Starting phenix.real_space_refine on Fri Jul 3 22:08:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnx_61630/07_2026/9jnx_61630.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnx_61630/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnx_61630/07_2026/9jnx_61630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnx_61630/07_2026/9jnx_61630.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnx_61630/07_2026/9jnx_61630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnx_61630/07_2026/9jnx_61630.cif" } 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-dev-6108/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: 3.40, per 1000 atoms: 0.20 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: 1.46 Conformation dependent library (CDL) restraints added in 585.8 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: 2.48 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: 4.12 Time building geometry restraints manager: 1.97 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: 23447 1.54 - 3.09: 1527 3.09 - 4.63: 158 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.600 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- 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= 0.520 Angle : 0.805 7.720 25173 Z= 0.647 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 0.80535 / 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 : 0.334 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: 0.8224 time to fit residues: 168.7833 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 : 0.480 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.3673 r_free = 0.3673 target = 0.088350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062419 restraints weight = 44604.552| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.26 r_work: 0.2887 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0869 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 : 0.702 8.147 25173 Z= 0.391 Chirality : 0.047 0.319 2852 Planarity : 0.005 0.052 2181 Dihedral : 30.371 177.028 4683 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.10 % Rotamer: Outliers : 0.87 % Allowed : 10.57 % Favored : 88.56 % 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: 0.42 (0.24), residues: 1318 helix: 1.57 (0.18), residues: 792 sheet: -1.55 (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 529 TYR 0.019 0.002 TYR K 545 PHE 0.021 0.001 PHE K 524 TRP 0.016 0.002 TRP K 364 HIS 0.007 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (17707) covalent geometry : angle 0.70162 / 0.39 (25173) hydrogen bonds : bond 0.05079 / 3.48 ( 949) hydrogen bonds : angle 3.46036 / 2.48 ( 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 177 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8841 (tt0) cc_final: 0.8392 (tt0) REVERT: A 76 GLN cc_start: 0.8677 (pp30) cc_final: 0.8404 (pp30) REVERT: A 120 MET cc_start: 0.8800 (mtm) cc_final: 0.8589 (mtt) REVERT: A 133 GLU cc_start: 0.8484 (mp0) cc_final: 0.8186 (mp0) REVERT: C 64 GLU cc_start: 0.8634 (tt0) cc_final: 0.8412 (pt0) REVERT: E 59 GLU cc_start: 0.8915 (pm20) cc_final: 0.8675 (pm20) REVERT: F 25 ASN cc_start: 0.9162 (m-40) cc_final: 0.8623 (m-40) REVERT: H 65 ASP cc_start: 0.8774 (t0) cc_final: 0.8567 (t0) REVERT: K 93 LYS cc_start: 0.6674 (mttm) cc_final: 0.6138 (pmtt) REVERT: K 525 SER cc_start: 0.8976 (t) cc_final: 0.8736 (p) REVERT: K 645 ARG cc_start: 0.8942 (tpp80) cc_final: 0.8409 (tpp80) REVERT: K 717 ASN cc_start: 0.8411 (m-40) cc_final: 0.8192 (t0) outliers start: 10 outliers final: 3 residues processed: 170 average time/residue: 0.8447 time to fit residues: 155.0197 Evaluate side-chains 150 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 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: 6.