Starting phenix.real_space_refine on Sun Jun 15 03:19:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnw_61629/06_2025/9jnw_61629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnw_61629/06_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_61629/06_2025/9jnw_61629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnw_61629/06_2025/9jnw_61629.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnw_61629/06_2025/9jnw_61629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnw_61629/06_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-5710/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: 9.48, 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: 4.46 Conformation dependent library (CDL) restraints added in 1.5 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: 7.03 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: 8.21 Time building geometry restraints manager: 5.14 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: 2.500 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.780 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.100 ------------------------------------------------------------------------------- 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 : 1.356 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: 1.8400 time to fit residues: 363.9269 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 : 1.452 ------------------------------------------------------------------------------- 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 = 0.093544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.067774 restraints weight = 46100.304| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.48 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 : 1.536 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: 0.8486 (t80) cc_final: 0.7712 (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: 0.8458 (mt-10) REVERT: E 76 GLN cc_start: 0.8452 (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: 0.9114 (mm110) cc_final: 0.8613 (mm110) REVERT: H 39 TYR cc_start: 0.8501 (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: 0.8447 (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: 1.6963 time to fit residues: 334.2635 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 : 1.426 ------------------------------------------------------------------------------- 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: 0.9990 chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 0.0870 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.093847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068224 restraints weight = 45541.964| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.45 r_work: 0.3064 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1727 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= 0.158 Angle : 0.617 7.815 25567 Z= 0.342 Chirality : 0.036 0.170 2888 Planarity : 0.004 0.043 2228 Dihedral : 29.786 167.103 4755 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.86 % Allowed : 14.82 % Favored : 83.32 % 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: 0.79 (0.24), residues: 1346 helix: 1.97 (0.19), residues: 806 sheet: -2.60 (0.70), residues: 62 loop : -1.65 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 267 HIS 0.004 0.001 HIS K 613 PHE 0.015 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 0.04680 ( 954) hydrogen bonds : angle 3.30767 ( 2462) covalent geometry : bond 0.00350 (17996) covalent geometry : angle 0.61667 (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 189 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9181 (pm20) cc_final: 0.8980 (pm20) REVERT: A 94 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: A 133 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 90 ASP cc_start: 0.8600 (t0) cc_final: 0.8375 (t0) REVERT: C 91 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7892 (tm-30) REVERT: D 39 TYR cc_start: 0.8354 (t80) cc_final: 0.7715 (t80) REVERT: D 65 ASP cc_start: 0.8929 (t0) cc_final: 0.8647 (t0) REVERT: E 76 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8087 (tp40) REVERT: F 93 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: G 104 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8888 (mm110) REVERT: H 54 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8426 (tmtt) REVERT: H 65 ASP cc_start: 0.9123 (t0) cc_final: 0.8867 (t0) REVERT: H 110 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: K 469 MET cc_start: 0.8616 (ttm) cc_final: 0.8378 (ttp) outliers start: 22 outliers final: 6 residues processed: 179 average time/residue: 1.7149 time to fit residues: 334.1976 Evaluate side-chains 162 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 418 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: 0.9990 chunk 144 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 128 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.0370 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.094680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069005 restraints weight = 45879.569| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.46 r_work: 0.3082 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2027 