Starting phenix.real_space_refine on Sun Aug 9 06:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7p_18987/08_2026/8r7p_18987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7p_18987/08_2026/8r7p_18987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r7p_18987/08_2026/8r7p_18987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7p_18987/08_2026/8r7p_18987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r7p_18987/08_2026/8r7p_18987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7p_18987/08_2026/8r7p_18987.map" } resolution = 2.53 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= 0.005 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: 5 Type Number sf(0) Gaussians S 156 5.16 5 C 11040 2.51 5 N 2700 2.21 5 O 2922 1.98 5 H 16908 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s 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: 33726 Number of models: 1 Model: "" Number of chains: 24 Chain: "L" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "C" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "D" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "E" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "F" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "G" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "H" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "I" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "J" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 6.28, per 1000 atoms: 0.19 Number of scatterers: 33726 At special positions: 0 Unit cell: (109.85, 103.35, 146.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 O 2922 8.00 N 2700 7.00 C 11040 6.00 H 16908 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 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: 3.26 Conformation dependent library (CDL) restraints added in 990.0 milliseconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 76.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'L' and resid 19 through 46 removed outlier: 5.489A pdb=" N GLU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR L 44 " --> pdb=" O ILE L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 101 Proline residue: L 89 - end of helix Processing helix chain 'L' and resid 195 through 222 Processing helix chain 'L' and resid 246 through 276 Processing helix chain 'L' and resid 276 through 282 removed outlier: 3.500A pdb=" N ILE L 280 " --> pdb=" O GLY L 276 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU L 282 " --> pdb=" O ARG L 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 46 removed outlier: 5.543A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 101 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.766A pdb=" N LEU A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 46 removed outlier: 5.386A pdb=" N GLU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 101 Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'C' and resid 20 through 46 removed outlier: 5.356A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 101 Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.837A pdb=" N LEU C 282 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 46 removed outlier: 5.458A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 101 Proline residue: D 89 - end of helix Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'D' and resid 276 through 282 Processing helix chain 'E' and resid 21 through 46 removed outlier: 5.518A pdb=" N GLU E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N THR E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 101 Proline residue: E 89 - end of helix Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'F' and resid 20 through 46 removed outlier: 5.500A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N THR F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 101 Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'F' and resid 276 through 282 removed outlier: 3.783A pdb=" N LEU F 282 " --> pdb=" O ARG F 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 46 removed outlier: 5.435A pdb=" N GLU G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR G 44 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 101 Proline residue: G 89 - end of helix Processing helix chain 'G' and resid 195 through 222 Processing helix chain 'G' and resid 246 through 276 Processing helix chain 'G' and resid 276 through 282 removed outlier: 3.613A pdb=" N LEU G 282 " --> pdb=" O ARG G 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 46 removed outlier: 5.372A pdb=" N GLU H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR H 44 " --> pdb=" O ILE H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 101 Proline residue: H 89 - end of helix Processing helix chain 'H' and resid 195 through 222 Processing helix chain 'H' and resid 246 through 276 Processing helix chain 'H' and resid 276 through 282 removed outlier: 3.888A pdb=" N LEU H 282 " --> pdb=" O ARG H 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 46 removed outlier: 5.392A pdb=" N GLU I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 101 Proline residue: I 89 - end of helix removed outlier: 3.525A pdb=" N SER I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 222 Processing helix chain 'I' and resid 246 through 276 Processing helix chain 'I' and resid 276 through 282 removed outlier: 3.573A pdb=" N LEU I 282 " --> pdb=" O ARG I 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 46 removed outlier: 5.367A pdb=" N GLU J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 101 Proline residue: J 89 - end of helix Processing helix chain 'J' and resid 195 through 222 Processing helix chain 'J' and resid 246 through 276 Processing helix chain 'J' and resid 276 through 282 removed outlier: 3.525A pdb=" N ILE J 280 " --> pdb=" O GLY J 276 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU J 282 " --> pdb=" O ARG J 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 46 removed outlier: 5.281A pdb=" N GLU K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 101 Proline residue: K 89 - end of helix Processing helix chain 'K' and resid 195 through 222 Processing helix chain 'K' and resid 246 through 276 Processing helix chain 'K' and resid 276 through 281 Processing sheet with id=AA1, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'G' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'H' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'K' and resid 54 through 55 1295 hydrogen bonds defined for protein. 3813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.01 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16872 1.03 - 1.23: 118 1.23 - 1.42: 7226 1.42 - 1.62: 9624 1.62 - 1.81: 204 Bond restraints: 34044 Sorted by residual: bond pdb=" CB LYS B 279 " pdb=" CG LYS B 279 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG LYS I 279 " pdb=" CD LYS I 279 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CB LYS I 279 " pdb=" CG LYS I 279 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CG LYS B 279 " pdb=" CD LYS B 279 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLN D 100 " pdb=" CG GLN D 100 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 ... (remaining 34039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 61101 1.83 - 3.66: 292 3.66 - 5.49: 28 5.49 - 7.32: 5 7.32 - 9.15: 2 Bond angle restraints: 61428 Sorted by residual: angle pdb=" CB LYS I 279 " pdb=" CG LYS I 279 " pdb=" CD LYS I 279 " ideal model delta sigma weight residual 111.30 120.45 -9.15 2.30e+00 1.89e-01 1.58e+01 angle pdb=" CB LYS B 279 " pdb=" CG LYS B 279 " pdb=" CD LYS B 279 " ideal model delta sigma weight residual 111.30 119.82 -8.52 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CB LYS D 279 " pdb=" CG LYS D 279 " pdb=" CD LYS D 279 " ideal model delta sigma weight residual 111.30 117.77 -6.47 2.30e+00 1.89e-01 7.93e+00 angle