Starting phenix.real_space_refine on Thu Aug 6 17:46:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnx_61630/08_2026/9jnx_61630.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnx_61630/08_2026/9jnx_61630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jnx_61630/08_2026/9jnx_61630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnx_61630/08_2026/9jnx_61630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jnx_61630/08_2026/9jnx_61630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnx_61630/08_2026/9jnx_61630.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 9692 2.51 5 N 3073 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16809 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: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 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: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4766 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 558} Chain breaks: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.16, per 1000 atoms: 0.19 Number of scatterers: 16809 At special positions: 0 Unit cell: (106.085, 123.405, 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 294 15.00 Mg 1 11.99 O 3724 8.00 N 3073 7.00 C 9692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 673.2 milliseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 13 sheets defined 63.2% alpha, 3.7% beta 145 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.736A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.503A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.773A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (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 26 through 37 removed outlier: 3.698A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.453A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) 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 removed outlier: 3.610A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.739A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.520A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.581A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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 removed outlier: 4.119A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.509A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.552A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (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: 3.877A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.744A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.870A pdb=" N THR K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 115 No H-bonds generated for 'chain 'K' and resid 114 through 115' Processing helix chain 'K' and resid 116 through 118 No H-bonds generated for 'chain 'K' and resid 116 through 118' Processing helix chain 'K' and resid 119 through 126 removed outlier: 4.398A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 137 removed outlier: 4.399A pdb=" N GLN K 135 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL K 136 " --> pdb=" O PHE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 253 through 256 Processing helix chain 'K' and resid 257 through 268 removed outlier: 3.730A pdb=" N LEU K 261 " --> pdb=" O LEU K 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU K 263 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.803A 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 303 through 309 Processing helix chain 'K' and resid 334 through 342 Processing helix chain 'K' and resid 360 through 371 Processing helix chain 'K' and resid 377 through 386 Processing helix chain 'K' and resid 396 through 406 Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 469 through 478 removed outlier: 3.715A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 494 through 498 removed outlier: 3.692A pdb=" N LEU K 497 " --> pdb=" O ASP K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 516 removed outlier: 3.811A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 541 Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 