent geometry : angle 0.78151 (25567) hydrogen bonds : bond 0.10219 ( 954) hydrogen bonds : angle 4.30709 ( 2462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8150 (tp30) REVERT: A 133 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8228 (mt-10) REVERT: D 90 GLU cc_start: 0.8463 (mp0) cc_final: 0.8053 (mp0) REVERT: E 50 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7919 (mt-10) REVERT: E 76 GLN cc_start: 0.8354 (tp-100) cc_final: 0.7995 (tp40) REVERT: E 106 ASP cc_start: 0.7892 (m-30) cc_final: 0.7503 (m-30) REVERT: G 104 GLN cc_start: 0.8674 (mm110) cc_final: 0.8284 (mm110) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.8810 time to fit residues: 173.6803 Evaluate side-chains 148 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.091686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.065792 restraints weight = 45696.202| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.45 r_work: 0.3003 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17996 Z= 0.209 Angle : 0.670 8.497 25567 Z= 0.370 Chirality : 0.038 0.184 2888 Planarity : 0.004 0.046 2228 Dihedral : 30.293 167.355 4755 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.91 % Favored : 93.02 % Rotamer: Outliers : 1.69 % Allowed : 10.25 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.25 (0.24), residues: 1346 helix: 1.52 (0.19), residues: 812 sheet: -2.94 (0.69), residues: 61 loop : -1.86 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.015 0.002 TYR K 320 PHE 0.016 0.002 PHE K 385 TRP 0.016 0.001 TRP K 267 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00473 (17996) covalent geometry : angle 0.66961 (25567) hydrogen bonds : bond 0.05513 ( 954) hydrogen bonds : angle 3.60692 ( 2462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.311 Fit side-chains REVERT: A 133 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8247 (mt-10) REVERT: B 84 MET cc_start: 0.9072 (mmm) cc_final: 0.8830 (mmp) REVERT: C 90 ASP cc_start: 0.8740 (t0) cc_final: 0.8234 (t0) REVERT: D 39 TYR cc_start: 0.8511 (t80) cc_final: 0.7730 (t80) REVERT: D 65 ASP cc_start: 0.8969 (t0) cc_final: 0.8659 (t0) REVERT: E 50 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8460 (mt-10) REVERT: E 76 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8157 (tp40) REVERT: E 115 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8743 (mttp) REVERT: F 93 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: G 104 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8660 (mm110) REVERT: H 39 TYR cc_start: 0.8535 (t80) cc_final: 0.8272 (t80) REVERT: H 65 ASP cc_start: 0.9137 (t0) cc_final: 0.8883 (t0) REVERT: H 102 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8005 (tp30) REVERT: H 110 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: K 335 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8546 (tpp) REVERT: K 469 MET cc_start: 0.8669 (ttm) cc_final: 0.8420 (ttp) REVERT: K 609 MET cc_start: 0.8933 (ptt) cc_final: 0.8494 (tmm) outliers start: 20 outliers final: 7 residues processed: 173 average time/residue: 0.8086 time to fit residues: 151.4314 Evaluate side-chains 156 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.091257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.064752 restraints weight = 45853.521| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.53 r_work: 0.2964 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17996 Z= 0.221 Angle : 0.650 7.988 25567 Z= 0.362 Chirality : 0.038 0.172 2888 Planarity : 0.004 0.046 2228 Dihedral : 30.111 167.153 4755 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.12 % Allowed : 14.82 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.46 (0.24), residues: 1346 helix: 1.70 (0.19), residues: 811 sheet: -2.75 (0.71), residues: 61 loop : -1.81 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.013 0.001 TYR K 320 PHE 0.015 0.002 PHE K 385 TRP 0.012 0.002 TRP K 384 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00503 (17996) covalent geometry : angle 0.65023 (25567) hydrogen bonds : bond 0.05490 ( 954) hydrogen bonds : angle 3.53247 ( 2462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9207 (pm20) cc_final: 0.8905 (pm20) REVERT: A 133 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8139 (mt-10) REVERT: C 90 ASP cc_start: 0.8572 (t0) cc_final: 0.8337 (t0) REVERT: C 91 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8013 (tm-30) REVERT: D 39 TYR cc_start: 0.8323 (t80) cc_final: 0.7680 (t80) REVERT: D 65 ASP cc_start: 0.8952 (t0) cc_final: 0.8657 (t0) REVERT: D 90 GLU cc_start: 0.9006 (mp0) cc_final: 0.8700 (mp0) REVERT: E 50 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8407 (mt-10) REVERT: E 76 GLN cc_start: 0.8413 (tp-100) cc_final: 0.8021 (tp40) REVERT: E 115 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8796 (mttp) REVERT: F 93 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7456 (mp10) REVERT: G 56 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: G 104 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8731 (mm110) REVERT: H 39 TYR cc_start: 0.8516 (t80) cc_final: 0.8279 (t80) REVERT: H 54 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8420 (tmtt) REVERT: H 65 ASP cc_start: 0.9103 (t0) cc_final: 0.8894 (t0) REVERT: H 90 GLU cc_start: 0.8838 (mp0) cc_final: 0.8120 (mp0) REVERT: H 110 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: K 469 MET cc_start: 0.8680 (ttm) cc_final: 0.8425 (ttp) REVERT: K 609 MET cc_start: 0.8956 (ptt) cc_final: 0.8750 (ppp) outliers start: 25 outliers final: 11 residues processed: 170 average time/residue: 0.8166 time to fit residues: 150.2471 Evaluate side-chains 167 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.090931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064370 restraints weight = 45675.059| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.54 r_work: 0.2953 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 17996 Z= 0.246 Angle : 0.658 8.154 25567 Z= 0.365 Chirality : 0.039 0.170 2888 Planarity : 0.004 0.049 2228 Dihedral : 30.112 167.399 4755 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.47 % Allowed : 16.77 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.47 (0.24), residues: 1346 helix: 1.67 (0.18), residues: 817 sheet: -2.74 (0.70), residues: 61 loop : -1.77 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.012 0.001 TYR K 596 PHE 0.014 0.002 PHE K 385 TRP 0.015 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00561 (17996) covalent geometry : angle 0.65784 (25567) hydrogen bonds : bond 0.05589 ( 954) hydrogen bonds : angle 3.52122 ( 2462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.543 Fit side-chains REVERT: A 59 GLU cc_start: 0.9217 (pm20) cc_final: 0.8812 (pm20) REVERT: A 133 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 24 ASP cc_start: 0.8249 (t0) cc_final: 0.8020 (t0) REVERT: C 90 ASP cc_start: 0.8578 (t0) cc_final: 0.8345 (t0) REVERT: C 91 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7947 (tm-30) REVERT: D 39 TYR cc_start: 0.8287 (t80) cc_final: 0.7660 (t80) REVERT: D 65 ASP cc_start: 0.8972 (t0) cc_final: 0.8663 (t0) REVERT: D 90 GLU cc_start: 0.9053 (mp0) cc_final: 0.8736 (mp0) REVERT: E 76 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8090 (tp40) REVERT: E 120 MET cc_start: 0.8017 (mtt) cc_final: 0.7640 (mtt) REVERT: F 93 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: G 56 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: G 104 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8718 (mm110) REVERT: H 39 TYR cc_start: 0.8526 (t80) cc_final: 0.8283 (t80) REVERT: H 54 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8459 (tmtt) REVERT: H 65 ASP cc_start: 0.9111 (t0) cc_final: 0.8896 (t0) REVERT: H 90 GLU cc_start: 0.8853 (mp0) cc_final: 0.8144 (mp0) REVERT: H 110 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: K 413 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7986 (mp) REVERT: K 424 LYS cc_start: 0.8436 (ttpt) cc_final: 0.7800 (ttpt) REVERT: K 469 MET cc_start: 0.8652 (ttm) cc_final: 0.8378 (ttp) outliers start: 41 outliers final: 17 residues processed: 178 average time/residue: 0.7694 time to fit residues: 148.8780 Evaluate side-chains 170 