Starting phenix.real_space_refine on Sun May 18 10:20:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnw_61629/05_2025/9jnw_61629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnw_61629/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnw_61629/05_2025/9jnw_61629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnw_61629/05_2025/9jnw_61629.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnw_61629/05_2025/9jnw_61629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnw_61629/05_2025/9jnw_61629.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.39, per 1000 atoms: 0.55 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: 4.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 7.41 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: 8.65 Time building geometry restraints manager: 4.83 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: 1.780 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.890 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP K 267 HIS 0.005 0.001 HIS B 18 PHE 0.023 0.002 PHE K 385 TYR 0.029 0.002 TYR K 320 ARG 0.010 0.001 ARG K 645 Details of bonding type rmsd hydrogen bonds : bond 0.10219 ( 954) hydrogen bonds : angle 4.30709 ( 2462) covalent geometry : bond 0.00790 (17996) covalent geometry : angle 0.78151 (25567) *********************** 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 : 1.425 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: 1.7397 time to fit residues: 344.7378 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 : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 HIS ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.093547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.067768 restraints weight = 46081.705| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.49 r_work: 0.3055 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17996 Z= 0.161 Angle : 0.639 8.513 25567 Z= 0.356 Chirality : 0.037 0.172 2888 Planarity : 0.004 0.042 2228 Dihedral : 30.015 167.610 4755 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 1.19 % Allowed : 11.09 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1346 helix: 1.75 (0.19), residues: 806 sheet: -2.83 (0.68), residues: 62 loop : -1.73 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 267 HIS 0.003 0.001 HIS K 613 PHE 0.014 0.001 PHE K 574 TYR 0.015 0.001 TYR H 39 ARG 0.005 0.000 ARG K 645 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 954) hydrogen bonds : angle 3.46998 ( 2462) covalent geometry : bond 0.00355 (17996) covalent geometry : angle 0.63929 (25567) *********************** 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 189 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 90 ASP cc_start: 0.8761 (t0) cc_final: 0.8290 (t0) REVERT: D 39 TYR cc_start: 0.8487 (t80) cc_final: 0.7713 (t80) REVERT: D 65 ASP cc_start: 0.8955 (t0) cc_final: 0.8631 (t0) REVERT: E 50 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8459 (mt-10) REVERT: E 76 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8083 (tp40) REVERT: F 93 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: G 104 GLN cc_start: 0.9115 (mm110) cc_final: 0.8613 (mm110) REVERT: H 39 TYR cc_start: 0.8502 (t80) cc_final: 0.8283 (t80) REVERT: H 65 ASP cc_start: 0.9134 (t0) cc_final: 0.8873 (t0) REVERT: H 110 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: K 469 MET cc_start: 0.8610 (ttm) cc_final: 0.8381 (ttp) outliers start: 14 outliers final: 4 residues processed: 181 average time/residue: 1.6895 time to fit residues: 332.8982 Evaluate side-chains 155 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 475 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 101 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN ** K 205 ASN ** 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 = 0.3758 r_free = 0.3758 target = 0.094065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068483 restraints weight = 45698.783| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.46 r_work: 0.3069 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17996 Z= 0.156 Angle : 0.613 7.755 25567 Z= 0.341 Chirality : 0.036 0.162 2888 Planarity : 0.004 0.043 2228 Dihedral : 29.755 167.053 4755 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.78 % Allowed : 14.99 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1346 helix: 1.93 (0.19), residues: 812 sheet: -2.59 (0.69), residues: 62 loop : -1.69 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 267 HIS 0.004 0.001 HIS K 613 PHE 0.013 0.001 PHE K 133 TYR 0.012 0.001 TYR K 543 ARG 0.004 0.000 ARG K 645 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 954) hydrogen bonds : angle 3.29433 ( 2462) covalent geometry : bond 0.00345 (17996) covalent geometry : angle 0.61332 (25567) *********************** 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 188 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8577 (tp30) REVERT: A 133 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8159 (mt-10) REVERT: C 90 ASP cc_start: 0.8603 (t0) cc_final: 0.8394 (t0) REVERT: C 91 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7927 (tm-30) REVERT: D 39 TYR cc_start: 0.8348 (t80) cc_final: 0.7775 (t80) REVERT: D 65 ASP cc_start: 