601 through 614 removed outlier: 4.177A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.913A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 658 removed outlier: 4.392A pdb=" N SER K 657 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 727 Processing helix chain 'K' and resid 730 through 735 removed outlier: 3.782A pdb=" N GLN K 735 " --> pdb=" O LEU K 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.931A 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: 7.109A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.156A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 301 through 302 removed outlier: 7.657A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 427 through 431 removed outlier: 6.335A pdb=" N LEU K 427 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL K 627 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 547 through 548 577 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3045 1.33 - 1.45: 5354 1.45 - 1.57: 8680 1.57 - 1.69: 585 1.69 - 1.81: 43 Bond restraints: 17707 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.34e-02 5.57e+03 2.33e+01 bond pdb=" C3' DT I 142 " pdb=" C2' DT I 142 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C1' DC I 143 " pdb=" N1 DC I 143 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" C3' DC I 70 " pdb=" O3' DC I 70 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.99e+00 bond pdb=" C3' DC J 3 " pdb=" C2' DC J 3 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.37e+00 ... (remaining 17702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 23426 1.54 - 3.09: 1545 3.09 - 4.63: 161 4.63 - 6.18: 35 6.18 - 7.72: 6 Bond angle restraints: 25173 Sorted by residual: angle pdb=" O4' DA I 98 " pdb=" C4' DA I 98 " pdb=" C3' DA I 98 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.22e+01 angle pdb=" O4' DA I 30 " pdb=" C4' DA I 30 " pdb=" C3' DA I 30 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.52e+01 angle pdb=" O4' DA I 39 " pdb=" C4' DA I 39 " pdb=" C3' DA I 39 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" O4' DG I 132 " pdb=" C4' DG I 132 " pdb=" C3' DG I 132 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.11e+01 ... (remaining 25168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 8434 35.12 - 70.24: 1455 70.24 - 105.36: 30 105.36 - 140.49: 5 140.49 - 175.61: 9 Dihedral angle restraints: 9933 sinusoidal: 6000 harmonic: 3933 Sorted by residual: dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 -144.53 -35.47 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA TYR K 545 " pdb=" C TYR K 545 " pdb=" N CYS K 546 " pdb=" CA CYS K 546 " ideal model delta harmonic sigma weight residual 180.00 146.23 33.77 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA HIS B 18 " pdb=" C HIS B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 9930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2310 0.058 - 0.117: 476 0.117 - 0.175: 61 0.175 - 0.233: 3 0.233 - 0.291: 2 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CB ILE K 329 " pdb=" CA ILE K 329 " pdb=" CG1 ILE K 329 " pdb=" CG2 ILE K 329 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE K 548 " pdb=" CA ILE K 548 " pdb=" CG1 ILE K 548 " pdb=" CG2 ILE K 548 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C3' DA I 20 " pdb=" C4' DA I 20 " pdb=" O3' DA I 20 " pdb=" C2' DA I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2849 not shown) Planarity restraints: 2181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO K 490 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 82 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO K 83 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO K 83 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 83 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " 0.023 2.00e-02 2.50e+03 1.02e-02 2.86e+00 pdb=" N9 DA I 39 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " -0.002 2.00e-02 2.50e+03 ... (remaining 2178 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 129 2.57 - 3.15: 13377 3.15 - 3.74: 29126 3.74 - 4.32: 40111 