pdb=" CG LYS I 279 " pdb=" CD LYS I 279 " pdb=" CE LYS I 279 " ideal model delta sigma weight residual 111.30 116.47 -5.17 2.30e+00 1.89e-01 5.05e+00 angle pdb=" CB MET E 21 " pdb=" CG MET E 21 " pdb=" SD MET E 21 " ideal model delta sigma weight residual 112.70 119.28 -6.58 3.00e+00 1.11e-01 4.81e+00 ... (remaining 61423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 14607 17.86 - 35.73: 1077 35.73 - 53.59: 344 53.59 - 71.46: 89 71.46 - 89.32: 11 Dihedral angle restraints: 16128 sinusoidal: 8532 harmonic: 7596 Sorted by residual: dihedral pdb=" CB GLU G 241 " pdb=" CG GLU G 241 " pdb=" CD GLU G 241 " pdb=" OE1 GLU G 241 " ideal model delta sinusoidal sigma weight residual 0.00 89.32 -89.32 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 241 " pdb=" CG GLU A 241 " pdb=" CD GLU A 241 " pdb=" OE1 GLU A 241 " ideal model delta sinusoidal sigma weight residual 0.00 86.02 -86.02 1 3.00e+01 1.11e-03 9.93e+00 dihedral pdb=" CB GLU L 43 " pdb=" CG GLU L 43 " pdb=" CD GLU L 43 " pdb=" OE1 GLU L 43 " ideal model delta sinusoidal sigma weight residual 0.00 85.67 -85.67 1 3.00e+01 1.11e-03 9.86e+00 ... (remaining 16125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1677 0.026 - 0.052: 542 0.052 - 0.079: 365 0.079 - 0.105: 85 0.105 - 0.131: 43 Chirality restraints: 2712 Sorted by residual: chirality pdb=" CA ILE G 73 " pdb=" N ILE G 73 " pdb=" C ILE G 73 " pdb=" CB ILE G 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE L 73 " pdb=" N ILE L 73 " pdb=" C ILE L 73 " pdb=" CB ILE L 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2709 not shown) Planarity restraints: 4836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 38 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C VAL H 38 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL H 38 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA H 39 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 38 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C VAL K 38 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL K 38 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA K 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 38 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C VAL B 38 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL B 38 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA B 39 " 0.007 2.00e-02 2.50e+03 ... (remaining 4833 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 2482 2.22 - 2.82: 72547 2.82 - 3.41: 91945 3.41 - 4.01: 124008 4.01 - 4.60: 186232 Nonbonded interactions: 477214 Sorted by model distance: nonbonded pdb="HE22 GLN B 59 " pdb=" OE1 GLN I 59 " model vdw 1.630 2.450 nonbonded pdb="HE22 GLN C 59 " pdb=" OE1 GLN H 59 " model vdw 1.650 2.450 nonbonded pdb=" HE ARG A 77 " pdb=" OE2 GLU B 249 " model vdw 1.709 2.450 nonbonded pdb=" H ARG F 246 " pdb=" O HOH F 401 " model vdw 1.710 2.450 nonbonded pdb=" H ARG K 246 " pdb=" O HOH K 401 " model vdw 1.710 2.450 ... (remaining 477209 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.010 Normalize map: mean=0, sd=1: 4.410 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: 0.280 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.290 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 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 : 0.003 0.040 17172 Z= 0.127 Angle : 0.463 9.150 23352 Z= 0.242 Chirality : 0.038 0.131 2712 Planarity : 0.003 0.027 2856 Dihedral : 14.575 89.319 6060 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.59 % Allowed : 14.90 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.48 (0.19), residues: 2028 helix: 3.86 (0.12), residues: 1548 sheet: -0.03 (0.38), residues: 204 loop : -0.41 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 206 TYR 0.011 0.001 TYR K 243 PHE 0.009 0.001 PHE F 213 TRP 0.005 0.001 TRP J 277 HIS 0.002 0.000 HIS I 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17136) covalent geometry : angle 0.46153 / 0.24 (23280) SS BOND : bond 0.00051 / 0.04 ( 36) SS BOND : angle 0.71395 / 0.56 ( 72) hydrogen bonds : bond 0.11188 / 7.34 ( 1295) hydrogen bonds : angle 4.00227 / 2.91 ( 3813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 301 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.3921 (mtp180) cc_final: 0.3465 (mmm-85) REVERT: L 43 GLU cc_start: 0.6047 (mt-10) cc_final: 0.4795 (mp0) REVERT: L 85 MET cc_start: 0.7055 (tpp) cc_final: 0.6699 (tpt) REVERT: L 197 ARG cc_start: 0.4340 (tpt170) cc_final: 0.3885 (tpt170) REVERT: L 230 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6324 (mt-10) REVERT: L 233 ARG cc_start: 0.6398 (ttm170) cc_final: 0.5681 (ttt180) REVERT: L 239 GLU cc_start: 0.7219 (tt0) cc_final: 0.6212 (tp30) REVERT: A 43 GLU cc_start: 0.6228 (mt-10) cc_final: 0.4961 (mp0) REVERT: A 85 MET cc_start: 0.6992 (tpp) cc_final: 0.6586 (tpt) REVERT: A 99 HIS cc_start: 0.3969 (OUTLIER) cc_final: 0.3606 (m90) REVERT: A 197 ARG cc_start: 0.5335 (ttt180) cc_final: 0.4946 (ttm170) REVERT: A 230 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6654 (mt-10) REVERT: A 233 ARG cc_start: 0.6354 (ttm170) cc_final: 0.5704 (ttt180) REVERT: A 238 LYS cc_start: 0.6528 (mtmt) cc_final: 0.5773 (mttm) REVERT: A 239 GLU cc_start: 0.7179 (tt0) cc_final: 0.6247 (tp30) REVERT: B 24 ARG cc_start: 0.4019 (mtp180) cc_final: 0.3541 (mmm-85) REVERT: B 43 GLU cc_start: 0.6575 (tt0) cc_final: 0.6006 (mm-30) REVERT: B 49 GLU cc_start: 0.7139 (pt0) cc_final: 0.6894 (pt0) REVERT: B 85 MET cc_start: 0.7092 (tpp) cc_final: 0.6782 (tpt) REVERT: B 86 VAL cc_start: 0.5690 (t) cc_final: 0.5312 (m) REVERT: B 197 ARG cc_start: 0.5139 (ttt180) cc_final: 0.4327 (ppt170) REVERT: B 230 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6578 (mt-10) REVERT: B 233 ARG cc_start: 0.6523 (ttm170) cc_final: 0.5753 (ttt180) REVERT: B 238 LYS cc_start: 0.6287 (mtmp) cc_final: 0.5710 (mttm) REVERT: B 239 GLU cc_start: 0.7167 (tt0) cc_final: 0.6232 (tp30) REVERT: C 24 ARG cc_start: 0.3731 (mtm180) cc_final: 0.3405 (mmm-85) REVERT: C 43 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5083 (mp0) REVERT: C 85 MET cc_start: 0.7151 (tpp) cc_final: 0.6731 (tpt) REVERT: C 197 ARG cc_start: 0.5298 (ttt180) cc_final: 0.5010 (ttt180) REVERT: C 230 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6379 (mt-10) REVERT: C 233 ARG cc_start: 0.6401 (ttm170) cc_final: 0.5692 (ttt180) REVERT: C 238 LYS cc_start: 0.6391 (mtmt) cc_final: 0.6146 (mtmp) REVERT: C 239 GLU cc_start: 0.7169 (tt0) cc_final: 0.6267 (tp30) REVERT: D 24 ARG cc_start: 0.3923 (mtp180) cc_final: 0.3524 (mmm-85) REVERT: D 43 GLU cc_start: 0.6408 (tt0) cc_final: 0.5152 (mp0) REVERT: D 48 ASP cc_start: 0.7174 (p0) cc_final: 0.6944 (p0) REVERT: D 52 MET cc_start: 0.7453 (mmt) cc_final: 0.7215 (mmt) REVERT: D 81 PHE cc_start: 0.6898 (t80) cc_final: 0.6596 (t80) REVERT: D 85 MET cc_start: 0.6873 (tpp) cc_final: 0.6530 (tpt) REVERT: D 87 CYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5475 (m) REVERT: D 230 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: D 233 ARG cc_start: 0.6524 (ttm170) cc_final: 0.5881 (ttt180) REVERT: D 238 LYS cc_start: 0.6529 (mtmt) cc_final: 0.5816 (mttm) REVERT: D 239 GLU cc_start: 0.7092 (tt0) cc_final: 0.6158 (tp30) REVERT: E 24 ARG cc_start: 0.3952 (mtp180) cc_final: 0.3437 (mmm-85) REVERT: E 43 GLU cc_start: 0.6518 (tt0) cc_final: 0.5169 (mp0) REVERT: E 49 GLU cc_start: 0.7092 (pt0) cc_final: 0.6871 (pt0) REVERT: E 85 MET cc_start: 0.7200 (tpp) cc_final: 0.6811 (tpt) REVERT: E 197 ARG cc_start: 0.5152 (ttt180) cc_final: 0.4931 (ttm170) REVERT: E 230 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6606 (mt-10) REVERT: E 233 ARG cc_start: 0.6029 (mtp180) cc_final: 0.5595 (ttp-170) REVERT: E 239 GLU cc_start: 0.7074 (tp30) cc_final: 0.6089 (tp30) REVERT: E 273 ASN cc_start: 0.5954 (t0) cc_final: 0.5714 (OUTLIER) REVERT: F 24 ARG cc_start: 0.3730 (mtp180) cc_final: 0.3234 (ptp90) REVERT: F 43 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5940 (mm-30) REVERT: F 48 ASP cc_start: 0.7249 (p0) cc_final: 0.6929 (p0) REVERT: F 81 PHE cc_start: 0.6891 (t80) cc_final: 0.6633 (t80) REVERT: F 85 MET cc_start: 0.6976 (tpp) cc_final: 0.6546 (tpt) REVERT: F 87 CYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5640 (m) REVERT: F 197 ARG cc_start: 0.5246 (ttt180) cc_final: 0.4896 (ttt180) REVERT: F 230 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6546 (mt-10) REVERT: F 233 ARG cc_start: 0.6474 (ttm170) cc_final: 0.5821 (ttt180) REVERT: F 239 GLU cc_start: 0.7077 (tt0) cc_final: 0.6802 (tt0) REVERT: G 24 ARG cc_start: 0.3716 (mtm180) cc_final: 0.3263 (mmm-85) REVERT: G 43 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5264 (mp0) REVERT: G 44 THR cc_start: 0.6974 (m) cc_final: 0.6556 (t) REVERT: G 49 GLU cc_start: 0.7148 (pt0) cc_final: 0.6917 (pt0) REVERT: G 85 MET cc_start: 0.6759 (mmm) cc_final: 0.6330 (tpp) REVERT: G 197 ARG cc_start: 0.5053 (ttt180) cc_final: 0.4825 (ttt180) REVERT: G 230 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6498 (mt-10) REVERT: G 233 ARG cc_start: 0.6502 (ttm170) cc_final: 0.5874 (ttt180) REVERT: G 238 LYS cc_start: 0.6250 (mtmp) cc_final: 0.5699 (mttm) REVERT: G 239 GLU cc_start: 0.7060 (tp30) cc_final: 0.6017 (tp30) REVERT: H 24 ARG cc_start: 0.3993 (mtp180) cc_final: 0.3645 (mmm-85) REVERT: H 43 GLU cc_start: 0.6622 (tp30) cc_final: 0.6001 (mm-30) REVERT: H 85 MET cc_start: 0.7008 (mmm) cc_final: 0.6720 (tpt) REVERT: H 86 VAL cc_start: 0.5946 (t) cc_final: 0.5551 (m) REVERT: H 197 ARG cc_start: 0.5351 (ttt180) cc_final: 0.5102 (ttt180) REVERT: H 230 GLU cc_start: 0.6891 (mt-10) cc_final: 0.5339 (mp0) REVERT: H 233 ARG cc_start: 0.6317 (ttm170) cc_final: 0.5545 (ttt180) REVERT: H 238 LYS cc_start: 0.6214 (mtmp) cc_final: 0.5682 (mttm) REVERT: H 239 GLU cc_start: 0.7007 (tp30) cc_final: 0.6040 (tp30) REVERT: I 24 ARG cc_start: 0.3901 (mtp180) cc_final: 0.3699 (mmm-85) REVERT: I 43 GLU cc_start: 0.6619 (tp30) cc_final: 0.6136 (mm-30) REVERT: I 48 ASP cc_start: 0.7284 (p0) cc_final: 0.6974 (p0) REVERT: I 81 PHE cc_start: 0.6847 (t80) cc_final: 0.6559 (t80) REVERT: I 85 MET cc_start: 0.7072 (mmm) cc_final: 0.6750 (tpt) REVERT: I 197 ARG cc_start: 0.5348 (ttt180) cc_final: 0.5138 (ttm170) REVERT: I 230 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6728 (mt-10) REVERT: I 233 ARG cc_start: 0.6431 (ttm170) cc_final: 0.5739 (ttt180) REVERT: I 238 LYS cc_start: 0.6504 (mtmt) cc_final: 0.5708 (mttm) REVERT: I 239 GLU cc_start: 0.7104 (tt0) cc_final: 0.6154 (tp30) REVERT: J 24 ARG cc_start: 0.3958 (mtp180) cc_final: 0.3585 (mmm-85) REVERT: J 85 MET cc_start: 0.6796 (mmm) cc_final: 0.6329 (tpt) REVERT: J 86 VAL cc_start: 0.5768 (t) cc_final: 0.5352 (m) REVERT: J 197 ARG cc_start: 0.5072 (ttt180) cc_final: 0.4851 (ttt180) REVERT: J 230 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6649 (mt-10) REVERT: J 233 ARG cc_start: 0.6535 (ttm170) cc_final: 0.5729 (ttt180) REVERT: J 238 LYS cc_start: 0.6294 (mtmt) cc_final: 0.5663 (mttm) REVERT: J 239 GLU cc_start: 0.7251 (tt0) cc_final: 0.6303 (tp30) REVERT: K 24 ARG cc_start: 0.3853 (mtp180) cc_final: 0.3474 (mmm-85) REVERT: K 43 GLU cc_start: 0.6511 (tp30) cc_final: 0.6033 (mm-30) REVERT: K 85 MET cc_start: 0.7015 (tpp) cc_final: 0.6586 (tpt) REVERT: K 86 VAL cc_start: 0.5866 (t) cc_final: 0.5427 (m) REVERT: K 197 ARG cc_start: 0.5285 (ttt180) cc_final: 0.5005 (ttt180) REVERT: K 230 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6405 (mt-10) REVERT: K 233 ARG cc_start: 0.6350 (ttm170) cc_final: 0.5688 (ttt180) REVERT: K 238 LYS cc_start: 0.6274 (mtmp) cc_final: 0.5625 (mttm) REVERT: K 239 GLU cc_start: 0.7121 (tt0) cc_final: 0.6116 (tp30) outliers start: 11 outliers final: 1 residues processed: 308 average time/residue: 1.5778 time to fit residues: 533.7616 Evaluate side-chains 243 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 43 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 207 ASN E 207 ASN F 273 ASN I 273 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.170113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.127312 restraints weight = 39999.773| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.32 r_work: 0.2907 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17172 Z= 0.162 Angle : 0.554 6.606 23352 Z= 0.304 Chirality : 0.042 0.160 2712 Planarity : 0.005 0.043 2856 Dihedral : 4.487 58.009 2296 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.18 % Allowed : 15.06 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.96 (0.18), residues: 2028 helix: 3.36 (0.12), residues: 1560 sheet: -0.26 (0.34), residues: 204 loop : 0.15 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 246 TYR 0.021 0.003 TYR J 67 PHE 0.016 0.002 PHE E 53 TRP 0.006 0.001 TRP J 277 HIS 0.004 0.001 HIS I 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (17136) covalent geometry : angle 0.55060 / 0.30 (23280) SS BOND : bond 0.00298 / 0.22 ( 36) SS BOND : angle 1.23696 / 0.93 ( 72) hydrogen bonds : bond 0.04902 / 3.28 ( 1295) hydrogen bonds : angle 3.76277 / 2.74 ( 3813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5321 (mtp180) cc_final: 0.4914 (mmm-85) REVERT: L 43 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7107 (mp0) REVERT: L 197 ARG cc_start: 0.5176 (tpt170) cc_final: 0.4777 (tpt170) REVERT: L 233 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7810 (ttt180) REVERT: L 239 GLU cc_start: 0.8460 (tt0) cc_final: 0.8009 (tp30) REVERT: A 24 ARG cc_start: 0.5351 (mtp180) cc_final: 0.4080 (mtp-110) REVERT: A 43 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7483 (mm-30) REVERT: A 85 MET cc_start: 0.8689 (tpp) cc_final: 0.8444 (tpt) REVERT: A 197 ARG cc_start: 0.6022 (ttt180) cc_final: 0.5680 (ttt180) REVERT: A 233 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7838 (ttt180) REVERT: A 238 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7632 (mttm) REVERT: A 239 GLU cc_start: 0.8501 (tt0) cc_final: 0.8033 (tp30) REVERT: B 24 ARG cc_start: 0.5420 (mtp180) cc_final: 0.4989 (mmm-85) REVERT: B 43 GLU cc_start: 0.8038 (tt0) cc_final: 0.7334 (mp0) REVERT: B 86 VAL cc_start: 0.7815 (t) cc_final: 0.7574 (m) REVERT: B 197 ARG cc_start: 0.5829 (ttt180) cc_final: 0.4936 (ppt170) REVERT: B 233 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7724 (ttt180) REVERT: B 239 GLU cc_start: 0.8473 (tt0) cc_final: 0.8071 (tp30) REVERT: C 24 ARG cc_start: 0.5411 (mtm180) cc_final: 0.5093 (mmm-85) REVERT: C 43 GLU cc_start: 0.7915 (tp30) cc_final: 0.7251 (mp0) REVERT: C 197 ARG cc_start: 0.5922 (ttt180) cc_final: 0.5602 (ttt180) REVERT: C 233 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7850 (ttt180) REVERT: C 239 GLU cc_start: 0.8445 (tt0) cc_final: 0.8005 (tp30) REVERT: D 24 ARG cc_start: 0.5296 (mtp180) cc_final: 0.4037 (mtp-110) REVERT: D 43 GLU cc_start: 0.7971 (tt0) cc_final: 0.7648 (mm-30) REVERT: D 197 ARG cc_start: 0.5884 (ttm170) cc_final: 0.5568 (ttt180) REVERT: D 233 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7860 (ttt180) REVERT: D 238 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7587 (mttm) REVERT: D 239 GLU cc_start: 0.8483 (tt0) cc_final: 0.7905 (tp30) REVERT: D 268 ASN cc_start: 0.8107 (m-40) cc_final: 0.7815 (m110) REVERT: E 24 ARG cc_start: 0.5311 (mtp180) cc_final: 0.4963 (mmm-85) REVERT: E 43 GLU cc_start: 0.8034 (tt0) cc_final: 0.7353 (mp0) REVERT: E 85 MET cc_start: 0.8677 (tpp) cc_final: 0.8450 (tpt) REVERT: E 197 ARG cc_start: 0.5916 (ttt180) cc_final: 0.4984 (ppt170) REVERT: E 239 GLU cc_start: 0.8292 (tp30) cc_final: 0.7780 (tp30) REVERT: F 24 ARG cc_start: 0.5178 (mtp180) cc_final: 0.3974 (mtp-110) REVERT: F 43 GLU cc_start: 0.7984 (tt0) cc_final: 0.7354 (mp0) REVERT: F 85 MET cc_start: 0.8635 (tpp) cc_final: 0.8427 (tpt) REVERT: F 197 ARG cc_start: 0.6022 (ttt180) cc_final: 