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= 0.151 Angle : 0.603 9.896 25567 Z= 0.335 Chirality : 0.035 0.154 2888 Planarity : 0.004 0.045 2228 Dihedral : 29.626 167.338 4755 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.86 % Allowed : 17.70 % Favored : 80.44 % 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: 0.84 (0.24), residues: 1346 helix: 1.98 (0.19), residues: 817 sheet: -2.48 (0.69), residues: 62 loop : -1.67 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 267 HIS 0.003 0.001 HIS K 121 PHE 0.021 0.001 PHE K 119 TYR 0.011 0.001 TYR K 543 ARG 0.004 0.000 ARG K 611 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 954) hydrogen bonds : angle 3.20573 ( 2462) covalent geometry : bond 0.00333 (17996) covalent geometry : angle 0.60296 (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 182 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9198 (pm20) cc_final: 0.8925 (pm20) REVERT: A 94 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8660 (tp30) REVERT: A 133 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8153 (mt-10) REVERT: C 90 ASP cc_start: 0.8583 (t0) cc_final: 0.8344 (t0) REVERT: C 91 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7860 (tm-30) REVERT: D 65 ASP cc_start: 0.8929 (t0) cc_final: 0.8640 (t0) REVERT: E 76 GLN cc_start: 0.8334 (tp-100) cc_final: 0.7961 (tp40) REVERT: E 120 MET cc_start: 0.7863 (mtt) cc_final: 0.7538 (mtt) REVERT: F 93 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: G 56 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: G 104 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8669 (mm110) REVERT: H 54 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8448 (tmtt) REVERT: H 65 ASP cc_start: 0.9123 (t0) cc_final: 0.8842 (t0) REVERT: K 222 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: K 469 MET cc_start: 0.8573 (ttm) cc_final: 0.8348 (ttp) REVERT: K 609 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8601 (ppp) outliers start: 22 outliers final: 6 residues processed: 174 average time/residue: 1.7579 time to fit residues: 332.9501 Evaluate side-chains 160 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU 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 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 54 LYS Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 20.0000 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.0060 chunk 135 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.093117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067375 restraints weight = 46035.896| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.43 r_work: 0.3044 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1980 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= 0.189 Angle : 0.623 8.584 25567 Z= 0.344 Chirality : 0.036 0.158 2888 Planarity : 0.004 0.047 2228 Dihedral : 29.692 167.257 4755 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.12 % Allowed : 19.31 % Favored : 78.58 % 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: 0.85 (0.24), residues: 1346 helix: 1.95 (0.19), residues: 817 sheet: -2.38 (0.70), residues: 61 loop : -1.61 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 PHE 0.034 0.002 PHE K 185 TYR 0.010 0.001 TYR K 543 ARG 0.003 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 954) hydrogen bonds : angle 3.26543 ( 2462) covalent geometry : bond 0.00428 (17996) covalent geometry : angle 0.62291 (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: 25 poor density : 158 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9182 (pm20) cc_final: 0.8805 (pm20) REVERT: A 65 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8617 (tm) REVERT: A 133 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 90 ASP cc_start: 0.8655 (t0) cc_final: 0.8449 (t0) REVERT: C 91 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 39 TYR cc_start: 0.8243 (t80) cc_final: 0.7684 (t80) REVERT: D 65 ASP cc_start: 0.8945 (t0) cc_final: 0.8653 (t0) REVERT: D 90 GLU cc_start: 0.9023 (mp0) cc_final: 0.8704 (mp0) REVERT: E 76 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7951 (tp40) REVERT: E 120 MET cc_start: 0.7944 (mtt) cc_final: 0.7608 (mtt) REVERT: F 93 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: G 56 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: G 104 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8684 (mm110) REVERT: H 54 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8467 (tmtt) REVERT: H 65 ASP cc_start: 0.9137 (t0) cc_final: 0.8878 (t0) REVERT: H 90 GLU cc_start: 0.8819 (mp0) cc_final: 0.8475 (mp0) REVERT: H 102 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7636 (tp30) REVERT: H 110 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: K 132 LYS cc_start: 0.9346 (pptt) cc_final: 0.9040 (tptp) REVERT: K 222 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: K 469 MET cc_start: 0.8639 (ttm) cc_final: 0.8391 (ttp) REVERT: K 609 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8416 (ppp) outliers start: 25 outliers final: 9 residues processed: 175 average time/residue: 1.6962 time to fit residues: 323.5898 Evaluate side-chains 165 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 