4.32 - 4.90: 59563 Nonbonded interactions: 142306 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 1.990 2.170 nonbonded pdb="MG MG K1201 " pdb=" O3A ADP K1202 " model vdw 2.074 2.170 nonbonded pdb=" O PHE K 122 " pdb=" OG SER K 125 " model vdw 2.135 3.040 nonbonded pdb=" O VAL K 398 " pdb=" ND1 HIS K 402 " model vdw 2.158 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.178 3.040 ... (remaining 142301 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' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 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)) } 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: 3.130 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:10.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.007 0.065 17707 Z= 0.521 Angle : 0.811 7.720 25173 Z= 0.652 Chirality : 0.048 0.291 2852 Planarity : 0.004 0.052 2181 Dihedral : 26.304 175.607 7383 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.56 % Rotamer: Outliers : 0.17 % Allowed : 0.43 % Favored : 99.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.23), residues: 1318 helix: 1.19 (0.19), residues: 775 sheet: -1.81 (0.72), residues: 63 loop : -1.91 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 83 TYR 0.017 0.002 TYR K 320 PHE 0.025 0.002 PHE K 524 TRP 0.022 0.002 TRP K 260 HIS 0.007 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.52 (17707) covalent geometry : angle 0.81052 / 0.65 (25173) hydrogen bonds : bond 0.11607 / 7.24 ( 949) hydrogen bonds : angle 4.47714 / 3.23 ( 2433) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8237 (tt0) cc_final: 0.7869 (tt0) REVERT: A 76 GLN cc_start: 0.8317 (pp30) cc_final: 0.8080 (pp30) REVERT: F 25 ASN cc_start: 0.9039 (m-40) cc_final: 0.8460 (m-40) REVERT: F 79 LYS cc_start: 0.8847 (mttp) cc_final: 0.8615 (mttm) REVERT: K 93 LYS cc_start: 0.6321 (mttm) cc_final: 0.5905 (pmtt) REVERT: K 377 ASP cc_start: 0.8612 (m-30) cc_final: 0.8279 (m-30) REVERT: K 418 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: K 525 SER cc_start: 0.8821 (t) cc_final: 0.8604 (p) REVERT: K 645 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8140 (tpp80) REVERT: K 717 ASN cc_start: 0.8213 (m-40) cc_final: 0.8013 (t0) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.7318 time to fit residues: 150.5446 Evaluate side-chains 147 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 418 GLU Chi-restraints excluded: chain K residue 420 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN F 93 GLN G 38 ASN K 86 ASN K 617 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.088429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.062466 restraints weight = 44633.522| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.26 r_work: 0.2890 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17707 Z= 0.169 Angle : 0.717 8.653 25173 Z= 0.394 Chirality : 0.048 0.341 2852 Planarity : 0.005 0.051 2181 Dihedral : 30.314 179.286 4683 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.75 % Favored : 93.17 % Rotamer: Outliers : 1.04 % Allowed : 10.31 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1318 helix: 1.58 (0.18), residues: 792 sheet: -1.54 (0.74), residues: 63 loop : -1.79 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 769 TYR 0.014 0.001 TYR F 51 PHE 0.020 0.001 PHE K 524 TRP 0.017 0.001 TRP K 364 HIS 0.008 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (17707) covalent geometry : angle 0.71748 / 0.39 (25173) hydrogen bonds : bond 0.04989 / 3.42 ( 949) hydrogen bonds : angle 3.43520 / 2.47 ( 2433) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8841 (tt0) cc_final: 0.8394 (tt0) REVERT: A 76 GLN cc_start: 0.8679 (pp30) cc_final: 0.8405 (pp30) REVERT: A 120 MET cc_start: 0.8762 (mtm) cc_final: 0.8549 (mtt) REVERT: A 133 GLU cc_start: 0.8498 (mp0) cc_final: 0.8195 (mp0) REVERT: C 64 GLU cc_start: 0.8648 (tt0) cc_final: 0.8418 (pt0) REVERT: E 59 GLU cc_start: 0.8884 (pm20) cc_final: 0.8631 (pm20) REVERT: F 25 ASN cc_start: 0.9167 (m-40) cc_final: 0.8632 (m-40) REVERT: H 65 ASP cc_start: 0.8745 (t0) cc_final: 0.8528 (t0) REVERT: K 93 LYS cc_start: 0.6658 (mttm) cc_final: 0.6134 (pmtt) REVERT: K 342 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8236 (tm-30) REVERT: K 377 ASP cc_start: 0.8940 (m-30) cc_final: 0.8731 (m-30) REVERT: K 525 SER cc_start: 0.8966 (t) cc_final: 0.8734 (p) REVERT: K 645 ARG cc_start: 0.8930 (tpp80) cc_final: 0.8400 (tpp80) REVERT: K 717 ASN cc_start: 0.8389 (m-40) cc_final: 0.8180 (t0) outliers start: 12 outliers final: 5 residues processed: 172 average time/residue: 0.7583 time to fit residues: 140.7726 Evaluate side-chains 153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 80 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 110 ASN E 68 GLN G 38 ASN K 617 GLN K 774 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.086412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060381 restraints weight = 45315.222| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.26 r_work: 0.2829 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17707 Z= 0.285 Angle : 0.752 8.510 25173 Z= 0.407 Chirality : 0.050 0.332 2852 Planarity : 0.005 0.053 2181 Dihedral : 30.550 179.625 4679 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.10 % Rotamer: Outliers : 2.51 % Allowed : 12.56 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1318 helix: 1.52 (0.18), residues: 793 sheet: -1.90 (0.71), residues: 65 loop : -1.75 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 76 TYR 0.016 0.002 TYR K 545 PHE 0.016 0.002 PHE K 737 TRP 0.014 0.002 TRP K 364 HIS 0.009 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.29 (17707) covalent geometry : angle 0.75246 / 0.41 (25173) hydrogen bonds : bond 0.06214 / 4.22 ( 949) hydrogen bonds : angle 3.45321 / 2.47 ( 2433) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8873 (tt0) cc_final: 0.8422 (tt0) REVERT: A 76 GLN cc_start: 0.8747 (pp30) cc_final: 0.8407 (pp30) REVERT: A 133 GLU cc_start: 0.8475 (mp0) cc_final: 0.8116 (mp0) REVERT: C 110 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8817 (p0) REVERT: E 59 GLU cc_start: 0.8956 (pm20) cc_final: 0.8661 (pm20) REVERT: E 94 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: F 25 ASN cc_start: 0.9176 (m-40) cc_final: 0.8541 (m-40) REVERT: F 84 MET cc_start: 0.8932 (mmm) cc_final: 0.8669 (mmm) REVERT: H 65 ASP cc_start: 0.8951 (t0) cc_final: 0.8658 (t0) REVERT: K 93 LYS cc_start: 0.6721 (mttm) cc_final: 0.6242 (pmtt) REVERT: K 342 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8328 (tm-30) REVERT: K 525 SER cc_start: 0.9030 (t) cc_final: 0.8754 (p) REVERT: K 645 ARG cc_start: 0.8985 (tpp80) cc_final: 0.8519 (tpp80) REVERT: K 717 ASN cc_start: 0.8433 (m-40) cc_final: 0.8217 (t0) outliers start: 29 outliers final: 13 residues processed: 173 average time/residue: 0.7753 time to fit residues: 145.0254 Evaluate side-chains 157 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 532 ASP Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 647 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 138 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.088092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061746 restraints weight = 44380.857| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.26 r_work: 0.2872 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17707 Z= 0.158 Angle : 0.679 8.280 25173 Z= 0.374 Chirality : 0.047 0.330 2852 Planarity : 0.004 0.056 2181 Dihedral : 30.440 179.014 4679 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 2.69 % Allowed : 14.90 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1318 helix: 1.79 (0.19), residues: 795 sheet: -1.78 (0.73), residues: 65 loop : -1.70 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.014 0.001 TYR K 545 PHE 0.012 0.001 PHE K 524 TRP 0.016 0.001 TRP K 364 HIS 0.008 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (17707) covalent geometry : angle 0.67880 / 0.37 (25173) hydrogen bonds : bond 0.04647 / 3.17 ( 949) hydrogen bonds : angle 3.18754 / 2.28 ( 2433) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8857 (tt0) cc_final: 0.8385 (tt0) REVERT: A 76 GLN cc_start: 