0.5133 (tpt170) REVERT: F 233 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7792 (ttt-90) REVERT: G 24 ARG cc_start: 0.5200 (mtm180) cc_final: 0.4807 (mmm-85) REVERT: G 43 GLU cc_start: 0.7962 (tp30) cc_final: 0.7324 (mp0) REVERT: G 85 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8295 (tpp) REVERT: G 197 ARG cc_start: 0.5771 (ttt180) cc_final: 0.4949 (tpt170) REVERT: G 233 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7758 (ttt180) REVERT: G 239 GLU cc_start: 0.8245 (tp30) cc_final: 0.7775 (tp30) REVERT: H 24 ARG cc_start: 0.5304 (mtp180) cc_final: 0.5014 (mmm-85) REVERT: H 43 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: H 85 MET cc_start: 0.8754 (mmm) cc_final: 0.8470 (tpt) REVERT: H 86 VAL cc_start: 0.7936 (t) cc_final: 0.7650 (m) REVERT: H 197 ARG cc_start: 0.5989 (ttt180) cc_final: 0.5630 (ttt180) REVERT: H 233 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7796 (ttt180) REVERT: H 239 GLU cc_start: 0.8179 (tp30) cc_final: 0.7605 (tp30) REVERT: I 43 GLU cc_start: 0.7938 (tp30) cc_final: 0.7633 (mm-30) REVERT: I 85 MET cc_start: 0.8782 (mmm) cc_final: 0.8475 (tpt) REVERT: I 197 ARG cc_start: 0.5959 (ttt180) cc_final: 0.5727 (ttm170) REVERT: I 233 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7826 (ttt180) REVERT: I 238 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7641 (mttm) REVERT: I 239 GLU cc_start: 0.8411 (tt0) cc_final: 0.7864 (tp30) REVERT: J 24 ARG cc_start: 0.5381 (mtp180) cc_final: 0.4991 (mmm-85) REVERT: J 43 GLU cc_start: 0.7841 (tp30) cc_final: 0.7546 (mm-30) REVERT: J 85 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8355 (tpp) REVERT: J 86 VAL cc_start: 0.7893 (t) cc_final: 0.7575 (m) REVERT: J 197 ARG cc_start: 0.5871 (ttt180) cc_final: 0.4955 (ppt170) REVERT: J 233 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7785 (ttt180) REVERT: J 238 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7601 (mttm) REVERT: J 239 GLU cc_start: 0.8556 (tt0) cc_final: 0.8133 (tp30) REVERT: J 278 ARG cc_start: 0.3891 (OUTLIER) cc_final: 0.3577 (ttp-110) REVERT: K 24 ARG cc_start: 0.5227 (mtp180) cc_final: 0.4889 (mmm-85) REVERT: K 43 GLU cc_start: 0.7882 (tp30) cc_final: 0.7550 (mm-30) REVERT: K 85 MET cc_start: 0.8776 (tpp) cc_final: 0.8549 (tpt) REVERT: K 86 VAL cc_start: 0.7909 (t) cc_final: 0.7553 (m) REVERT: K 197 ARG cc_start: 0.5918 (ttt180) cc_final: 0.5138 (ttp80) REVERT: K 233 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7771 (ttt180) REVERT: K 239 GLU cc_start: 0.8492 (tt0) cc_final: 0.7931 (tp30) REVERT: K 278 ARG cc_start: 0.3899 (OUTLIER) cc_final: 0.3679 (ttp-110) outliers start: 22 outliers final: 2 residues processed: 275 average time/residue: 1.6654 time to fit residues: 500.4808 Evaluate side-chains 248 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 240 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 278 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 130 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 50 GLN L 268 ASN A 50 GLN A 273 ASN B 50 GLN B 207 ASN B 273 ASN C 50 GLN C 273 ASN D 50 GLN E 50 GLN E 207 ASN F 50 GLN F 268 ASN F 273 ASN G 50 GLN H 50 GLN H 207 ASN H 273 ASN I 50 GLN I 207 ASN I 268 ASN I 273 ASN J 268 ASN K 50 GLN K 273 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.169296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.126502 restraints weight = 39798.533| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.37 r_work: 0.2877 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17172 Z= 0.152 Angle : 0.516 5.534 23352 Z= 0.282 Chirality : 0.040 0.137 2712 Planarity : 0.004 0.037 2856 Dihedral : 3.476 12.568 2280 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.91 % Allowed : 13.73 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.88 (0.18), residues: 2028 helix: 3.29 (0.12), residues: 1560 sheet: -0.39 (0.34), residues: 204 loop : 0.27 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 246 TYR 0.020 0.003 TYR B 67 PHE 0.012 0.001 PHE D 53 TRP 0.005 0.001 TRP J 277 HIS 0.003 0.001 HIS I 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (17136) covalent geometry : angle 0.51426 / 0.28 (23280) SS BOND : bond 0.00289 / 0.20 ( 36) SS BOND : angle 0.95422 / 0.72 ( 72) hydrogen bonds : bond 0.04870 / 3.24 ( 1295) hydrogen bonds : angle 3.71780 / 2.71 ( 3813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5282 (mtp180) cc_final: 0.4843 (mmm-85) REVERT: L 43 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7163 (mp0) REVERT: L 197 ARG cc_start: 0.5087 (tpt170) cc_final: 0.4713 (tpt170) REVERT: L 233 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7777 (ttt180) REVERT: L 239 GLU cc_start: 0.8467 (tt0) cc_final: 0.8009 (tp30) REVERT: L 278 ARG cc_start: 0.4176 (OUTLIER) cc_final: 0.3897 (ttp-110) REVERT: A 24 ARG cc_start: 0.5237 (mtp180) cc_final: 0.3961 (mtp-110) REVERT: A 43 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7435 (mm-30) REVERT: A 85 MET cc_start: 0.8732 (tpp) cc_final: 0.8525 (tpt) REVERT: A 86 VAL cc_start: 0.7667 (t) cc_final: 0.7325 (m) REVERT: A 197 ARG cc_start: 0.6027 (ttt180) cc_final: 0.5088 (tpt170) REVERT: A 233 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7857 (ttt180) REVERT: A 238 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7672 (mttm) REVERT: A 239 GLU cc_start: 0.8614 (tt0) cc_final: 0.8121 (tp30) REVERT: A 279 LYS cc_start: 0.4318 (OUTLIER) cc_final: 0.3992 (mppt) REVERT: B 24 ARG cc_start: 0.5368 (mtp180) cc_final: 0.4928 (mmm-85) REVERT: B 43 GLU cc_start: 0.8009 (tt0) cc_final: 0.7383 (mp0) REVERT: B 86 VAL cc_start: 0.7803 (t) cc_final: 0.7533 (m) REVERT: B 197 ARG cc_start: 0.5757 (ttt180) cc_final: 0.4838 (ppt170) REVERT: B 233 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7801 (ttt180) REVERT: B 239 GLU cc_start: 0.8582 (tt0) cc_final: 0.8132 (tp30) REVERT: C 24 ARG cc_start: 0.5303 (mtm180) cc_final: 0.4995 (mmm-85) REVERT: C 43 GLU cc_start: 0.7915 (tp30) cc_final: 0.7219 (mp0) REVERT: C 197 ARG cc_start: 0.5912 (ttt180) cc_final: 0.5550 (ttt180) REVERT: C 233 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7798 (ttt180) REVERT: C 239 GLU cc_start: 0.8537 (tt0) cc_final: 0.8266 (tt0) REVERT: D 24 ARG cc_start: 0.5306 (mtp180) cc_final: 0.4990 (mmm-85) REVERT: D 43 GLU cc_start: 0.8000 (tt0) cc_final: 0.7457 (mp0) REVERT: D 197 ARG cc_start: 0.5920 (ttm170) cc_final: 0.5598 (ttt180) REVERT: D 233 ARG cc_start: 0.8285 (ttm170) cc_final: 0.7847 (ttt180) REVERT: D 238 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7627 (mttm) REVERT: D 239 GLU cc_start: 0.8558 (tt0) cc_final: 0.7919 (tp30) REVERT: D 268 ASN cc_start: 0.8079 (m-40) cc_final: 0.7796 (m110) REVERT: E 24 ARG cc_start: 0.5280 (mtp180) cc_final: 0.4896 (mmm-85) REVERT: E 43 GLU cc_start: 0.8051 (tt0) cc_final: 0.7388 (mp0) REVERT: E 197 ARG cc_start: 0.5869 (ttt180) cc_final: 0.4907 (ppt170) REVERT: E 239 GLU cc_start: 0.8427 (tp30) cc_final: 0.7898 (tp30) REVERT: F 24 ARG cc_start: 0.5336 (mtp180) cc_final: 0.4062 (mtp-110) REVERT: F 43 GLU cc_start: 0.8021 (tt0) cc_final: 0.7732 (mm-30) REVERT: F 197 ARG cc_start: 0.6015 (ttt180) cc_final: 0.5086 (tpt170) REVERT: F 233 ARG cc_start: 0.8306 (ttm170) cc_final: 0.7850 (ttt180) REVERT: G 24 ARG cc_start: 0.5186 (mtm180) cc_final: 0.4769 (mmm-85) REVERT: G 43 GLU cc_start: 0.7995 (tp30) cc_final: 0.7376 (mp0) REVERT: G 85 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8343 (tpp) REVERT: G 197 ARG cc_start: 0.5842 (ttt180) cc_final: 0.4909 (ppt170) REVERT: G 233 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7725 (ttt180) REVERT: G 239 GLU cc_start: 0.8372 (tp30) cc_final: 0.7842 (tp30) REVERT: H 24 ARG cc_start: 0.5259 (mtp180) cc_final: 0.4923 (mmm-85) REVERT: H 43 GLU cc_start: 0.7834 (tp30) cc_final: 0.7244 (mp0) REVERT: H 85 MET cc_start: 0.8770 (mmm) cc_final: 0.8511 (tpt) REVERT: H 86 VAL cc_start: 0.7870 (t) cc_final: 