0.8925 (t0) cc_final: 0.8647 (t0) REVERT: E 76 GLN cc_start: 0.8413 (tp-100) cc_final: 0.8091 (tp40) REVERT: F 93 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: G 104 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8680 (mm110) REVERT: H 54 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8440 (tmtt) REVERT: H 65 ASP cc_start: 0.9123 (t0) cc_final: 0.8866 (t0) REVERT: H 110 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: K 469 MET cc_start: 0.8617 (ttm) cc_final: 0.8377 (ttp) outliers start: 21 outliers final: 5 residues processed: 178 average time/residue: 1.5999 time to fit residues: 311.1420 Evaluate side-chains 159 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU 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 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 475 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 7 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 chunk 135 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.095069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069526 restraints weight = 45857.808| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.46 r_work: 0.3092 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17996 Z= 0.147 Angle : 0.602 9.412 25567 Z= 0.335 Chirality : 0.035 0.157 2888 Planarity : 0.004 0.046 2228 Dihedral : 29.570 167.400 4755 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.86 % Allowed : 17.61 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1346 helix: 2.00 (0.19), residues: 817 sheet: -2.42 (0.70), residues: 62 loop : -1.67 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 267 HIS 0.003 0.001 HIS B 75 PHE 0.020 0.001 PHE K 119 TYR 0.011 0.001 TYR K 543 ARG 0.003 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 954) hydrogen bonds : angle 3.19167 ( 2462) covalent geometry : bond 0.00324 (17996) covalent geometry : angle 0.60165 (25567) *********************** 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 183 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 59 LYS cc_start: 0.8958 (tttm) cc_final: 0.8721 (tttm) REVERT: B 63 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8379 (mt-10) REVERT: C 73 ASN cc_start: 0.8182 (m-40) cc_final: 0.7930 (t0) REVERT: C 90 ASP cc_start: 0.8562 (t0) cc_final: 0.8357 (t0) REVERT: C 91 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 65 ASP cc_start: 0.8917 (t0) cc_final: 0.8630 (t0) REVERT: E 76 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7974 (tp40) REVERT: E 94 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: E 120 MET cc_start: 0.7820 (mtt) cc_final: 0.7499 (mtt) REVERT: F 93 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: G 56 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8587 (tt0) REVERT: G 104 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8680 (mm110) REVERT: H 54 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8511 (tmtt) REVERT: H 65 ASP cc_start: 0.9118 (t0) cc_final: 0.8838 (t0) REVERT: H 90 GLU cc_start: 0.8813 (mp0) cc_final: 0.8441 (mp0) REVERT: H 110 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: K 469 MET cc_start: 0.8559 (ttm) cc_final: 0.8341 (ttp) outliers start: 22 outliers final: 6 residues processed: 176 average time/residue: 1.5676 time to fit residues: 301.2816 Evaluate side-chains 158 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU 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 H residue 36 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.093286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067486 restraints weight = 46026.722| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.43 r_work: 0.3049 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2074 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= 0.184 Angle : 0.618 8.612 25567 Z= 0.342 Chirality : 0.036 0.158 2888 Planarity : 0.004 0.049 2228 Dihedral : 29.658 167.322 4755 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1346 helix: 1.98 (0.19), residues: 817 sheet: -2.32 (0.70), residues: 61 loop : -1.63 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 384 HIS 0.005 0.001 HIS K 121 PHE 0.025 0.002 PHE K 185 TYR 0.010 0.001 TYR K 543 ARG 0.005 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 954) hydrogen bonds : angle 3.22590 ( 2462) covalent geometry : bond 0.00416 (17996) covalent geometry : angle 0.61801 (25567) *********************** 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 183 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8169 (mt-10) REVERT: C 91 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8033 (tm-30) REVERT: D 65 ASP cc_start: 0.8940 (t0) cc_final: 0.8650 (t0) REVERT: D 90 GLU cc_start: 0.9019 (mp0) cc_final: 0.8761 (mp0) REVERT: E 76 GLN cc_start: 0.8302 (tp-100) cc_final: 0.7902 (tp40) REVERT: E 120 MET cc_start: 0.7952 (mtt) cc_final: 0.7597 (mtt) REVERT: F 93 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: G 104 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8685 (mm110) REVERT: H 54 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8430 (tmtt) REVERT: H 65 ASP cc_start: 0.9131 (t0) cc_final: 0.8870 (t0) REVERT: H 102 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7675 (tp30) REVERT: H 110 