0.8718 (pp30) cc_final: 0.8366 (pp30) REVERT: A 120 MET cc_start: 0.8816 (mtm) cc_final: 0.8592 (mtt) REVERT: A 133 GLU cc_start: 0.8476 (mp0) cc_final: 0.8043 (mp0) REVERT: C 95 LYS cc_start: 0.9226 (tttp) cc_final: 0.8932 (ttmm) REVERT: E 59 GLU cc_start: 0.8897 (pm20) cc_final: 0.8579 (pm20) REVERT: F 25 ASN cc_start: 0.9174 (m-40) cc_final: 0.8534 (m-40) REVERT: H 65 ASP cc_start: 0.8866 (t0) cc_final: 0.8555 (t0) REVERT: K 93 LYS cc_start: 0.6873 (mttm) cc_final: 0.6479 (pmtt) REVERT: K 525 SER cc_start: 0.8948 (t) cc_final: 0.8699 (p) REVERT: K 645 ARG cc_start: 0.8948 (tpp80) cc_final: 0.8491 (tpp80) REVERT: K 717 ASN cc_start: 0.8406 (m-40) cc_final: 0.8200 (t0) outliers start: 31 outliers final: 9 residues processed: 178 average time/residue: 0.7362 time to fit residues: 141.7551 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 87 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 131 optimal weight: 0.0980 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN B 25 ASN E 68 GLN G 38 ASN K 505 GLN K 617 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.085676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.059365 restraints weight = 44153.434| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.24 r_work: 0.2807 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 17707 Z= 0.343 Angle : 0.802 9.686 25173 Z= 0.425 Chirality : 0.052 0.361 2852 Planarity : 0.005 0.054 2181 Dihedral : 30.688 179.791 4679 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.94 % Rotamer: Outliers : 3.38 % Allowed : 15.68 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1318 helix: 1.51 (0.18), residues: 796 sheet: -2.16 (0.69), residues: 65 loop : -1.80 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.016 0.002 TYR A 54 PHE 0.017 0.002 PHE E 67 TRP 0.012 0.002 TRP K 364 HIS 0.008 0.002 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.34 (17707) covalent geometry : angle 0.80224 / 0.43 (25173) hydrogen bonds : bond 0.06886 / 4.68 ( 949) hydrogen bonds : angle 3.46309 / 2.48 ( 2433) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8899 (tt0) cc_final: 0.8434 (tt0) REVERT: A 76 GLN cc_start: 0.8798 (pp30) cc_final: 0.8439 (pp30) REVERT: A 133 GLU cc_start: 0.8496 (mp0) cc_final: 0.7994 (mp0) REVERT: B 19 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7965 (pmm150) REVERT: C 91 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7848 (tm-30) REVERT: D 82 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9024 (mtpp) REVERT: E 59 GLU cc_start: 0.8951 (pm20) cc_final: 0.8632 (pm20) REVERT: F 25 ASN cc_start: 0.9185 (m-40) cc_final: 0.8549 (m-40) REVERT: H 54 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8905 (mmtm) REVERT: H 56 MET cc_start: 0.9408 (tpp) cc_final: 0.9123 (tpp) REVERT: H 65 ASP cc_start: 0.8991 (t0) cc_final: 0.8694 (t0) REVERT: H 90 GLU cc_start: 0.8887 (mp0) cc_final: 0.8634 (mm-30) REVERT: K 93 LYS cc_start: 0.6937 (mttm) cc_final: 0.6472 (pmtt) REVERT: K 645 ARG cc_start: 0.8992 (tpp80) cc_final: 0.8436 (tpp80) REVERT: K 717 ASN cc_start: 0.8449 (m-40) cc_final: 0.8229 (t0) outliers start: 39 outliers final: 18 residues processed: 171 average time/residue: 0.7788 time to fit residues: 143.9607 Evaluate side-chains 158 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 1 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN K 617 GLN K 723 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061674 restraints weight = 44032.305| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.24 r_work: 0.2869 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17707 Z= 0.146 Angle : 0.689 8.916 25173 Z= 0.374 Chirality : 0.047 0.343 2852 Planarity : 0.004 0.055 2181 Dihedral : 30.545 179.126 4679 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 2.43 % Allowed : 17.33 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1318 helix: 1.80 (0.19), residues: 797 sheet: -2.01 (0.69), residues: 65 loop : -1.67 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.015 0.001 TYR K 596 PHE 0.019 0.001 PHE K 737 TRP 0.017 0.001 TRP K 364 