0.7569 (m) REVERT: H 197 ARG cc_start: 0.6014 (ttt180) cc_final: 0.5663 (ttt180) REVERT: H 233 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7793 (ttt180) REVERT: H 239 GLU cc_start: 0.8384 (tp30) cc_final: 0.7756 (tp30) REVERT: I 43 GLU cc_start: 0.7979 (tp30) cc_final: 0.7662 (mm-30) REVERT: I 85 MET cc_start: 0.8789 (mmm) cc_final: 0.8523 (tpt) REVERT: I 86 VAL cc_start: 0.7842 (t) cc_final: 0.7548 (m) REVERT: I 197 ARG cc_start: 0.6019 (ttt180) cc_final: 0.5641 (ttt180) REVERT: I 233 ARG cc_start: 0.8267 (ttm170) cc_final: 0.7816 (ttt180) REVERT: I 238 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7589 (mttm) REVERT: I 239 GLU cc_start: 0.8525 (tt0) cc_final: 0.7920 (tp30) REVERT: J 24 ARG cc_start: 0.5288 (mtp180) cc_final: 0.4883 (mmm-85) REVERT: J 43 GLU cc_start: 0.7876 (tp30) cc_final: 0.7659 (mm-30) REVERT: J 85 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8388 (tpp) REVERT: J 86 VAL cc_start: 0.7838 (t) cc_final: 0.7524 (m) REVERT: J 197 ARG cc_start: 0.5856 (ttt180) cc_final: 0.4895 (ppt170) REVERT: J 233 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7766 (ttt180) REVERT: J 238 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7644 (mttm) REVERT: J 239 GLU cc_start: 0.8658 (tt0) cc_final: 0.8148 (tp30) REVERT: J 278 ARG cc_start: 0.3928 (OUTLIER) cc_final: 0.3569 (ttp-110) REVERT: K 24 ARG cc_start: 0.5200 (mtp180) cc_final: 0.4832 (mmm-85) REVERT: K 43 GLU cc_start: 0.7935 (tp30) cc_final: 0.7212 (mp0) REVERT: K 85 MET cc_start: 0.8812 (tpp) cc_final: 0.8570 (tpt) REVERT: K 86 VAL cc_start: 0.7829 (t) cc_final: 0.7439 (m) REVERT: K 197 ARG cc_start: 0.5914 (ttt180) cc_final: 0.5052 (ttp80) REVERT: K 233 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7770 (ttt180) REVERT: K 239 GLU cc_start: 0.8577 (tt0) cc_final: 0.7992 (tp30) REVERT: K 268 ASN cc_start: 0.8151 (m-40) cc_final: 0.7947 (m110) REVERT: K 278 ARG cc_start: 0.3893 (OUTLIER) cc_final: 0.3652 (ttp-110) outliers start: 17 outliers final: 3 residues processed: 259 average time/residue: 1.6197 time to fit residues: 458.7233 Evaluate side-chains 241 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 232 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 278 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 128 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 207 ASN B 273 ASN C 273 ASN E 207 ASN E 268 ASN E 273 ASN F 207 ASN F 273 ASN H 207 ASN H 273 ASN I 207 ASN I 273 ASN J 50 GLN J 268 ASN K 273 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.170075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127139 restraints weight = 39710.367| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.34 r_work: 0.2890 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17172 Z= 0.121 Angle : 0.486 4.503 23352 Z= 0.265 Chirality : 0.039 0.136 2712 Planarity : 0.004 0.036 2856 Dihedral : 3.406 10.991 2280 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.80 % Allowed : 13.19 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.90 (0.18), residues: 2028 helix: 3.31 (0.12), residues: 1560 sheet: -0.37 (0.34), residues: 204 loop : 0.24 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 206 TYR 0.017 0.002 TYR B 67 PHE 0.011 0.001 PHE C 53 TRP 0.004 0.001 TRP J 277 HIS 0.002 0.001 HIS I 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17136) covalent geometry : angle 0.48461 / 0.26 (23280) SS BOND : bond 0.00232 / 0.16 ( 36) SS BOND : angle 0.78507 / 0.60 ( 72) hydrogen bonds : bond 0.04374 / 2.92 ( 1295) hydrogen bonds : angle 3.59770 / 2.63 ( 3813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5267 (mtp180) cc_final: 0.4847 (mmm-85) REVERT: L 43 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7179 (mp0) REVERT: L 197 ARG cc_start: 0.5071 (tpt170) cc_final: 0.4143 (ppt170) REVERT: L 233 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7801 (ttt180) REVERT: L 278 ARG cc_start: 0.4179 (OUTLIER) cc_final: 0.3872 (ttp-110) REVERT: A 24 ARG cc_start: 0.5234 (mtp180) cc_final: 0.3951 (mtp-110) REVERT: A 86 VAL cc_start: 0.7681 (t) cc_final: 0.7331 (m) REVERT: A 197 ARG cc_start: 0.6025 (ttt180) cc_final: 0.5107 (tpt170) REVERT: A 233 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7839 (ttt180) REVERT: A 238 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7595 (mttm) REVERT: A 239 GLU cc_start: 0.8596 (tt0) cc_final: 0.8091 (tp30) REVERT: A 279 LYS cc_start: 0.4363 (OUTLIER) cc_final: 0.4037 (mppt) REVERT: B 24 ARG cc_start: 0.5370 (mtp180) cc_final: 0.4933 (mmm-85) REVERT: B 43 GLU cc_start: 0.7991 (tt0) cc_final: 0.7372 (mp0) REVERT: B 86 VAL cc_start: 0.7788 (t) cc_final: 0.7519 (m) REVERT: B 197 ARG cc_start: 0.5849 (ttt180) cc_final: 0.4863 (ppt170) REVERT: B 233 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7796 (ttt180) REVERT: B 239 GLU cc_start: 0.8579 (tt0) cc_final: 0.8113 (tp30) REVERT: C 24 ARG cc_start: 0.5305 (mtm180) cc_final: 0.5020 (mmm-85) REVERT: C 43 GLU cc_start: 0.7889 (tp30) cc_final: 0.7222 (mp0) REVERT: C 197 ARG cc_start: 0.5976 (ttt180) cc_final: 0.5101 (ppt170) REVERT: C 233 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7789 (ttt180) REVERT: C 239 GLU cc_start: 0.8492 (tt0) cc_final: 0.8279 (tt0) REVERT: D 24 ARG cc_start: 0.5313 (mtp180) cc_final: 0.5004 (mmm-85) REVERT: D 43 GLU cc_start: 0.8013 (tt0) cc_final: 0.7461 (mp0) REVERT: D 197 ARG cc_start: 0.5923 (ttm170) cc_final: 0.4830 (ppt170) REVERT: D 233 ARG cc_start: 0.8292 (ttm170) cc_final: 0.7839 (ttt180) REVERT: D 238 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7569 (mttm) REVERT: D 239 GLU cc_start: 0.8552 (tt0) cc_final: 0.7921 (tp30) REVERT: D 268 ASN cc_start: 0.8071 (m-40) cc_final: 0.7830 (m110) REVERT: E 24 ARG cc_start: 0.5299 (mtp180) cc_final: 0.4894 (mmm-85) REVERT: E 43 GLU cc_start: 0.8010 (tt0) cc_final: 0.7396 (mp0) REVERT: E 197 ARG cc_start: 0.5914 (ttt180) cc_final: 0.4962 (tpt170) REVERT: E 239 GLU cc_start: 0.8390 (tp30) cc_final: 0.7866 (tp30) REVERT: F 24 ARG cc_start: 0.5362 (mtp180) cc_final: 0.4102 (mtp-110) REVERT: F 43 GLU cc_start: 0.7999 (tt0) cc_final: 0.7457 (mp0) REVERT: F 197 ARG cc_start: 0.6055 (ttt180) cc_final: 0.5138 (tpt170) REVERT: F 233 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7838 (ttt180) REVERT: G 24 ARG cc_start: 0.5208 (mtm180) cc_final: 0.4810 (mmm-85) REVERT: G 43 GLU cc_start: 0.7987 (tt0) cc_final: 0.7393 (mp0) REVERT: G 85 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8334 (tpp) REVERT: G 197 ARG cc_start: 0.5890 (ttt180) cc_final: 0.4958 (ppt170) REVERT: G 233 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7806 (ttt180) REVERT: G 239 GLU cc_start: 0.8367 (tp30) cc_final: 0.7807 (tp30) REVERT: H 24 ARG cc_start: 0.5278 (mtp180) cc_final: 0.4953 (mmm-85) REVERT: H 43 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: H 85 MET cc_start: 0.8758 (mmm) cc_final: 0.8513 (tpt) REVERT: H 86 VAL cc_start: 0.7818 (t) cc_final: 0.7480 (m) REVERT: H 197 ARG cc_start: 0.6022 (ttt180) cc_final: 0.5190 (ttp80) REVERT: H 233 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7777 (ttt180) REVERT: H 239 GLU cc_start: 0.8391 (tp30) cc_final: 0.8093 (tt0) REVERT: I 43 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: I 85 MET cc_start: 0.8779 (mmm) cc_final: 0.8517 (tpt) REVERT: I 86 VAL cc_start: 0.7825 (t) cc_final: 0.7528 (m) REVERT: I 197 ARG cc_start: 0.6058 (ttt180) cc_final: 0.5120 (tpt170) REVERT: I 233 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7798 (ttt180) REVERT: I 239 GLU cc_start: 0.8519 (tt0) cc_final: 0.7902 (tp30) REVERT: J 24 ARG cc_start: 0.5405 (mtp180) cc_final: 0.5079 (mmm-85) REVERT: J 43 GLU cc_start: 0.7851 (tp30) cc_final: 0.7329 (mp0) REVERT: J 85 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8371 (tpp) REVERT: J 86 VAL cc_start: 0.7805 (t) cc_final: 0.7487 (m) REVERT: J 197 ARG cc_start: 0.5865 (ttt180) cc_final: 