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 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 475 CYS Chi-restraints excluded: chain K residue 609 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.093352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067179 restraints weight = 45879.917| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.46 r_work: 0.3036 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2042 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= 0.190 Angle : 0.629 9.448 25567 Z= 0.346 Chirality : 0.036 0.155 2888 Planarity : 0.004 0.045 2228 Dihedral : 29.686 167.895 4755 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.54 % Allowed : 19.73 % Favored : 77.73 % 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: 0.78 (0.24), residues: 1346 helix: 1.89 (0.19), residues: 823 sheet: -2.32 (0.69), residues: 61 loop : -1.68 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP K 384 HIS 0.004 0.001 HIS K 121 PHE 0.020 0.002 PHE K 185 TYR 0.010 0.001 TYR K 320 ARG 0.003 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 954) hydrogen bonds : angle 3.25031 ( 2462) covalent geometry : bond 0.00430 (17996) covalent geometry : angle 0.62934 (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 188 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9161 (pm20) cc_final: 0.8755 (pm20) REVERT: A 65 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8630 (tm) REVERT: A 120 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7384 (mtt) REVERT: A 133 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 24 ASP cc_start: 0.8117 (t0) cc_final: 0.7916 (t0) REVERT: C 90 ASP cc_start: 0.8671 (t0) cc_final: 0.8462 (t0) REVERT: D 39 TYR cc_start: 0.8224 (t80) cc_final: 0.7668 (t80) REVERT: D 65 ASP cc_start: 0.8940 (t0) cc_final: 0.8668 (t0) REVERT: D 82 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9113 (mmtm) REVERT: D 90 GLU cc_start: 0.9054 (mp0) cc_final: 0.8793 (mp0) REVERT: E 76 GLN cc_start: 0.8361 (tp-100) cc_final: 0.7966 (tp40) REVERT: E 120 MET cc_start: 0.8010 (mtt) cc_final: 0.7692 (mtt) REVERT: F 93 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: G 104 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8789 (mm110) REVERT: H 54 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8477 (tmtt) REVERT: H 65 ASP cc_start: 0.9134 (t0) cc_final: 0.8882 (t0) REVERT: H 110 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: K 132 LYS cc_start: 0.9334 (pptt) cc_final: 0.9018 (tptp) REVERT: K 222 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: K 315 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8233 (mmtp) REVERT: K 469 MET cc_start: 0.8678 (ttm) cc_final: 0.8428 (ttp) outliers start: 30 outliers final: 13 residues processed: 175 average time/residue: 1.7450 time to fit residues: 332.2750 Evaluate side-chains 168 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 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 185 PHE 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 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: 0.6980 chunk 129 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.093728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.068019 restraints weight = 45613.399| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.43 r_work: 0.3058 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2207 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= 0.170 Angle : 0.622 8.653 25567 Z= 0.342 Chirality : 0.036 0.178 2888 Planarity : 0.004 0.050 2228 Dihedral : 29.568 168.271 4755 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.03 % Allowed : 20.75 % Favored : 77.22 % 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: 811 sheet: -2.22 (0.70), residues: 61 loop : -1.62 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 PHE 0.016 0.001 PHE K 119 TYR 0.010 0.001 TYR K 543 ARG 0.003 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 954) hydrogen bonds : angle 3.20691 ( 2462) covalent geometry : bond 0.00382 (17996) covalent geometry : angle 0.62215 (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 180 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9145 (pm20) cc_final: 0.8746 (pm20) REVERT: A 65 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8630 (tm) REVERT: A 120 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7336 (mtt) REVERT: A 133 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8157 (mt-10) REVERT: B 24 ASP cc_start: 0.8057 (t0) cc_final: 0.7803 (t0) REVERT: B 84 MET cc_start: 0.9065 (mmm) cc_final: 0.8824 (mmp) REVERT: C 73 ASN cc_start: 0.8582 (m110) cc_final: 0.8035 (t0) REVERT: D 39 TYR cc_start: 0.8152 (t80) cc_final: 0.7620 (t80) REVERT: D 65 ASP cc_start: 0.8931 (t0) cc_final: 0.8676 (t0) REVERT: D 82 LYS cc_start: 0.9316 (mmmm) cc_final: 0.9108 (mmtm) REVERT: D 90 GLU cc_start: 0.9044 (mp0) cc_final: 0.8729 (mp0) REVERT: E 76 GLN cc_start: 0.8302 (tp-100) cc_final: 0.7949 (tp40) REVERT: E 120 MET cc_start: 0.8002 (mtt) cc_final: 0.7657 (mtt) REVERT: F 93 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: G 104 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8777 (mm110) REVERT: H 54 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8432 (tmtt) REVERT: H 65 ASP cc_start: 0.9132 (t0) cc_final: 0.8835 (t0) REVERT: H 110 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: K 132 LYS cc_start: 0.9322 (pptt) cc_final: 0.9029 (tptp) REVERT: K 222 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: K 315 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8198 (mmtp) REVERT: K 469 MET cc_start: 0.8646 (ttm) cc_final: 0.8397 (ttp) outliers start: 24 outliers final: 13 residues processed: 170 average time/residue: 1.7292 time to fit residues: 320.1343 Evaluate side-chains 171 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 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 315 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 146 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.094294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068467 restraints weight = 45593.485| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.45 r_work: 0.3062 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2331 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= 0.166 Angle : 0.622 7.997 25567 Z= 0.342 Chirality : 0.036 0.150 2888 Planarity : 0.004 0.050 2228 Dihedral : 29.523 168.436 4755 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.20 % Allowed : 21.08 % Favored : 76.71 % 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: 0.90 (0.24), residues: 1346 helix: 1.99 (0.19), residues: 814 sheet: -2.13 (0.70), residues: 61 loop : -1.59 (0.29), residues: 471 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 0.013 0.001 PHE K 119 TYR 0.010 0.001 TYR K 743 ARG 0.008 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 954) hydrogen bonds : angle 3.17174 ( 2462) covalent geometry : bond 0.00372 (17996) covalent geometry : angle 0.62249 (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 182 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9144 (pm20) cc_final: 0.8773 (pm20) REVERT: A 65 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8636 (tm) REVERT: A 120 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7338 (mtt) REVERT: A 133 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 24 ASP cc_start: 0.8059 (t0) cc_final: 0.7840 (t0) REVERT: B 84 MET cc_start: 0.9042 (mmm) cc_final: 0.8805 (mmp) REVERT: C 73 ASN cc_start: 0.8483 (m110) cc_final: 0.8010 (t0) REVERT: D 39 TYR cc_start: 0.8139 (t80) cc_final: 0.7615 (t80) REVERT: D 65 ASP cc_start: 0.8915 (t0) cc_final: 0.8678 (t0) REVERT: D 82 LYS cc_start: 0.9307 (mmmm) cc_final: 0.9102 (mmtm) REVERT: E 76 GLN cc_start: 0.8322 (tp-100) cc_final: 0.7935 (tp40) REVERT: E 120 MET cc_start: 0.8004 (mtt) cc_final: 0.7708 (mtt) REVERT: F 93 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: G 104 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8779 (mm110) REVERT: H 54 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8435 (tmtt) REVERT: H 65 ASP cc_start: 0.9136 (t0) cc_final: 0.8861 (t0) REVERT: H 110 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8331 (pt0) REVERT: K 132 LYS cc_start: 0.9310 (pptt) cc_final: 0.9022 (tptp) REVERT: K 222 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: K 315 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8192 (mmtp) REVERT: K 469 MET cc_start: 0.8622 (ttm) cc_final: 0.8375 (ttp) outliers start: 26 outliers final: 13 residues processed: 173 average time/residue: 1.7500 time to fit residues: 329.5770 Evaluate side-chains 172 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 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 315 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 69 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.094911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069099 restraints weight = 45696.642| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.46 r_work: 0.3079 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2442 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= 0.153 Angle : 0.627 8.203 25567 Z= 0.343 Chirality : 0.036 0.158 2888 Planarity : 0.004 0.050 2228 Dihedral : 29.473 168.760 4755 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.86 % Allowed : 21.51 % 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: 0.91 (0.24), residues: 1346 helix: 1.98 (0.19), residues: 814 sheet: -2.02 (0.71), residues: 61 loop : -1.57 (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 0.016 0.001 PHE K 133 TYR 0.010 0.001 TYR K 543 ARG 0.011 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 954) hydrogen bonds : angle 3.18798 ( 2462) covalent geometry : bond 0.00338 (17996) covalent geometry : angle 0.62682 (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 176 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 2.270 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9141 (pm20) cc_final: 0.8773 (pm20) REVERT: A 65 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8620 (tm) REVERT: A 94 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: A 120 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7326 (mtt) REVERT: A 133 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 24 ASP cc_start: 0.8113 (t0) cc_final: 0.7889 (t0) REVERT: C 73 ASN cc_start: 0.8368 (m110) cc_final: 0.7947 (t0) REVERT: D 39 TYR cc_start: 