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 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: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN G 38 ASN K 617 GLN K 774 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.087004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060913 restraints weight = 45154.491| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.28 r_work: 0.2844 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17707 Z= 0.237 Angle : 0.710 7.792 25173 Z= 0.390 Chirality : 0.048 0.306 2852 Planarity : 0.005 0.055 2181 Dihedral : 30.543 177.337 4679 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 2.25 % Allowed : 12.39 % Favored : 85.36 % 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: 0.49 (0.24), residues: 1318 helix: 1.63 (0.19), residues: 792 sheet: -1.81 (0.72), residues: 65 loop : -1.73 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.016 0.002 TYR K 545 PHE 0.016 0.002 PHE K 737 TRP 0.015 0.001 TRP K 364 HIS 0.009 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (17707) covalent geometry : angle 0.70981 / 0.39 (25173) hydrogen bonds : bond 0.05696 / 3.87 ( 949) hydrogen bonds : angle 3.37749 / 2.42 ( 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 188 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8861 (tt0) cc_final: 0.8397 (tt0) REVERT: A 76 GLN cc_start: 0.8724 (pp30) cc_final: 0.8384 (pp30) REVERT: A 120 MET cc_start: 0.8843 (mtm) cc_final: 0.8631 (mtt) REVERT: A 133 GLU cc_start: 0.8438 (mp0) cc_final: 0.7901 (mp0) REVERT: C 64 GLU cc_start: 0.8722 (tt0) cc_final: 0.8383 (pt0) REVERT: E 59 GLU cc_start: 0.8941 (pm20) cc_final: 0.8685 (pm20) REVERT: E 94 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: F 25 ASN cc_start: 0.9191 (m-40) cc_final: 0.8552 (m-40) REVERT: H 65 ASP cc_start: 0.8937 (t0) cc_final: 0.8640 (t0) REVERT: K 93 LYS cc_start: 0.6709 (mttm) cc_final: 0.6229 (pmtt) REVERT: K 525 SER cc_start: 0.9046 (t) cc_final: 0.8766 (p) REVERT: K 645 ARG cc_start: 0.8978 (tpp80) cc_final: 0.8513 (tpp80) REVERT: K 717 ASN cc_start: 0.8424 (m-40) cc_final: 0.8211 (t0) outliers start: 26 outliers final: 10 residues processed: 174 average time/residue: 0.7972 time to fit residues: 149.9250 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU 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 538 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: 0.8980 chunk 44 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.088684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.062821 restraints weight = 44181.085| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.23 r_work: 0.2894 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17707 Z= 0.143 Angle : 0.655 8.681 25173 Z= 0.365 Chirality : 0.045 0.294 2852 Planarity : 0.004 0.056 2181 Dihedral : 30.412 177.416 4679 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 2.51 % Allowed : 14.90 % Favored : 82.58 % 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: 0.78 (0.24), residues: 1318 helix: 1.87 (0.19), residues: 793 sheet: -1.71 (0.73), residues: 65 loop : -1.63 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.012 0.001 TYR K 545 PHE 0.013 0.001 PHE K 524 TRP 0.017 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (17707) covalent geometry : angle 0.65533 / 0.36 (25173) hydrogen bonds : bond 0.04392 / 3.00 ( 949) hydrogen bonds : angle 3.12189 / 2.24 ( 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 195 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8851 (tt0) cc_final: 0.8385 (tt0) REVERT: A 76 GLN cc_start: 0.8680 (pp30) cc_final: 0.8356 (pp30) REVERT: A 120 MET cc_start: 0.8716 (mtm) cc_final: 0.8495 (mtt) REVERT: A 133 GLU cc_start: 0.8487 (mp0) cc_final: 0.8080 (mp0) REVERT: C 64 GLU cc_start: 0.8680 (tt0) cc_final: 0.8320 (pt0) REVERT: C 110 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8411 (p0) REVERT: E 59 GLU cc_start: 0.8876 (pm20) cc_final: 0.8551 (pm20) REVERT: F 25 ASN cc_start: 0.9174 (m-40) cc_final: 0.8538 (m-40) REVERT: H 65 ASP cc_start: 0.8847 (t0) cc_final: 0.8540 (t0) REVERT: K 93 LYS cc_start: 0.6912 (mttm) cc_final: 0.6466 (pmtt) REVERT: K 525 SER cc_start: 0.8919 (t) cc_final: 0.8662 (p) REVERT: K 645 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8493 (tpp80) REVERT: K 717 ASN cc_start: 0.8394 (m-40) cc_final: 0.8183 (t0) outliers start: 29 outliers final: 11 residues processed: 183 average time/residue: 0.7448 time to fit residues: 147.7065 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 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 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 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: 0.6980 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 10.