0.4855 (ppt170) REVERT: J 233 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7765 (ttt180) REVERT: J 238 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7661 (mttm) REVERT: J 239 GLU cc_start: 0.8623 (tt0) cc_final: 0.8095 (tp30) REVERT: J 269 LEU cc_start: 0.8073 (mt) cc_final: 0.7785 (mm) REVERT: J 278 ARG cc_start: 0.3873 (OUTLIER) cc_final: 0.3592 (ttp-110) REVERT: K 24 ARG cc_start: 0.5202 (mtp180) cc_final: 0.4843 (mmm-85) REVERT: K 43 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: K 85 MET cc_start: 0.8786 (tpp) cc_final: 0.8563 (tpt) REVERT: K 86 VAL cc_start: 0.7788 (t) cc_final: 0.7410 (m) REVERT: K 197 ARG cc_start: 0.5926 (ttt180) cc_final: 0.5073 (ttp80) REVERT: K 233 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7751 (ttt180) REVERT: K 239 GLU cc_start: 0.8572 (tt0) cc_final: 0.8009 (tp30) outliers start: 15 outliers final: 4 residues processed: 253 average time/residue: 1.6262 time to fit residues: 450.3802 Evaluate side-chains 247 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 233 ARG Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 43 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 144 optimal weight: 0.0470 chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.0040 chunk 88 optimal weight: 0.6980 overall best weight: 1.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 273 ASN C 273 ASN D 273 ASN E 268 ASN F 207 ASN F 273 ASN G 268 ASN H 273 ASN I 207 ASN I 273 ASN J 268 ASN K 273 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.170294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127740 restraints weight = 40047.677| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.42 r_work: 0.2885 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17172 Z= 0.117 Angle : 0.474 4.368 23352 Z= 0.259 Chirality : 0.039 0.133 2712 Planarity : 0.004 0.070 2856 Dihedral : 3.388 11.362 2280 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.69 % Allowed : 13.09 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.97 (0.18), residues: 2028 helix: 3.35 (0.12), residues: 1560 sheet: -0.29 (0.34), residues: 204 loop : 0.24 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 278 TYR 0.017 0.002 TYR B 67 PHE 0.011 0.001 PHE F 53 TRP 0.003 0.001 TRP J 277 HIS 0.002 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (17136) covalent geometry : angle 0.47302 / 0.26 (23280) SS BOND : bond 0.00224 / 0.15 ( 36) SS BOND : angle 0.76305 / 0.58 ( 72) hydrogen bonds : bond 0.04265 / 2.84 ( 1295) hydrogen bonds : angle 3.56620 / 2.60 ( 3813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 248 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5244 (mtp180) cc_final: 0.4837 (mmm-85) REVERT: L 43 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7112 (mm-30) REVERT: L 197 ARG cc_start: 0.5085 (tpt170) cc_final: 0.4188 (ppt170) REVERT: L 233 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7781 (ttt180) REVERT: L 278 ARG cc_start: 0.4041 (OUTLIER) cc_final: 0.3789 (ttp-110) REVERT: A 24 ARG cc_start: 0.5249 (mtp180) cc_final: 0.3963 (mtp-110) REVERT: A 86 VAL cc_start: 0.7685 (t) cc_final: 0.7329 (m) REVERT: A 197 ARG cc_start: 0.6062 (ttt180) cc_final: 0.5129 (tpt170) REVERT: A 233 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7814 (ttt180) REVERT: A 238 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7594 (mttm) REVERT: A 239 GLU cc_start: 0.8515 (tt0) cc_final: 0.7979 (tp30) REVERT: A 279 LYS cc_start: 0.4336 (OUTLIER) cc_final: 0.4005 (mppt) REVERT: B 24 ARG cc_start: 0.5400 (mtp180) cc_final: 0.4957 (mmm-85) REVERT: B 43 GLU cc_start: 0.7992 (tt0) cc_final: 0.7397 (mp0) REVERT: B 86 VAL cc_start: 0.7777 (t) cc_final: 0.7517 (m) REVERT: B 197 ARG cc_start: 0.5907 (ttt180) cc_final: 0.4971 (tpt170) REVERT: B 233 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7776 (ttt180) REVERT: B 239 GLU cc_start: 0.8467 (tt0) cc_final: 0.7976 (tp30) REVERT: C 24 ARG cc_start: 0.5344 (mtm180) cc_final: 0.5060 (mmm-85) REVERT: C 43 GLU cc_start: 0.7881 (tp30) cc_final: 0.7295 (mp0) REVERT: C 197 ARG cc_start: 0.5950 (ttt180) cc_final: 0.5152 (ttp80) REVERT: C 233 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7816 (ttt180) REVERT: C 239 GLU cc_start: 0.8468 (tt0) cc_final: 0.8249 (tt0) REVERT: D 24 ARG cc_start: 0.5277 (mtp180) cc_final: 0.4954 (mmm-85) REVERT: D 43 GLU cc_start: 0.8007 (tt0) cc_final: 0.7449 (mp0) REVERT: D 197 ARG cc_start: 0.5995 (ttm170) cc_final: 0.4861 (ppt170) REVERT: D 233 ARG cc_start: 0.8281 (ttm170) cc_final: 0.7805 (ttt180) REVERT: D 238 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7551 (mttm) REVERT: D 239 GLU cc_start: 0.8510 (tt0) cc_final: 0.8264 (tt0) REVERT: E 24 ARG cc_start: 0.5311 (mtp180) cc_final: 0.4902 (mmm-85) REVERT: E 43 GLU cc_start: 0.8004 (tt0) cc_final: 0.7390 (mp0) REVERT: E 197 ARG cc_start: 0.5956 (ttt180) cc_final: 0.5007 (tpt170) REVERT: E 239 GLU cc_start: 0.8342 (tp30) cc_final: 0.7802 (tp30) REVERT: F 24 ARG cc_start: 0.5364 (mtp180) cc_final: 0.4083 (mtp-110) REVERT: F 43 GLU cc_start: 0.8029 (tt0) cc_final: 0.7484 (mp0) REVERT: F 197 ARG cc_start: 0.6061 (ttt180) cc_final: 0.5155 (tpt170) REVERT: F 233 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7817 (ttt180) REVERT: G 24 ARG cc_start: 0.5288 (mtm180) cc_final: 0.4887 (mmm-85) REVERT: G 43 GLU cc_start: 0.7977 (tt0) cc_final: 0.7397 (mp0) REVERT: G 85 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8303 (tpp) REVERT: G 197 ARG cc_start: 0.5931 (ttt180) cc_final: 0.4996 (ppt170) REVERT: G 233 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7775 (ttt180) REVERT: G 239 GLU cc_start: 0.8324 (tp30) cc_final: 0.7761 (tp30) REVERT: H 24 ARG cc_start: 0.5308 (mtp180) cc_final: 0.4986 (mmm-85) REVERT: H 43 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: H 85 MET cc_start: 0.8766 (mmm) cc_final: 0.8520 (tpt) REVERT: H 86 VAL cc_start: 0.7826 (t) cc_final: 0.7495 (m) REVERT: H 197 ARG cc_start: 0.6064 (ttt180) cc_final: 0.5240 (ttp80) REVERT: H 233 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7761 (ttt180) REVERT: H 239 GLU cc_start: 0.8418 (tp30) cc_final: 0.8112 (tt0) REVERT: I 43 GLU cc_start: 0.7951 (tp30) cc_final: 0.7655 (mm-30) REVERT: I 85 MET cc_start: 0.8782 (mmm) cc_final: 0.8532 (tpt) REVERT: I 86 VAL cc_start: 0.7831 (t) cc_final: 0.7531 (m) REVERT: I 197 ARG cc_start: 0.6084 (ttt180) cc_final: 0.5142 (tpt170) REVERT: I 233 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7765 (ttt180) REVERT: I 239 GLU cc_start: 0.8486 (tt0) cc_final: 0.8263 (tt0) REVERT: J 24 ARG cc_start: 0.5418 (mtp180) cc_final: 0.5096 (mmm-85) REVERT: J 43 GLU cc_start: 0.7831 (tp30) cc_final: 0.7338 (mp0) REVERT: J 85 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8349 (tpp) REVERT: J 86 VAL cc_start: 0.7790 (t) cc_final: 0.7474 (m) REVERT: J 197 ARG cc_start: 0.5952 (ttt180) cc_final: 0.5008 (tpt170) REVERT: J 233 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7747 (ttt180) REVERT: J 238 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7655 (mttm) REVERT: J 239 GLU cc_start: 0.8543 (tt0) cc_final: 0.7975 (tp30) REVERT: J 278 ARG cc_start: 0.3838 (OUTLIER) cc_final: 0.3610 (ttp-110) REVERT: K 24 ARG cc_start: 0.5231 (mtp180) cc_final: 0.4805 (mmm-85) REVERT: K 43 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: K 85 MET cc_start: 0.8764 (tpp) cc_final: 0.8541 (tpt) REVERT: K 86 VAL cc_start: 0.7769 (t) cc_final: 0.7399 (m) REVERT: K 197 ARG cc_start: 0.5987 (ttt180) cc_final: 0.5128 (ttp80) REVERT: K 233 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7729 (ttt180) REVERT: K 239 GLU cc_start: 0.8513 (tt0) cc_final: 0.8293 (tt0) outliers start: 13 outliers final: 3 residues processed: 252 average time/residue: 1.5686 time to fit residues: 433.4949 Evaluate side-chains 248 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 233 ARG Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 