0.8118 (t80) cc_final: 0.7585 (t80) REVERT: E 76 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7958 (tp40) REVERT: E 79 LYS cc_start: 0.8968 (tttp) cc_final: 0.8758 (tttm) REVERT: E 120 MET cc_start: 0.7967 (mtt) cc_final: 0.7672 (mtt) REVERT: F 93 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: G 104 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8946 (mm110) REVERT: H 31 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8512 (mtmm) REVERT: H 54 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8419 (tmtt) REVERT: H 65 ASP cc_start: 0.9137 (t0) cc_final: 0.8863 (t0) REVERT: H 90 GLU cc_start: 0.8806 (mp0) cc_final: 0.8469 (mp0) REVERT: H 110 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: K 115 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8329 (mm) REVERT: K 132 LYS cc_start: 0.9318 (pptt) cc_final: 0.9039 (tptp) REVERT: K 222 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: K 315 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8157 (mmtp) REVERT: K 469 MET cc_start: 0.8572 (ttm) cc_final: 0.8326 (ttp) outliers start: 22 outliers final: 8 residues processed: 168 average time/residue: 2.0341 time to fit residues: 372.8170 Evaluate side-chains 168 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 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 115 LEU 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 538 CYS 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: 2.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.093622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067487 restraints weight = 45395.045| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.46 r_work: 0.3041 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17996 Z= 0.195 Angle : 0.657 10.979 25567 Z= 0.356 Chirality : 0.037 0.172 2888 Planarity : 0.004 0.050 2228 Dihedral : 29.575 168.627 4755 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.95 % Allowed : 22.35 % Favored : 75.70 % 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: 0.83 (0.24), residues: 1346 helix: 1.90 (0.18), residues: 816 sheet: -2.19 (0.67), residues: 64 loop : -1.56 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE K 119 TYR 0.016 0.001 TYR K 743 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 954) hydrogen bonds : angle 3.25159 ( 2462) covalent geometry : bond 0.00443 (17996) covalent geometry : angle 0.65663 (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 175 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9125 (pm20) cc_final: 0.8701 (pm20) REVERT: A 65 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8669 (tm) REVERT: A 120 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7457 (mtt) REVERT: A 133 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8186 (mt-10) REVERT: C 73 ASN cc_start: 0.8542 (m110) cc_final: 0.8038 (t0) REVERT: D 39 TYR cc_start: 0.8203 (t80) cc_final: 0.7651 (t80) REVERT: D 90 GLU cc_start: 0.8896 (mp0) cc_final: 0.8381 (mp0) REVERT: E 76 GLN cc_start: 0.8365 (tp-100) cc_final: 0.7969 (tp40) REVERT: E 120 MET cc_start: 0.8063 (mtt) cc_final: 0.7785 (mtt) REVERT: F 93 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: G 104 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8793 (mm110) REVERT: H 54 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8508 (tmtt) REVERT: H 65 ASP cc_start: 0.9135 (t0) cc_final: 0.8876 (t0) REVERT: H 90 GLU cc_start: 0.8784 (mp0) cc_final: 0.8429 (mp0) REVERT: H 110 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: K 132 LYS cc_start: 0.9312 (pptt) cc_final: 0.9056 (tptp) REVERT: K 222 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: K 469 MET cc_start: 0.8633 (ttm) cc_final: 0.8371 (ttp) outliers start: 23 outliers final: 10 residues processed: 167 average time/residue: 1.7262 time to fit residues: 314.0408 Evaluate side-chains 164 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 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 538 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 15 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 148 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.094461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068578 restraints weight = 45668.155| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.46 r_work: 0.3066 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17996 Z= 0.159 Angle : 0.640 10.400 25567 Z= 0.348 Chirality : 0.036 0.150 2888 Planarity : 0.004 0.049 2228 Dihedral : 29.520 169.239 4755 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.69 % Allowed : 22.27 % Favored : 76.04 % 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: 0.89 (0.24), residues: 1346 helix: 1.95 (0.18), residues: 816 sheet: -2.08 (0.68), residues: 64 loop : -1.53 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 267 HIS 0.005 0.001 HIS K 111 PHE 0.012 0.001 PHE K 119 TYR 0.015 0.001 TYR K 743 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 954) hydrogen bonds : angle 3.18358 ( 2462) covalent geometry : bond 0.00358 (17996) covalent geometry : angle 0.64025 (25567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11029.09 seconds wall clock time: 191 minutes 33.99 seconds (11493.99 seconds total)