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: K 222 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: K 413 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.8058 (mp) REVERT: K 469 MET cc_start: 0.8636 (ttm) cc_final: 0.8386 (ttp) outliers start: 24 outliers final: 9 residues processed: 177 average time/residue: 1.6461 time to fit residues: 317.8857 Evaluate side-chains 161 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL 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 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 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 413 ILE 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 71 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3743 r_free = 0.3743 target = 0.093337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067526 restraints weight = 45732.993| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.42 r_work: 0.3047 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2136 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= 0.183 Angle : 0.627 9.649 25567 Z= 0.345 Chirality : 0.036 0.174 2888 Planarity : 0.004 0.048 2228 Dihedral : 29.628 168.013 4755 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.54 % Allowed : 19.48 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1346 helix: 1.89 (0.19), residues: 825 sheet: -2.25 (0.71), residues: 60 loop : -1.67 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 PHE 0.018 0.002 PHE K 185 TYR 0.016 0.001 TYR K 743 ARG 0.003 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 954) hydrogen bonds : angle 3.25134 ( 2462) covalent geometry : bond 0.00414 (17996) covalent geometry : angle 0.62688 (25567) *********************** 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 : 1.445 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7344 (mtt) REVERT: A 133 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8185 (mt-10) REVERT: C 73 ASN cc_start: 0.8593 (m110) cc_final: 0.8032 (t0) REVERT: D 39 TYR cc_start: 0.8283 (t80) cc_final: 0.7677 (t80) REVERT: D 65 ASP cc_start: 0.8925 (t0) cc_final: 0.8648 (t0) REVERT: D 82 LYS cc_start: 0.9310 (mmmm) cc_final: 0.9098 (mmtm) REVERT: D 90 GLU cc_start: 0.9043 (mp0) cc_final: 0.8726 (mp0) REVERT: E 76 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7951 (tp40) REVERT: E 120 MET cc_start: 0.7993 (mtt) cc_final: 0.7634 (mtt) REVERT: F 93 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: G 104 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8774 (mm110) REVERT: H 54 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8417 (tmtt) REVERT: H 65 ASP cc_start: 0.9126 (t0) cc_final: 0.8873 (t0) REVERT: H 90 GLU cc_start: 0.8849 (mp0) cc_final: 0.8508 (mp0) REVERT: H 110 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: K 132 LYS cc_start: 0.9343 (pptt) cc_final: 0.9025 (tptp) REVERT: K 222 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: K 315 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8232 (mmtp) REVERT: K 413 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8010 (mp) REVERT: K 469 MET cc_start: 0.8667 (ttm) cc_final: 0.8419 (ttp) outliers start: 30 outliers final: 12 residues processed: 173 average time/residue: 1.7193 time to fit residues: 323.9762 Evaluate side-chains 167 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET 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 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 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 315 LYS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 538 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3766 r_free = 0.3766 target = 0.094745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068922 restraints weight = 45670.666| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.46 r_work: 0.3076 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17996 Z= 0.155 Angle : 0.616 7.927 25567 Z= 0.338 Chirality : 0.035 0.158 2888 Planarity : 0.004 0.049 2228 Dihedral : 29.475 168.422 4755 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.03 % Allowed : 20.58 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1346 helix: 2.02 (0.19), residues: 814 sheet: -2.14 (0.71), residues: 61 loop : -1.59 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 PHE 0.019 0.001 PHE K 133 TYR 0.010 0.001 TYR K 543 ARG 0.005 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 954) hydrogen bonds : angle 3.14592 ( 2462) covalent geometry : bond 0.00345 (17996) covalent geometry : angle 0.61568 (25567) *********************** 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 184 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7264 (mtt) REVERT: B 19 ARG cc_start: 0.8721 (mpp80) cc_final: 0.8313 (ptm-80) REVERT: C 73 ASN cc_start: 0.8444 (m110) cc_final: 0.8009 (t0) REVERT: D 39 TYR cc_start: 0.8204 (t80) cc_final: 0.7637 (t80) REVERT: D 65 ASP cc_start: 0.8924 (t0) cc_final: 0.8720 (t0) REVERT: D 82 LYS cc_start: 0.9307 (mmmm) cc_final: 0.9101 (mmtm) REVERT: E 76 GLN cc_start: 0.8284 (tp-100) cc_final: 0.7939 (tp40) REVERT: E 120 MET cc_start: 0.7935 (mtt) cc_final: 0.7630 (mtt) REVERT: F 93 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: G 104 