43 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 140 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 268 ASN A 273 ASN B 273 ASN C 273 ASN D 268 ASN D 273 ASN E 268 ASN F 207 ASN F 273 ASN G 207 ASN G 268 ASN H 268 ASN H 273 ASN I 207 ASN I 273 ASN J 207 ASN J 268 ASN J 273 ASN K 268 ASN K 273 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.167657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.124562 restraints weight = 39490.398| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.61 r_work: 0.2815 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17172 Z= 0.195 Angle : 0.563 4.842 23352 Z= 0.311 Chirality : 0.042 0.141 2712 Planarity : 0.005 0.039 2856 Dihedral : 3.697 12.394 2280 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.91 % Allowed : 13.14 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.47 (0.18), residues: 2028 helix: 3.03 (0.12), residues: 1560 sheet: -0.66 (0.34), residues: 204 loop : 0.09 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 206 TYR 0.024 0.003 TYR B 67 PHE 0.014 0.002 PHE A 53 TRP 0.005 0.001 TRP C 277 HIS 0.004 0.001 HIS I 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (17136) covalent geometry : angle 0.56032 / 0.31 (23280) SS BOND : bond 0.00377 / 0.26 ( 36) SS BOND : angle 1.14341 / 0.84 ( 72) hydrogen bonds : bond 0.05166 / 3.46 ( 1295) hydrogen bonds : angle 3.88187 / 2.83 ( 3813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5345 (mtp180) cc_final: 0.4988 (mmm-85) REVERT: L 43 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7181 (mm-30) REVERT: L 197 ARG cc_start: 0.5077 (tpt170) cc_final: 0.4152 (ppt170) REVERT: L 233 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7888 (ttt180) REVERT: L 268 ASN cc_start: 0.8137 (m-40) cc_final: 0.7842 (m110) REVERT: L 271 GLU cc_start: 0.7004 (tt0) cc_final: 0.6371 (tp30) REVERT: L 278 ARG cc_start: 0.4042 (OUTLIER) cc_final: 0.3784 (ttp-110) REVERT: A 24 ARG cc_start: 0.5328 (mtp180) cc_final: 0.4081 (mtp-110) REVERT: A 43 GLU cc_start: 0.8004 (mt-10) cc_final: 0.6984 (pm20) REVERT: A 86 VAL cc_start: 0.7726 (t) cc_final: 0.7341 (m) REVERT: A 197 ARG cc_start: 0.6066 (ttt180) cc_final: 0.5600 (tpp80) REVERT: A 233 ARG cc_start: 0.8313 (ttm170) cc_final: 0.7879 (ttt180) REVERT: A 279 LYS cc_start: 0.4314 (OUTLIER) cc_final: 0.4086 (mppt) REVERT: B 24 ARG cc_start: 0.5393 (mtp180) cc_final: 0.4931 (mmm-85) REVERT: B 43 GLU cc_start: 0.8134 (tt0) cc_final: 0.7455 (mp0) REVERT: B 86 VAL cc_start: 0.7858 (t) cc_final: 0.7521 (m) REVERT: B 197 ARG cc_start: 0.5927 (ttt180) cc_final: 0.4965 (tpt170) REVERT: B 233 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7906 (ttt180) REVERT: B 239 GLU cc_start: 0.8600 (tt0) cc_final: 0.8044 (tp30) REVERT: C 24 ARG cc_start: 0.5412 (mtm180) cc_final: 0.5129 (mmm-85) REVERT: C 43 GLU cc_start: 0.8004 (tp30) cc_final: 0.7379 (mp0) REVERT: C 197 ARG cc_start: 0.6033 (ttt180) cc_final: 0.5181 (ttp80) REVERT: C 233 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7936 (ttt180) REVERT: D 24 ARG cc_start: 0.5401 (mtp180) cc_final: 0.4173 (mtp-110) REVERT: D 43 GLU cc_start: 0.8084 (tt0) cc_final: 0.7450 (mp0) REVERT: D 197 ARG cc_start: 0.5993 (ttm170) cc_final: 0.4808 (ppt170) REVERT: D 233 ARG cc_start: 0.8323 (ttm170) cc_final: 0.7858 (ttt180) REVERT: D 238 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7680 (mttm) REVERT: D 239 GLU cc_start: 0.8627 (tt0) cc_final: 0.8367 (tt0) REVERT: D 268 ASN cc_start: 0.8084 (m-40) cc_final: 0.7802 (m110) REVERT: E 24 ARG cc_start: 0.5363 (mtp180) cc_final: 0.4919 (mmm-85) REVERT: E 43 GLU cc_start: 0.8147 (tt0) cc_final: 0.7472 (mp0) REVERT: E 197 ARG cc_start: 0.5968 (ttt180) cc_final: 0.4996 (tpt170) REVERT: E 239 GLU cc_start: 0.8517 (tp30) cc_final: 0.8207 (tt0) REVERT: F 24 ARG cc_start: 0.5355 (mtp180) cc_final: 0.4096 (mtp-110) REVERT: F 43 GLU cc_start: 0.8144 (tt0) cc_final: 0.7851 (mm-30) REVERT: F 197 ARG cc_start: 0.6088 (ttt180) cc_final: 0.5625 (ttt180) REVERT: F 233 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7793 (ttt180) REVERT: G 24 ARG cc_start: 0.5333 (mtm180) cc_final: 0.5111 (mmm-85) REVERT: G 43 GLU cc_start: 0.8083 (tt0) cc_final: 0.7452 (mp0) REVERT: G 85 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: G 197 ARG cc_start: 0.5984 (ttt180) cc_final: 0.4996 (tpt170) REVERT: G 233 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7699 (ttt180) REVERT: G 239 GLU cc_start: 0.8502 (tp30) cc_final: 0.7895 (tp30) REVERT: H 24 ARG cc_start: 0.5367 (mtp180) cc_final: 0.4994 (mmm-85) REVERT: H 43 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: H 85 MET cc_start: 0.8802 (mmm) cc_final: 0.8566 (tpt) REVERT: H 86 VAL cc_start: 0.7831 (t) cc_final: 0.7515 (m) REVERT: H 197 ARG cc_start: 0.6103 (ttt180) cc_final: 0.5174 (ttp80) REVERT: H 233 ARG cc_start: 0.8290 (ttm170) cc_final: 0.7944 (ttt180) REVERT: H 239 GLU cc_start: 0.8554 (tp30) cc_final: 0.8261 (tt0) REVERT: H 268 ASN cc_start: 0.8137 (m-40) cc_final: 0.7860 (m110) REVERT: I 43 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7787 (mm-30) REVERT: I 85 MET cc_start: 0.8799 (mmm) cc_final: 0.8583 (tpt) REVERT: I 86 VAL cc_start: 0.7845 (t) cc_final: 0.7504 (m) REVERT: I 100 GLN cc_start: 0.4563 (OUTLIER) cc_final: 0.4122 (tt0) REVERT: I 197 ARG cc_start: 0.6140 (ttt180) cc_final: 0.5146 (tpt170) REVERT: I 233 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7847 (ttt180) REVERT: I 239 GLU cc_start: 0.8590 (tt0) cc_final: 0.8356 (tt0) REVERT: J 24 ARG cc_start: 0.5448 (mtp180) cc_final: 0.5100 (mmm-85) REVERT: J 43 GLU cc_start: 0.8026 (tp30) cc_final: 0.7392 (mp0) REVERT: J 85 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8395 (tpp) REVERT: J 86 VAL cc_start: 0.7822 (t) cc_final: 0.7481 (m) REVERT: J 197 ARG cc_start: 0.6127 (ttt180) cc_final: 0.5119 (ttp80) REVERT: J 233 ARG cc_start: 0.8286 (ttm170) cc_final: 0.7958 (ttt180) REVERT: J 278 ARG cc_start: 0.3931 (OUTLIER) cc_final: 0.3647 (ttp-110) REVERT: K 24 ARG cc_start: 0.5250 (mtp180) cc_final: 0.4800 (mmm-85) REVERT: K 43 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: K 85 MET cc_start: 0.8785 (tpp) cc_final: 0.8568 (tpt) REVERT: K 86 VAL cc_start: 0.7789 (t) cc_final: 0.7397 (m) REVERT: K 197 ARG cc_start: 0.5996 (ttt180) cc_final: 0.5021 (ttp80) REVERT: K 207 ASN cc_start: 0.7965 (t0) cc_final: 0.7516 (m-40) REVERT: K 233 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7924 (ttt180) outliers start: 17 outliers final: 5 residues processed: 244 average time/residue: 1.7635 time to fit residues: 470.6795 Evaluate side-chains 245 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 233 ARG Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 43 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 165 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.2023 > 50:) chunk 68 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 207 ASN B 273 ASN C 273 ASN D 273 ASN E 207 ASN E 268 ASN E 273 ASN F 207 ASN F 273 ASN H 273 ASN I 207 ASN I 273 ASN J 207 ASN J 268 ASN J 273 ASN K 273 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.168501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.124634 restraints weight = 39705.420| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.74 r_work: 0.2986 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17172 Z= 0.150 Angle : 0.517 4.166 23352 Z= 0.285 Chirality : 0.040 0.136 2712 Planarity : 0.004 0.039 2856 Dihedral : 3.615 11.920 2280 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.01 % Allowed : 13.03 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.49 (0.18), residues: 2028 helix: 3.05 (0.12), residues: 1560 sheet: -0.68 (0.33), residues: 204 loop : 0.04 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 278 TYR 0.020 0.003 TYR E 67 PHE 0.012 0.001 PHE F 53 TRP 0.004 0.001 TRP J 277 HIS 0.003 0.001 