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.086210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.059798 restraints weight = 44206.264| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.30 r_work: 0.2818 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 17707 Z= 0.319 Angle : 0.766 9.623 25173 Z= 0.411 Chirality : 0.050 0.335 2852 Planarity : 0.005 0.056 2181 Dihedral : 30.670 177.891 4679 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 3.12 % Allowed : 15.86 % Favored : 81.02 % 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: 0.44 (0.24), residues: 1318 helix: 1.59 (0.18), residues: 794 sheet: -2.06 (0.69), residues: 65 loop : -1.73 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.019 0.002 TYR K 545 PHE 0.016 0.002 PHE E 67 TRP 0.012 0.002 TRP K 364 HIS 0.007 0.002 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.32 (17707) covalent geometry : angle 0.76598 / 0.41 (25173) hydrogen bonds : bond 0.06469 / 4.40 ( 949) hydrogen bonds : angle 3.39141 / 2.43 ( 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 188 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8904 (tt0) cc_final: 0.8435 (tt0) REVERT: A 76 GLN cc_start: 0.8775 (pp30) cc_final: 0.8406 (pp30) REVERT: A 133 GLU cc_start: 0.8516 (mp0) cc_final: 0.8022 (mp0) REVERT: C 91 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7832 (tm-30) REVERT: C 110 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8479 (p0) REVERT: D 82 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9031 (mtpp) REVERT: E 59 GLU cc_start: 0.8934 (pm20) cc_final: 0.8621 (pm20) REVERT: F 25 ASN cc_start: 0.9186 (m-40) cc_final: 0.8523 (m-40) REVERT: H 54 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8875 (mmtm) REVERT: H 65 ASP cc_start: 0.8983 (t0) cc_final: 0.8689 (t0) REVERT: H 90 GLU cc_start: 0.8875 (mp0) cc_final: 0.8314 (mm-30) REVERT: K 93 LYS cc_start: 0.6872 (mttm) cc_final: 0.6465 (pmtt) REVERT: K 645 ARG cc_start: 0.8972 (tpp80) cc_final: 0.8475 (tpp80) REVERT: K 717 ASN cc_start: 0.8424 (m-40) cc_final: 0.8208 (t0) outliers start: 36 outliers final: 18 residues processed: 174 average time/residue: 0.7637 time to fit residues: 143.6211 Evaluate side-chains 165 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 79 LYS 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 C residue 113 SER 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: 0.9980 chunk 113 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 617 GLN K 723 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.062052 restraints weight = 44022.528| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.23 r_work: 0.2877 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1552 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= 0.145 Angle : 0.666 9.369 25173 Z= 0.366 Chirality : 0.045 0.311 2852 Planarity : 0.004 0.056 2181 Dihedral : 30.546 178.063 4679 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 2.08 % Allowed : 17.94 % Favored : 79.98 % 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: 0.75 (0.24), residues: 1318 helix: 1.85 (0.19), residues: 796 sheet: -1.86 (0.71), residues: 65 loop : -1.65 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.012 0.001 TYR K 596 PHE 0.024 0.001 PHE K 737 TRP 0.017 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (17707) covalent geometry : angle 0.66582 / 0.37 (25173) hydrogen bonds : bond 0.04439 / 3.02 ( 949) hydrogen bonds : angle 3.13475 / 2.24 ( 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 179 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 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: 0.8842 (tt0) cc_final: 0.8366 (tt0) REVERT: A 76 GLN cc_start: 0.8708 (pp30) cc_final: 0.8374 (pp30) REVERT: A 133 GLU cc_start: 0.8544 (mp0) cc_final: 0.8083 (mp0) REVERT: C 64 GLU cc_start: 