HIS 0.008 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (17707) covalent geometry : angle 0.68875 / 0.37 (25173) hydrogen bonds : bond 0.04555 / 3.10 ( 949) hydrogen bonds : angle 3.14121 / 2.25 ( 2433) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8843 (tt0) cc_final: 0.8359 (tt0) REVERT: A 76 GLN cc_start: 0.8722 (pp30) cc_final: 0.8378 (pp30) REVERT: A 133 GLU cc_start: 0.8511 (mp0) cc_final: 0.8001 (mp0) REVERT: D 102 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8542 (mm-30) REVERT: E 59 GLU cc_start: 0.8840 (pm20) cc_final: 0.8531 (pm20) REVERT: F 25 ASN cc_start: 0.9181 (m-40) cc_final: 0.8565 (m-40) REVERT: H 48 ASP cc_start: 0.8820 (p0) cc_final: 0.8489 (p0) REVERT: H 65 ASP cc_start: 0.8880 (t0) cc_final: 0.8580 (t0) REVERT: K 93 LYS cc_start: 0.6860 (mttm) cc_final: 0.6510 (pmtt) REVERT: K 525 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8613 (p) REVERT: K 717 ASN cc_start: 0.8354 (m-40) cc_final: 0.8138 (t0) outliers start: 28 outliers final: 14 residues processed: 169 average time/residue: 0.7288 time to fit residues: 134.0388 Evaluate side-chains 164 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 116 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 154 optimal weight: 0.0170 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 ASN K 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.089187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062986 restraints weight = 44082.280| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.25 r_work: 0.2904 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 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 : 0.002 0.044 17707 Z= 0.135 Angle : 0.664 8.797 25173 Z= 0.365 Chirality : 0.045 0.311 2852 Planarity : 0.004 0.056 2181 Dihedral : 30.305 179.529 4679 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 2.17 % Allowed : 18.89 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.24), residues: 1318 helix: 1.98 (0.19), residues: 799 sheet: -1.72 (0.73), residues: 63 loop : -1.55 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.011 0.001 TYR F 51 PHE 0.014 0.001 PHE E 67 TRP 0.017 0.001 TRP K 364 HIS 0.008 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (17707) covalent geometry : angle 0.66409 / 0.37 (25173) hydrogen bonds : bond 0.04145 / 2.84 ( 949) hydrogen bonds : angle 2.99148 / 2.14 ( 2433) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8843 (tt0) cc_final: 0.8349 (tt0) REVERT: A 76 GLN cc_start: 0.8692 (pp30) cc_final: 0.8325 (pp30) REVERT: A 133 GLU cc_start: 0.8502 (mp0) cc_final: 0.8202 (mp0) REVERT: C 91 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7836 (tm-30) REVERT: C 95 LYS cc_start: 0.9181 (tttp) cc_final: 0.8976 (ttmt) REVERT: D 76 ARG cc_start: 0.9006 (mtm-85) cc_final: 0.8782 (mtp-110) REVERT: E 59 GLU cc_start: 0.8814 (pm20) cc_final: 0.8527 (pm20) REVERT: E 133 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: F 25 ASN cc_start: 0.9189 (m-40) cc_final: 0.8544 (m-40) REVERT: H 48 ASP cc_start: 0.8812 (p0) cc_final: 0.8476 (p0) REVERT: H 65 ASP cc_start: 0.8845 (t0) cc_final: 0.8554 (t0) REVERT: H 90 GLU cc_start: 0.8773 (mp0) cc_final: 0.8558 (mm-30) REVERT: K 93 LYS cc_start: 0.6863 (mttm) cc_final: 0.6504 (pmtt) REVERT: K 525 SER cc_start: 0.8894 (t) cc_final: 0.8671 (p) REVERT: K 645 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8213 (tpp80) REVERT: K 717 ASN cc_start: 0.8359 (m-40) cc_final: 0.8082 (m-40) outliers start: 25 outliers final: 12 residues processed: 169 average time/residue: 0.7912 time to fit residues: 144.8014 Evaluate side-chains 161 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 91 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 155 optimal weight: 0.0470 chunk 134 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.089018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.062940 restraints weight = 44349.667| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.25 r_work: 0.2899 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17707 Z= 0.143 Angle : 0.664 10.035 25173 Z= 