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.093839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.068177 restraints weight = 45913.971| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.46 r_work: 0.3060 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17996 Z= 0.154 Angle : 0.611 9.547 25567 Z= 0.340 Chirality : 0.036 0.146 2888 Planarity : 0.004 0.045 2228 Dihedral : 29.745 168.428 4755 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.03 % Allowed : 19.31 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.82 (0.24), residues: 1346 helix: 1.94 (0.19), residues: 817 sheet: -2.49 (0.69), residues: 62 loop : -1.63 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 186 TYR 0.012 0.001 TYR K 543 PHE 0.020 0.001 PHE K 185 TRP 0.032 0.002 TRP K 384 HIS 0.018 0.001 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00342 (17996) covalent geometry : angle 0.61060 (25567) hydrogen bonds : bond 0.04653 ( 954) hydrogen bonds : angle 3.25681 ( 2462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9164 (pm20) cc_final: 0.8801 (pm20) REVERT: A 133 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8224 (mt-10) REVERT: B 24 ASP cc_start: 0.8289 (t0) cc_final: 0.8067 (t0) REVERT: C 90 ASP cc_start: 0.8630 (t0) cc_final: 0.8416 (t0) REVERT: D 39 TYR cc_start: 0.8168 (t80) cc_final: 0.7597 (t80) REVERT: D 65 ASP cc_start: 0.8946 (t0) cc_final: 0.8683 (t0) REVERT: D 90 GLU cc_start: 0.9054 (mp0) cc_final: 0.8815 (mp0) REVERT: E 76 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8010 (tp40) REVERT: E 120 MET cc_start: 0.7890 (mtt) cc_final: 0.7531 (mtt) REVERT: F 93 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: G 104 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8739 (mm110) REVERT: H 54 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8504 (tmtt) REVERT: H 65 ASP cc_start: 0.9131 (t0) cc_final: 0.8849 (t0) REVERT: H 90 GLU cc_start: 0.8882 (mp0) cc_final: 0.8255 (mp0) REVERT: H 110 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: K 132 LYS cc_start: 0.9308 (pptt) cc_final: 0.9062 (tptp) REVERT: K 222 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: K 469 MET cc_start: 0.8623 (ttm) cc_final: 0.8380 (ttp) REVERT: K 609 MET cc_start: 0.8951 (ptt) cc_final: 0.8592 (tmm) outliers start: 24 outliers final: 10 residues processed: 184 average time/residue: 0.7646 time to fit residues: 153.3097 Evaluate side-chains 166 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 475 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.091187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064612 restraints weight = 45732.044| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.53 r_work: 0.2960 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17996 Z= 0.249 Angle : 0.667 7.897 25567 Z= 0.367 Chirality : 0.038 0.154 2888 Planarity : 0.004 0.044 2228 Dihedral : 29.939 167.255 4755 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.54 % Allowed : 21.17 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 aren not related in a simple way. whole: 0.64 (0.24), residues: 1346 helix: 1.76 (0.18), residues: 820 sheet: -2.54 (0.70), residues: 60 loop : -1.66 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.012 0.001 TYR H 39 PHE 0.017 0.002 PHE K 385 TRP 0.046 0.003 TRP K 384 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00570 (17996) covalent geometry : angle 0.66724 (25567) hydrogen bonds : bond 0.05560 ( 954) hydrogen bonds : angle 3.43747 ( 2462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9183 (pm20) cc_final: 0.8712 (pm20) REVERT: A 133 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8206 (mt-10) REVERT: C 90 ASP cc_start: 0.8616 (t0) cc_final: 0.8380 (t0) REVERT: D 39 TYR cc_start: 0.8238 (t80) cc_final: 0.7613 (t80) REVERT: D 44 GLN cc_start: 0.8822 (mt0) cc_final: 0.8499 (mt0) REVERT: D 65 ASP cc_start: 0.8989 (t0) cc_final: 0.8686 (t0) REVERT: D 90 GLU cc_start: 0.9048 (mp0) cc_final: 0.8791 (mp0) REVERT: E 76 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8054 (tp40) REVERT: E 120 MET cc_start: 0.7944 (mtt) cc_final: 0.7614 (mtt) REVERT: F 93 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: G 104 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8725 (mm110) REVERT: H 54 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8457 (tmtt) REVERT: H 65 ASP cc_start: 0.9124 (t0) cc_final: 0.8881 (t0) REVERT: H 90 GLU cc_start: 0.8899 (mp0) cc_final: 0.8121 (mp0) REVERT: H 110 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: K 132 LYS cc_start: 0.9301 (pptt) cc_final: 0.9042 (tptp) REVERT: K 222 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: K 413 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8064 (mp) REVERT: K 424 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8004 (ttpt) REVERT: K 469 MET cc_start: 0.8699 (ttm) cc_final: 0.8437 (ttp) outliers start: 30 outliers final: 18 residues processed: 174 average time/residue: 0.7714 time to fit residues: 145.7479 Evaluate side-chains 171 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 525 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.091466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064834 restraints weight = 45692.309| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.55 r_work: 0.2963 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17996 Z= 0.230 Angle : 0.657 7.647 25567 Z= 0.362 Chirality : 0.038 0.156 2888 Planarity : 0.004 0.043 2228 Dihedral : 29.922 168.198 4755 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.13 % Allowed : 20.91 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 aren not related in a simple way. whole: 0.60 (0.24), residues: 1346 helix: 1.72 (0.18), residues: 820 sheet: -2.53 (0.70), residues: 60 loop : -1.64 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.017 0.001 TYR K 743 PHE 0.014 0.002 PHE K 133 TRP 0.035 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00525 (17996) covalent geometry : angle 0.65678 (25567) hydrogen bonds : bond 0.05345 ( 954) hydrogen bonds : angle 3.40018 ( 2462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9163 (pm20) cc_final: 0.8679 (pm20) REVERT: A 133 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 24 ASP cc_start: 0.8127 (t0) cc_final: 0.7892 (t0) REVERT: C 90 ASP cc_start: 0.8634 (t0) cc_final: 0.8407 (t0) REVERT: D 39 TYR cc_start: 0.8244 (t80) cc_final: 0.7625 (t80) REVERT: D 65 ASP cc_start: 0.8971 (t0) cc_final: 0.8671 (t0) REVERT: D 90 GLU cc_start: 0.9056 (mp0) cc_final: 0.8800 (mp0) REVERT: E 76 GLN cc_start: 0.8403 (tp-100) cc_final: 0.7984 (tp40) REVERT: E 120 MET cc_start: 0.7957 (mtt) cc_final: 0.7625 (mtt) REVERT: F 93 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: G 104 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8722 (mm110) REVERT: H 54 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8484 (tmtt) REVERT: H 65 ASP cc_start: 0.9133 (t0) cc_final: 0.8892 (t0) REVERT: H 90 GLU cc_start: 0.8909 (mp0) cc_final: 0.8136 (mp0) REVERT: H 110 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: K 132 LYS cc_start: 0.9314 (pptt) cc_final: 0.9070 (tptp) REVERT: K 222 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: K 469 MET cc_start: 0.8689 (ttm) cc_final: 0.8382 (ttp) outliers start: 37 outliers final: 21 residues processed: 177 average time/residue: 0.7609 time to fit residues: 146.9104 Evaluate side-chains 173 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 538 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 134 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.092425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066011 restraints weight = 45690.373| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.54 r_work: 0.2995 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17996 Z= 0.187 Angle : 0.641 7.569 25567 Z= 0.353 Chirality : 0.037 0.160 2888 Planarity : 0.004 0.044 2228 Dihedral : 29.770 168.565 4755 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.54 % Allowed : 22.18 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 aren not related in a simple way. whole: 0.74 (0.24), residues: 1346 helix: 1.86 (0.18), residues: 816 sheet: -2.29 (0.70), residues: 58 loop : -1.67 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 131 TYR 0.011 0.001 TYR K 543 PHE 0.011 