0.8733 (tt0) cc_final: 0.8525 (pt0) REVERT: C 110 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8487 (p0) REVERT: E 59 GLU cc_start: 0.8848 (pm20) cc_final: 0.8544 (pm20) REVERT: E 133 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: F 25 ASN cc_start: 0.9181 (m-40) cc_final: 0.8533 (m-40) REVERT: H 48 ASP cc_start: 0.8794 (p0) cc_final: 0.8463 (p0) REVERT: H 65 ASP cc_start: 0.8878 (t0) cc_final: 0.8579 (t0) REVERT: K 93 LYS cc_start: 0.6885 (mttm) cc_final: 0.6512 (pmtt) REVERT: K 525 SER cc_start: 0.8895 (t) cc_final: 0.8672 (p) REVERT: K 645 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8423 (tpp80) REVERT: K 717 ASN cc_start: 0.8392 (m-40) cc_final: 0.8127 (t0) outliers start: 24 outliers final: 13 residues processed: 170 average time/residue: 0.7994 time to fit residues: 146.9286 Evaluate side-chains 163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 86 SER 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 G residue 101 THR Chi-restraints excluded: chain H residue 53 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 ASN K 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.088222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062326 restraints weight = 43886.823| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.23 r_work: 0.2882 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1641 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= 0.159 Angle : 0.673 10.304 25173 Z= 0.369 Chirality : 0.045 0.303 2852 Planarity : 0.004 0.057 2181 Dihedral : 30.459 178.960 4679 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 2.34 % Allowed : 18.28 % Favored : 79.38 % 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: 0.87 (0.24), residues: 1318 helix: 1.92 (0.19), residues: 797 sheet: -1.78 (0.71), residues: 63 loop : -1.56 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.009 0.001 TYR F 51 PHE 0.013 0.001 PHE E 67 TRP 0.015 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (17707) covalent geometry : angle 0.67269 / 0.37 (25173) hydrogen bonds : bond 0.04506 / 3.08 ( 949) hydrogen bonds : angle 3.08529 / 2.20 ( 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 181 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8848 (tt0) cc_final: 0.8359 (tt0) REVERT: A 76 GLN cc_start: 0.8705 (pp30) cc_final: 0.8337 (pp30) REVERT: A 120 MET cc_start: 0.8771 (mtm) cc_final: 0.8563 (mtt) REVERT: A 133 GLU cc_start: 0.8567 (mp0) cc_final: 0.8252 (mp0) REVERT: C 64 GLU cc_start: 0.8689 (tt0) cc_final: 0.8462 (pt0) REVERT: C 110 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8492 (p0) REVERT: D 68 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8530 (tp30) REVERT: E 59 GLU cc_start: 0.8860 (pm20) cc_final: 0.8564 (pm20) REVERT: E 133 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: F 25 ASN cc_start: 0.9187 (m-40) cc_final: 0.8546 (m-40) REVERT: H 48 ASP cc_start: 0.8847 (p0) cc_final: 0.8517 (p0) REVERT: H 65 ASP cc_start: 0.8890 (t0) cc_final: 0.8564 (t0) REVERT: K 93 LYS cc_start: 0.6881 (mttm) cc_final: 0.6514 (pmtt) REVERT: K 525 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8658 (p) REVERT: K 717 ASN cc_start: 0.8333 (m-40) cc_final: 0.8042 (m-40) outliers start: 27 outliers final: 15 residues processed: 169 average time/residue: 0.8072 time to fit residues: 147.7293 Evaluate side-chains 164 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER 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 G residue 101 THR 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=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: 0.9980 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.088786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.062953 restraints weight = 44329.228| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.23 r_work: 0.2894 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1735 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= 0.148 Angle : 0.660 9.327 25173 Z= 0.363 Chirality : 0.044 0.297 2852 Planarity : 0.004 0.058 2181 Dihedral : 30.435 179.651 4679 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 