0.363 Chirality : 0.045 0.303 2852 Planarity : 0.004 0.057 2181 Dihedral : 30.308 179.441 4679 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 2.25 % Allowed : 19.24 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1318 helix: 1.98 (0.19), residues: 805 sheet: -1.74 (0.72), residues: 63 loop : -1.53 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 23 TYR 0.014 0.001 TYR K 726 PHE 0.022 0.001 PHE K 737 TRP 0.016 0.001 TRP K 364 HIS 0.008 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (17707) covalent geometry : angle 0.66408 / 0.36 (25173) hydrogen bonds : bond 0.04193 / 2.88 ( 949) hydrogen bonds : angle 2.97497 / 2.13 ( 2433) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8820 (tt0) cc_final: 0.8322 (tt0) REVERT: A 76 GLN cc_start: 0.8685 (pp30) cc_final: 0.8321 (pp30) REVERT: A 120 MET cc_start: 0.8717 (mtm) cc_final: 0.8499 (mtt) REVERT: A 133 GLU cc_start: 0.8532 (mp0) cc_final: 0.8233 (mp0) REVERT: C 91 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7866 (tm-30) REVERT: C 95 LYS cc_start: 0.9189 (tttp) cc_final: 0.8978 (ttmt) REVERT: D 68 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8519 (tp30) REVERT: E 59 GLU cc_start: 0.8805 (pm20) cc_final: 0.8505 (pm20) REVERT: E 133 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: F 25 ASN cc_start: 0.9193 (m-40) cc_final: 0.8541 (m-40) REVERT: H 31 LYS cc_start: 0.8638 (mptt) cc_final: 0.8333 (mmpt) REVERT: H 39 TYR cc_start: 0.8990 (t80) cc_final: 0.8245 (t80) REVERT: H 48 ASP cc_start: 0.8807 (p0) cc_final: 0.8488 (p0) REVERT: H 65 ASP cc_start: 0.8873 (t0) cc_final: 0.8543 (t0) REVERT: K 93 LYS cc_start: 0.6855 (mttm) cc_final: 0.6501 (pmtt) REVERT: K 525 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8627 (p) REVERT: K 645 ARG cc_start: 0.8734 (tpp80) cc_final: 0.8247 (tpp80) REVERT: K 717 ASN cc_start: 0.8370 (m-40) cc_final: 0.8098 (m-40) outliers start: 26 outliers final: 15 residues processed: 167 average time/residue: 0.8102 time to fit residues: 146.8474 Evaluate side-chains 162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 578 THR Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN D 46 HIS E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.063431 restraints weight = 44177.426| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.23 r_work: 0.2913 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17707 Z= 0.141 Angle : 0.671 9.356 25173 Z= 0.366 Chirality : 0.045 0.298 2852 Planarity : 0.004 0.058 2181 Dihedral : 30.285 178.568 4679 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.22 % Favored : 93.70 % Rotamer: Outliers : 2.17 % Allowed : 19.67 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1318 helix: 2.00 (0.19), residues: 806 sheet: -1.68 (0.72), residues: 63 loop : -1.49 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.011 0.001 TYR H 80 PHE 0.013 0.001 PHE E 67 TRP 0.016 0.001 TRP K 364 HIS 0.008 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (17707) covalent geometry : angle 0.67088 / 0.37 (25173) hydrogen bonds : bond 0.04078 / 2.80 ( 949) hydrogen bonds : angle 2.95477 / 2.11 ( 2433) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8823 (tt0) cc_final: 0.8329 (tt0) REVERT: A 76 GLN cc_start: 0.8677 (pp30) cc_final: 0.8316 (pp30) REVERT: A 120 MET cc_start: 0.8708 (mtm) cc_final: 0.8498 (mtt) REVERT: A 133 GLU cc_start: 0.8554 (mp0) cc_final: 0.8272 (mp0) REVERT: C 91 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 95 LYS cc_start: 0.9185 (tttp) cc_final: 0.8969 (ttmt) REVERT: D 65 ASP cc_start: 0.9099 (t0) cc_final: 0.8865 (t0) REVERT: E 59 GLU cc_start: 0.8791 (pm20) cc_final: 0.8518 (pm20) REVERT: F 25 ASN cc_start: 0.9196 (m-40) cc_final: 0.8566 (m-40) REVERT: H 31 LYS cc_start: 0.8653 (mptt) cc_final: 0.8349 (mmpt) REVERT: H 39 TYR cc_start: 0.8979 (t80) cc_final: 0.8326 (t80) REVERT: H 48 ASP cc_start: 0.8817 (p0) cc_final: 0.8497 (p0) REVERT: H 65 ASP cc_start: 0.8853 (t0) cc_final: 0.8541 (t0) REVERT: K 93 LYS cc_start: 0.6832 (mttm) cc_final: 0.6489 (pmtt) REVERT: K 525 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8557 (p) REVERT: K 645 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8248 (tpp80) REVERT: K 717 ASN cc_start: 0.8354 (m-40) cc_final: 0.8081 (m-40) outliers start: 25 outliers final: 15 residues processed: 166 average time/residue: 0.8488 time to fit residues: 152.6106 Evaluate side-chains 163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 578 THR Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN D 46 HIS E 68 GLN K 739 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.089103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.063296 restraints weight = 43968.534| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.23 r_work: 0.2905 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17707 Z= 0.150 Angle : 0.669 9.780 25173 Z= 0.363 Chirality : 0.044 0.296 2852 Planarity : 0.004 0.058 2181 Dihedral : 30.273 178.011 4679 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 1.91 % Allowed : 20.36 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1318 helix: 2.02 (0.19), residues: 805 sheet: -1.68 (0.72), residues: 63 loop : -1.50 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.012 0.001 TYR K 726 PHE 0.025 0.001 PHE K 737 TRP 0.015 0.001 TRP K 364 HIS 0.008 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (17707) covalent geometry : angle 0.66913 / 0.36 (25173) hydrogen bonds : bond 0.04176 / 2.86 ( 949) hydrogen bonds : angle 2.97125 / 2.12 ( 2433) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8814 (tt0) cc_final: 0.8338 (tt0) REVERT: A 76 GLN cc_start: 0.8686 (pp30) cc_final: 0.8323 (pp30) REVERT: A 120 MET cc_start: 0.8708 (mtm) cc_final: 0.8489 (mtt) REVERT: A 133 GLU cc_start: 0.8536 (mp0) cc_final: 0.8241 (mp0) REVERT: C 91 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7865 (tm-30) REVERT: C 95 LYS cc_start: 0.9186 (tttp) cc_final: 0.8973 (ttmt) REVERT: D 65 ASP cc_start: 0.9083 (t0) cc_final: 0.8852 (t0) REVERT: E 59 GLU cc_start: 0.8745 (pm20) cc_final: 0.8397 (pm20) REVERT: F 25 ASN cc_start: 0.9203 (m-40) cc_final: 0.8573 (m-40) REVERT: H 31 LYS cc_start: 0.8655 (mptt) cc_final: 0.8363 (mmpt) REVERT: H 39 TYR cc_start: 0.8991 (t80) cc_final: 0.8341 (t80) REVERT: H 48 ASP cc_start: 0.8804 (p0) cc_final: 0.8500 (p0) REVERT: H 65 ASP cc_start: 0.8863 (t0) cc_final: 0.8545 (t0) REVERT: H 90 GLU cc_start: 0.8816 (mp0) cc_final: 0.8585 (mm-30) REVERT: K 93 LYS cc_start: 0.6809 (mttm) cc_final: 0.6472 (pmtt) REVERT: K 525 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8552 (p) REVERT: K 645 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8128 (tpp80) REVERT: K 717 ASN cc_start: 0.8376 (m-40) cc_final: 0.8105 (m-40) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 0.8094 time to fit residues: 141.0344 Evaluate side-chains 161 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 146 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 26 optimal weight: 0.0870 chunk 85 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN K 739 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.089439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063425 restraints weight = 44011.230| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.26 r_work: 0.2912 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17707 Z= 0.138 Angle : 0.668 9.896 25173 Z= 0.363 Chirality : 0.044 0.294 2852 Planarity : 0.004 0.058 2181 Dihedral : 30.256 177.862 4679 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 1.65 % Allowed : 20.45 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1318 helix: 2.03 (0.19), residues: 805 sheet: -1.61 (0.72), residues: 63 loop : -1.50 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.013 0.001 TYR K 545 PHE 0.015 0.001 PHE E 67 TRP 0.015 0.001 TRP K 364 HIS 0.008 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (17707) covalent geometry : angle 0.66789 / 0.36 (25173) hydrogen bonds : bond 0.04049 / 2.77 ( 949) hydrogen bonds : angle 2.94990 / 2.10 ( 2433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4829.48 seconds wall clock time: 83 minutes 3.11 seconds (4983.11 seconds total)