0.001 PHE K 385 TRP 0.031 0.002 TRP K 267 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00425 (17996) covalent geometry : angle 0.64114 (25567) hydrogen bonds : bond 0.04944 ( 954) hydrogen bonds : angle 3.28926 ( 2462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9128 (pm20) cc_final: 0.8678 (pm20) REVERT: A 133 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 24 ASP cc_start: 0.8163 (t0) cc_final: 0.7917 (t0) REVERT: C 90 ASP cc_start: 0.8631 (t0) cc_final: 0.8405 (t0) REVERT: D 39 TYR cc_start: 0.8142 (t80) cc_final: 0.7540 (t80) REVERT: D 65 ASP cc_start: 0.8948 (t0) cc_final: 0.8645 (t0) REVERT: D 90 GLU cc_start: 0.9045 (mp0) cc_final: 0.8803 (mp0) REVERT: E 76 GLN cc_start: 0.8401 (tp-100) cc_final: 0.7978 (tp40) REVERT: E 120 MET cc_start: 0.7982 (mtt) cc_final: 0.7633 (mtt) REVERT: F 93 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: G 104 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8709 (mm110) REVERT: H 54 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8419 (tmtt) REVERT: H 65 ASP cc_start: 0.9130 (t0) cc_final: 0.8833 (t0) REVERT: H 90 GLU cc_start: 0.8889 (mp0) cc_final: 0.8139 (mp0) REVERT: H 110 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: K 132 LYS cc_start: 0.9358 (pptt) cc_final: 0.9075 (tptp) REVERT: K 222 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: K 338 GLN cc_start: 0.8984 (mt0) cc_final: 0.8760 (mt0) REVERT: K 469 MET cc_start: 0.8716 (ttm) cc_final: 0.8512 (ttp) outliers start: 30 outliers final: 19 residues processed: 177 average time/residue: 0.8336 time to fit residues: 160.4022 Evaluate side-chains 173 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 538 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.093429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067121 restraints weight = 45947.790| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.56 r_work: 0.3016 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17996 Z= 0.164 Angle : 0.636 9.500 25567 Z= 0.349 Chirality : 0.036 0.147 2888 Planarity : 0.004 0.049 2228 Dihedral : 29.624 168.743 4755 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.12 % Allowed : 23.12 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 aren not related in a simple way. whole: 0.84 (0.24), residues: 1346 helix: 1.93 (0.19), residues: 814 sheet: -1.80 (0.77), residues: 51 loop : -1.68 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.011 0.001 TYR K 543 PHE 0.012 0.001 PHE K 750 TRP 0.031 0.002 TRP K 267 HIS 0.004 0.001 HIS K 211 Details of bonding type rmsd covalent geometry : bond 0.00368 (17996) covalent geometry : angle 0.63588 (25567) hydrogen bonds : bond 0.04667 ( 954) hydrogen bonds : angle 3.21539 ( 2462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9143 (pm20) cc_final: 0.8752 (pm20) REVERT: A 133 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 24 ASP cc_start: 0.8149 (t0) cc_final: 0.7877 (t0) REVERT: C 73 ASN cc_start: 0.8431 (m110) cc_final: 0.7936 (t0) REVERT: C 90 ASP cc_start: 0.8620 (t0) cc_final: 0.8420 (t0) REVERT: D 39 TYR cc_start: 0.8097 (t80) cc_final: 0.7567 (t80) REVERT: D 65 ASP cc_start: 0.8933 (t0) cc_final: 0.8668 (t0) REVERT: D 90 GLU cc_start: 0.9048 (mp0) cc_final: 0.8825 (mp0) REVERT: E 76 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7964 (tp40) REVERT: E 120 MET cc_start: 0.7917 (mtt) cc_final: 0.7630 (mtt) REVERT: F 93 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: G 104 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8711 (mm110) REVERT: H 54 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8399 (tmtt) REVERT: H 65 ASP cc_start: 0.9144 (t0) cc_final: 0.8818 (t0) REVERT: H 90 GLU cc_start: 0.8885 (mp0) cc_final: 0.8159 (mp0) REVERT: H 110 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: K 132 LYS cc_start: 0.9373 (pptt) cc_final: 0.9121 (tptp) REVERT: K 222 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: K 338 GLN cc_start: 0.8976 (mt0) cc_final: 0.8747 (mt0) REVERT: K 469 MET cc_start: 0.8679 (ttm) cc_final: 0.8478 (ttp) outliers start: 25 outliers final: 19 residues processed: 167 average time/residue: 