1.99 % Allowed : 19.50 % Favored : 78.51 % 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: 0.92 (0.24), residues: 1318 helix: 1.91 (0.18), residues: 805 sheet: -1.74 (0.72), residues: 63 loop : -1.52 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 645 TYR 0.015 0.001 TYR K 726 PHE 0.022 0.001 PHE K 737 TRP 0.015 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (17707) covalent geometry : angle 0.65999 / 0.36 (25173) hydrogen bonds : bond 0.04237 / 2.90 ( 949) hydrogen bonds : angle 3.03051 / 2.16 ( 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 172 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8829 (tt0) cc_final: 0.8337 (tt0) REVERT: A 76 GLN cc_start: 0.8691 (pp30) cc_final: 0.8329 (pp30) REVERT: A 120 MET cc_start: 0.8733 (mtm) cc_final: 0.8531 (mtt) REVERT: A 133 GLU cc_start: 0.8527 (mp0) cc_final: 0.8066 (mp0) REVERT: C 64 GLU cc_start: 0.8719 (tt0) cc_final: 0.8476 (pt0) REVERT: C 110 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8497 (p0) REVERT: E 59 GLU cc_start: 0.8825 (pm20) cc_final: 0.8531 (pm20) REVERT: E 133 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: F 25 ASN cc_start: 0.9194 (m-40) cc_final: 0.8559 (m-40) REVERT: H 48 ASP cc_start: 0.8834 (p0) cc_final: 0.8502 (p0) REVERT: H 65 ASP cc_start: 0.8880 (t0) cc_final: 0.8568 (t0) REVERT: K 93 LYS cc_start: 0.6859 (mttm) cc_final: 0.6505 (pmtt) REVERT: K 525 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8593 (p) REVERT: K 645 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8244 (tpp80) REVERT: K 717 ASN cc_start: 0.8325 (m-40) cc_final: 0.8040 (m-40) outliers start: 23 outliers final: 12 residues processed: 161 average time/residue: 0.7891 time to fit residues: 137.9593 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 110 ASN 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 G residue 101 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 148 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 135 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN G 38 ASN ** G 73 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 = 0.3686 r_free = 0.3686 target = 0.089192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063179 restraints weight = 44105.898| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.25 r_work: 0.2906 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1832 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= 0.137 Angle : 0.656 8.291 25173 Z= 0.361 Chirality : 0.044 0.289 2852 Planarity : 0.004 0.058 2181 Dihedral : 30.384 179.841 4679 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 2.08 % Allowed : 19.41 % 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: 1.97 (0.18), residues: 805 sheet: -1.72 (0.72), residues: 63 loop : -1.50 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.015 0.001 TYR K 545 PHE 0.014 0.001 PHE E 67 TRP 0.016 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (17707) covalent geometry : angle 0.65552 / 0.36 (25173) hydrogen bonds : bond 0.04096 / 2.80 ( 949) hydrogen bonds : angle 2.97886 / 2.12 ( 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 175 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8834 (tt0) cc_final: 0.8341 (tt0) REVERT: A 76 GLN cc_start: 0.8679 (pp30) cc_final: 0.8324 (pp30) REVERT: A 133 GLU cc_start: 0.8527 (mp0) cc_final: 0.8229 (mp0) REVERT: C 64 GLU cc_start: 0.8719 (tt0) cc_final: 0.8465 (pt0) REVERT: C 91 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 95 LYS cc_start: 0.9192 (tttp) cc_final: 0.8978 (ttmt) REVERT: C 110 ASN cc_start: 0.9132 (t0) cc_final: 0.8484 (p0) REVERT: D 68 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8498 (tp30) REVERT: E 59 GLU cc_start: 0.8814 (pm20) cc_final: 0.8524 (pm20) REVERT: E 133 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: F 25 ASN cc_start: 0.9198 (m-40) cc_final: 0.8556 (m-40) REVERT: H 48 ASP cc_start: 0.8857 (p0) cc_final: 0.8531 (p0) REVERT: H 65 ASP cc_start: 0.8864 (t0) cc_final: 0.8545 (t0) REVERT: K 93 LYS cc_start: 0.6855 (mttm) cc_final: 0.6503 (pmtt) REVERT: K 525 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8563 (p) REVERT: K 645 ARG cc_start: 0.8736 (tpp80) cc_final: 0.8228 (tpp80) REVERT: K 717 ASN cc_start: 0.8330 (m-40) cc_final: 0.8044 (m-40) outliers start: 24 outliers final: 14 residues processed: 163 average time/residue: 0.8176 time to fit residues: 144.2402 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 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 43 VAL Chi-restraints excluded: chain C residue 113 SER 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 G residue 101 THR 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 546 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 52 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.088823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062652 restraints weight = 44024.323| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.26 r_work: 0.2894 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17707 Z= 0.158 Angle : 0.670 9.522 25173 Z= 0.366 Chirality : 0.044 0.292 2852 Planarity : 0.004 0.057 2181 Dihedral : 30.396 179.220 4679 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 1.73 % Allowed : 20.19 % Favored : 78.08 % 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: 1.96 (0.18), residues: 805 sheet: -1.73 (0.71), residues: 63 loop : -1.49 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.014 0.001 TYR K 545 PHE 0.024 0.001 PHE K 737 TRP 0.014 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (17707) covalent geometry : angle 0.67027 / 0.37 (25173) hydrogen bonds : bond 0.04269 / 2.92 ( 949) hydrogen bonds : angle 3.00151 / 2.14 ( 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 167 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8848 (tt0) cc_final: 0.8375 (tt0) REVERT: A 76 GLN cc_start: 0.8686 (pp30) cc_final: 0.8326 (pp30) REVERT: A 133 GLU cc_start: 0.8536 (mp0) cc_final: 0.8067 (mp0) REVERT: C 64 GLU cc_start: 0.8731 (tt0) cc_final: 0.8440 (pt0) REVERT: C 91 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7824 (tm-30) REVERT: C 95 LYS cc_start: 0.9189 (tttp) cc_final: 0.8983 (ttmt) REVERT: C 110 ASN cc_start: 0.9130 (t0) cc_final: 0.8490 (p0) REVERT: E 59 GLU cc_start: 0.8831 (pm20) cc_final: 0.8542 (pm20) REVERT: F 25 ASN cc_start: 0.9200 (m-40) cc_final: 0.8558 (m-40) REVERT: H 48 ASP cc_start: 0.8839 (p0) cc_final: 0.8517 (p0) REVERT: H 65 ASP cc_start: 0.8886 (t0) cc_final: 0.8539 (t0) REVERT: K 93 LYS cc_start: 0.6853 (mttm) cc_final: 0.6504 (pmtt) REVERT: K 525 SER cc_start: 0.8802 (t) cc_final: 0.8541 (p) REVERT: K 645 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8247 (tpp80) REVERT: K 717 ASN cc_start: 0.8325 (m-40) cc_final: 0.8038 (m-40) outliers start: 20 outliers final: 15 residues processed: 160 average time/residue: 0.7929 time to fit residues: 137.3290 Evaluate side-chains 160 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 113 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 146 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 52 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN G 38 ASN ** G 73 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 = 0.3689 r_free = 0.3689 target = 0.089146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063368 restraints weight = 44112.219| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.24 r_work: 0.2907 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17707 Z= 0.138 Angle : 0.660 9.248 25173 Z= 0.362 Chirality : 0.044 0.288 2852 Planarity : 0.004 0.057 2181 Dihedral : 30.385 179.271 4679 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1318 helix: 1.99 (0.18), residues: 805 sheet: -1.69 (0.71), residues: 63 loop : -1.47 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.014 0.001 TYR K 545 PHE 0.015 0.001 PHE E 67 TRP 0.015 0.001 TRP K 364 HIS 0.006 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (17707) covalent geometry : angle 0.65992 / 0.36 (25173) hydrogen bonds : bond 0.04127 / 2.82 ( 949) hydrogen bonds : angle 2.97968 / 2.13 ( 2433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4863.05 seconds wall clock time: 83 minutes 40.34 seconds (5020.34 seconds total)