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8726 (mm110) REVERT: H 31 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8488 (mtmm) REVERT: H 54 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8411 (tmtt) REVERT: H 65 ASP cc_start: 0.9137 (t0) cc_final: 0.8865 (t0) REVERT: H 110 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: K 132 LYS cc_start: 0.9327 (pptt) cc_final: 0.9036 (tptp) REVERT: K 222 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: K 413 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7998 (mp) REVERT: K 469 MET cc_start: 0.8632 (ttm) cc_final: 0.8389 (ttp) outliers start: 24 outliers final: 12 residues processed: 175 average time/residue: 1.5871 time to fit residues: 302.5486 Evaluate side-chains 166 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 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 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 115 LEU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 475 CYS 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 146 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3759 r_free = 0.3759 target = 0.094360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068546 restraints weight = 45581.945| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.43 r_work: 0.3065 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17996 Z= 0.171 Angle : 0.627 7.704 25567 Z= 0.343 Chirality : 0.036 0.153 2888 Planarity : 0.004 0.049 2228 Dihedral : 29.499 168.407 4755 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.37 % Allowed : 20.83 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1346 helix: 1.98 (0.18), residues: 816 sheet: -2.08 (0.71), residues: 60 loop : -1.59 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.001 PHE K 133 TYR 0.009 0.001 TYR K 543 ARG 0.008 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 954) hydrogen bonds : angle 3.16508 ( 2462) covalent geometry : bond 0.00386 (17996) covalent geometry : angle 0.62701 (25567) *********************** 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 185 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8618 (tm) REVERT: A 120 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7334 (mtt) REVERT: A 133 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 59 LYS cc_start: 0.9041 (tttm) cc_final: 0.8838 (tmtp) REVERT: C 73 ASN cc_start: 0.8450 (m110) cc_final: 0.8019 (t0) REVERT: D 39 TYR cc_start: 0.8219 (t80) cc_final: 0.7655 (t80) REVERT: D 82 LYS cc_start: 0.9299 (mmmm) cc_final: 0.9094 (mmtm) REVERT: E 76 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7867 (tp40) REVERT: E 81 ASP cc_start: 0.9125 (p0) cc_final: 0.8903 (p0) REVERT: E 120 MET cc_start: 0.8000 (mtt) cc_final: 0.7698 (mtt) REVERT: F 93 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: G 104 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8775 (mm110) REVERT: H 31 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8525 (mtmm) REVERT: H 54 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8427 (tmtt) REVERT: H 65 ASP cc_start: 0.9146 (t0) cc_final: 0.8845 (t0) REVERT: H 110 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: K 132 LYS cc_start: 0.9320 (pptt) cc_final: 0.9041 (tptp) REVERT: K 222 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: K 315 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (mmtp) REVERT: K 413 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.8018 (mp) REVERT: K 469 MET cc_start: 0.8639 (ttm) cc_final: 0.8388 (ttp) outliers start: 28 outliers final: 14 residues processed: 175 average time/residue: 1.5624 time to fit residues: 298.2342 Evaluate side-chains 171 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET 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 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 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 315 LYS Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 413 ILE 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 69 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.095123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069328 restraints weight = 45627.920| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.45 r_work: 0.3085 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17996 Z= 0.158 Angle : 0.624 7.905 25567 Z= 0.341 Chirality : 0.035 0.155 2888 Planarity : 0.004 0.049 2228 Dihedral : 29.406 168.961 4755 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.03 % Allowed : 21.34 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1346 helix: 1.99 (0.19), residues: 814 sheet: -2.07 (0.70), residues: 61 loop : -1.52 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 267 HIS 0.004 0.001 HIS K 111 PHE 0.010 0.001 PHE K 122 TYR 0.013 0.001 TYR K 743 ARG 0.007 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 954) hydrogen bonds : angle 3.18040 ( 2462) covalent geometry : bond 0.00354 (17996) covalent geometry : angle 0.62357 (25567) *********************** 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 179 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8634 (tm) REVERT: A 120 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7283 (mtt) REVERT: A 133 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8236 (mt-10) REVERT: C 73 ASN cc_start: 0.8329 (m110) cc_final: 0.7960 (t0) REVERT: D 39 TYR cc_start: 0.8198 (t80) cc_final: 0.7627 (t80) REVERT: E 76 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7839 (tp40) REVERT: E 81 ASP cc_start: 0.9156 (p0) cc_final: 0.8947 (p0) REVERT: E 120 MET cc_start: 0.7938 (mtt) cc_final: 0.7650 (mtt) REVERT: F 93 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: G 104 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8741 (mm110) REVERT: H 31 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8519 (mtmm) REVERT: H 65 ASP cc_start: 0.9143 (t0) cc_final: 0.8870 (t0) REVERT: H 90 GLU cc_start: 0.8783 (mp0) cc_final: 0.8506 (mp0) REVERT: H 110 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: K 132 LYS cc_start: 0.9345 (pptt) cc_final: 0.9094 (tptp) REVERT: K 222 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: K 469 MET cc_start: 0.8564 (ttm) cc_final: 0.8321 (ttp) REVERT: K 706 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7154 (mt) outliers start: 24 outliers final: 13 residues processed: 171 average time/residue: 1.5924 time to fit residues: 296.7972 Evaluate side-chains 167 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 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 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 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 = 0.3764 r_free = 0.3764 target = 0.094629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068701 restraints weight = 45335.132| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.44 r_work: 0.3073 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17996 Z= 0.170 Angle : 0.636 10.424 25567 Z= 0.347 Chirality : 0.036 0.170 2888 Planarity : 0.004 0.049 2228 Dihedral : 29.431 169.143 4755 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.61 % Allowed : 22.02 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1346 helix: 1.95 (0.18), residues: 816 sheet: -1.48 (0.82), residues: 50 loop : -1.57 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 267 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.001 PHE K 133 TYR 0.015 0.001 TYR K 743 ARG 0.007 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 954) hydrogen bonds : angle 3.21613 ( 2462) covalent geometry : bond 0.00386 (17996) covalent geometry : angle 0.63556 (25567) ********************** 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 171 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8646 (tm) REVERT: A 120 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7333 (mtt) REVERT: A 133 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8251 (mt-10) REVERT: B 24 ASP cc_start: 0.8184 (t0) cc_final: 0.7952 (t0) REVERT: C 73 ASN cc_start: 0.8353 (m110) cc_final: 0.7957 (t0) REVERT: D 39 TYR cc_start: 0.8240 (t80) cc_final: 0.7667 (t80) REVERT: E 76 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7863 (tp40) REVERT: E 80 THR cc_start: 0.9201 (m) cc_final: 0.8858 (m) REVERT: E 120 MET cc_start: 0.7988 (mtt) cc_final: 0.7699 (mtt) REVERT: F 93 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: G 104 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8777 (mm110) REVERT: H 31 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8522 (mtmm) REVERT: H 65 ASP cc_start: 0.9150 (t0) cc_final: 0.8823 (t0) REVERT: H 110 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: K 132 LYS cc_start: 0.9364 (pptt) cc_final: 0.9085 (tptp) REVERT: K 222 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: K 469 MET cc_start: 0.8604 (ttm) cc_final: 0.8348 (ttp) outliers start: 19 outliers final: 12 residues processed: 165 average time/residue: 1.6144 time to fit residues: 291.1507 Evaluate side-chains 166 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 100 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 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 363 LEU 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 15 optimal weight: 0.0670 chunk 126 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 131 optimal weight: 0.0020 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9730 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.094864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069053 restraints weight = 45872.650| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.46 r_work: 0.3079 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17996 Z= 0.167 Angle : 0.632 10.155 25567 Z= 0.345 Chirality : 0.036 0.165 2888 Planarity : 0.004 0.049 2228 Dihedral : 29.390 169.536 4755 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.95 % Allowed : 21.59 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1346 helix: 1.96 (0.19), residues: 816 sheet: -2.07 (0.67), residues: 64 loop : -1.47 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 267 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE K 122 TYR 0.014 0.001 TYR K 743 ARG 0.010 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 954) hydrogen bonds : angle 3.17074 ( 2462) covalent geometry : bond 0.00378 (17996) covalent geometry : angle 0.63217 (25567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10352.38 seconds wall clock time: 178 minutes 52.22 seconds (10732.22 seconds total)