0.8397 time to fit residues: 152.6148 Evaluate side-chains 169 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 538 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 145 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.093408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067061 restraints weight = 45478.733| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.53 r_work: 0.3017 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17996 Z= 0.171 Angle : 0.638 10.260 25567 Z= 0.349 Chirality : 0.036 0.152 2888 Planarity : 0.004 0.051 2228 Dihedral : 29.592 168.771 4755 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.46 % Allowed : 23.20 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 aren not related in a simple way. whole: 0.87 (0.24), residues: 1346 helix: 1.93 (0.18), residues: 816 sheet: -1.68 (0.78), residues: 50 loop : -1.64 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 108 TYR 0.014 0.001 TYR K 743 PHE 0.011 0.001 PHE K 122 TRP 0.026 0.002 TRP K 267 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00387 (17996) covalent geometry : angle 0.63832 (25567) hydrogen bonds : bond 0.04732 ( 954) hydrogen bonds : angle 3.21719 ( 2462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9114 (pm20) cc_final: 0.8686 (pm20) REVERT: A 65 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8553 (tm) REVERT: A 133 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 24 ASP cc_start: 0.8202 (t0) cc_final: 0.7998 (t0) REVERT: B 59 LYS cc_start: 0.8930 (tttm) cc_final: 0.8728 (tmtp) REVERT: C 73 ASN cc_start: 0.8410 (m110) cc_final: 0.7975 (t0) REVERT: D 39 TYR cc_start: 0.8122 (t80) cc_final: 0.7583 (t80) REVERT: D 65 ASP cc_start: 0.8933 (t0) cc_final: 0.8669 (t0) REVERT: D 90 GLU cc_start: 0.9047 (mp0) cc_final: 0.8812 (mp0) REVERT: E 76 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7903 (tp40) REVERT: E 120 MET cc_start: 0.7939 (mtt) cc_final: 0.7650 (mtt) REVERT: F 93 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: G 104 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8716 (mm110) REVERT: H 54 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8399 (tmtt) REVERT: H 65 ASP cc_start: 0.9135 (t0) cc_final: 0.8846 (t0) REVERT: H 90 GLU cc_start: 0.8888 (mp0) cc_final: 0.8150 (mp0) REVERT: H 110 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: K 132 LYS cc_start: 0.9320 (pptt) cc_final: 0.9059 (tptp) REVERT: K 222 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6473 (mp0) REVERT: K 338 GLN cc_start: 0.8990 (mt0) cc_final: 0.8763 (mt0) REVERT: K 469 MET cc_start: 0.8703 (ttm) cc_final: 0.8495 (ttp) outliers start: 29 outliers final: 20 residues processed: 168 average time/residue: 0.8539 time to fit residues: 156.0801 Evaluate side-chains 173 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 538 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 38 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 0.0020 chunk 77 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.093842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.067459 restraints weight = 45574.015| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.55 r_work: 0.3029 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17996 Z= 0.155 Angle : 0.638 10.378 25567 Z= 0.348 Chirality : 0.036 0.153 2888 Planarity : 0.004 0.052 2228 Dihedral : 29.583 168.902 4755 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.12 % Allowed : 23.54 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 aren not related in a simple way. whole: 0.90 (0.24), residues: 1346 helix: 1.95 (0.18), residues: 816 sheet: -1.62 (0.79), residues: 50 loop : -1.63 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.015 0.001 TYR K 743 PHE 0.010 0.001 PHE K 122 TRP 0.026 0.002 TRP K 267 HIS 0.004 0.001 HIS K 211 Details of bonding type rmsd covalent geometry : bond 0.00345 (17996) covalent geometry : angle 0.63756 (25567) hydrogen bonds : bond 0.04659 ( 954) hydrogen bonds : angle 3.18861 ( 2462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5217.25 seconds wall clock time: 89 minutes 39.57 seconds (5379.57 seconds total)