HIS J 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (17136) covalent geometry : angle 0.51509 / 0.28 (23280) SS BOND : bond 0.00299 / 0.20 ( 36) SS BOND : angle 0.89848 / 0.67 ( 72) hydrogen bonds : bond 0.04773 / 3.19 ( 1295) hydrogen bonds : angle 3.76061 / 2.74 ( 3813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5406 (mtp180) cc_final: 0.5074 (mmm-85) REVERT: L 43 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7108 (mm-30) REVERT: L 197 ARG cc_start: 0.5100 (tpt170) cc_final: 0.4199 (ppt170) REVERT: L 233 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7804 (ttt180) REVERT: L 271 GLU cc_start: 0.7016 (tt0) cc_final: 0.6423 (tp30) REVERT: L 278 ARG cc_start: 0.3952 (OUTLIER) cc_final: 0.3750 (ttp-110) REVERT: A 24 ARG cc_start: 0.5302 (mtp180) cc_final: 0.4062 (mtp-110) REVERT: A 43 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7025 (pm20) REVERT: A 86 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7393 (m) REVERT: A 197 ARG cc_start: 0.6097 (ttt180) cc_final: 0.5616 (tpp80) REVERT: A 233 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7824 (ttt180) REVERT: A 279 LYS cc_start: 0.4421 (OUTLIER) cc_final: 0.4169 (mppt) REVERT: B 24 ARG cc_start: 0.5442 (mtp180) cc_final: 0.5037 (mmm-85) REVERT: B 43 GLU cc_start: 0.7965 (tt0) cc_final: 0.7464 (mp0) REVERT: B 86 VAL cc_start: 0.7895 (t) cc_final: 0.7584 (m) REVERT: B 197 ARG cc_start: 0.5989 (ttt180) cc_final: 0.5069 (tpt170) REVERT: B 233 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7607 (ttt180) REVERT: B 239 GLU cc_start: 0.8346 (tt0) cc_final: 0.7835 (tp30) REVERT: C 24 ARG cc_start: 0.5444 (mtm180) cc_final: 0.5199 (mmm-85) REVERT: C 43 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: C 197 ARG cc_start: 0.6049 (ttt180) cc_final: 0.5252 (ttp80) REVERT: C 233 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7832 (ttt180) REVERT: C 268 ASN cc_start: 0.8235 (m-40) cc_final: 0.7919 (m-40) REVERT: D 24 ARG cc_start: 0.5321 (mtp180) cc_final: 0.5017 (mmm-85) REVERT: D 43 GLU cc_start: 0.7990 (tt0) cc_final: 0.7473 (mp0) REVERT: D 197 ARG cc_start: 0.6045 (ttm170) cc_final: 0.4946 (ppt170) REVERT: D 233 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7668 (ttt180) REVERT: D 239 GLU cc_start: 0.8379 (tt0) cc_final: 0.8156 (tt0) REVERT: E 24 ARG cc_start: 0.5356 (mtp180) cc_final: 0.4968 (mmm-85) REVERT: E 43 GLU cc_start: 0.8001 (tt0) cc_final: 0.7456 (mp0) REVERT: E 197 ARG cc_start: 0.6041 (ttt180) cc_final: 0.5103 (tpt170) REVERT: E 239 GLU cc_start: 0.8238 (tp30) cc_final: 0.8024 (tt0) REVERT: F 24 ARG cc_start: 0.5330 (mtp180) cc_final: 0.4942 (mmm-85) REVERT: F 43 GLU cc_start: 0.7988 (tt0) cc_final: 0.7503 (mp0) REVERT: F 197 ARG cc_start: 0.6142 (ttt180) cc_final: 0.5615 (tpp80) REVERT: F 233 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7721 (ttt180) REVERT: G 43 GLU cc_start: 0.7923 (tt0) cc_final: 0.7446 (mp0) REVERT: G 85 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8265 (tpp) REVERT: G 197 ARG cc_start: 0.6038 (ttt180) cc_final: 0.5103 (tpt170) REVERT: G 233 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7719 (ttt180) REVERT: G 239 GLU cc_start: 0.8232 (tp30) cc_final: 0.8029 (tt0) REVERT: H 24 ARG cc_start: 0.5418 (mtp180) cc_final: 0.5090 (mmm-85) REVERT: H 43 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: H 86 VAL cc_start: 0.7867 (t) cc_final: 0.7578 (m) REVERT: H 197 ARG cc_start: 0.6101 (ttt180) cc_final: 0.5227 (ttp80) REVERT: H 233 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7836 (ttt180) REVERT: H 239 GLU cc_start: 0.8221 (tp30) cc_final: 0.7992 (tt0) REVERT: H 268 ASN cc_start: 0.8119 (m-40) cc_final: 0.7886 (m110) REVERT: I 43 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: I 100 GLN cc_start: 0.4639 (OUTLIER) cc_final: 0.4236 (tt0) REVERT: I 197 ARG cc_start: 0.6182 (ttt180) cc_final: 0.5656 (tpp80) REVERT: I 233 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7792 (ttt180) REVERT: J 24 ARG cc_start: 0.5484 (mtp180) cc_final: 0.5178 (mmm-85) REVERT: J 43 GLU cc_start: 0.7879 (tp30) cc_final: 0.7365 (mp0) REVERT: J 85 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8317 (tpp) REVERT: J 86 VAL cc_start: 0.7840 (t) cc_final: 0.7526 (m) REVERT: J 197 ARG cc_start: 0.6204 (ttt180) cc_final: 0.5669 (tpp80) REVERT: J 233 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7761 (ttt180) REVERT: J 278 ARG cc_start: 0.3834 (OUTLIER) cc_final: 0.3616 (ttp-110) REVERT: K 24 ARG cc_start: 0.5266 (mtp180) cc_final: 0.4874 (mmm-85) REVERT: K 43 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: K 86 VAL cc_start: 0.7819 (t) cc_final: 0.7447 (m) REVERT: K 197 ARG cc_start: 0.6017 (ttt180) cc_final: 0.5117 (ttp80) REVERT: K 233 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7711 (ttt180) REVERT: K 268 ASN cc_start: 0.8154 (m-40) cc_final: 0.7938 (m110) outliers start: 19 outliers final: 5 residues processed: 240 average time/residue: 1.6097 time to fit residues: 421.9031 Evaluate side-chains 250 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 233 ARG Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 43 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 117 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 62 optimal weight: 0.0040 chunk 106 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 268 ASN A 273 ASN B 268 ASN B 273 ASN C 273 ASN D 273 ASN F 207 ASN F 273 ASN G 268 ASN H 273 ASN I 207 ASN I 273 ASN J 268 ASN J 273 ASN K 273 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.168566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.123753 restraints weight = 39360.089| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.70 r_work: 0.2853 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17172 Z= 0.168 Angle : 0.536 4.472 23352 Z= 0.295 Chirality : 0.041 0.138 2712 Planarity : 0.004 0.040 2856 Dihedral : 3.671 12.228 2280 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.18 % Allowed : 13.03 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.38 (0.18), residues: 2028 helix: 2.97 (0.12), residues: 1560 sheet: -0.75 (0.33), residues: 204 loop : 0.01 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 278 TYR 0.022 0.003 TYR B 67 PHE 0.013 0.002 PHE A 53 TRP 0.004 0.001 TRP C 277 HIS 0.003 0.001 HIS J 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (17136) covalent geometry : angle 0.53403 / 0.29 (23280) SS BOND : bond 0.00337 / 0.23 ( 36) SS BOND : angle 0.96424 / 0.71 ( 72) hydrogen bonds : bond 0.04939 / 3.30 ( 1295) hydrogen bonds : angle 3.82742 / 2.79 ( 3813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5262 (mtp180) cc_final: 0.4909 (mmm-85) REVERT: L 43 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7084 (mm-30) REVERT: L 197 ARG cc_start: 0.5036 (tpt170) cc_final: 0.4103 (ppt170) REVERT: L 207 ASN cc_start: 0.7869 (t0) cc_final: 0.7360 (m-40) REVERT: L 233 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7797 (ttt180) REVERT: L 271 GLU cc_start: 0.6937 (tt0) cc_final: 0.6341 (tp30) REVERT: L 278 ARG cc_start: 0.3926 (OUTLIER) cc_final: 0.3718 (ttp-110) REVERT: A 24 ARG cc_start: 0.5283 (mtp180) cc_final: 0.4902 (mmm-85) REVERT: A 43 GLU cc_start: 0.7901 (mt-10) cc_final: 0.6903 (pm20) REVERT: A 86 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7265 (m) REVERT: A 197 ARG cc_start: 0.6026 (ttt180) cc_final: 0.5526 (tpp80) REVERT: A 233 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7832 (ttt180) REVERT: A 279 LYS cc_start: 0.4311 (OUTLIER) cc_final: 0.4077 (mppt) REVERT: B 24 ARG cc_start: 0.5350 (mtp180) cc_final: 0.4907 (mmm-85) REVERT: B 43 GLU cc_start: 0.8040 (tt0) cc_final: 0.7388 (mp0) REVERT: B 86 VAL cc_start: 0.7789 (t) cc_final: 0.7454 (m) REVERT: B 197 ARG cc_start: 0.5987 (ttt180) cc_final: 0.5474 (tpp80) REVERT: B 233 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7819 (ttt180) REVERT: C 24 ARG cc_start: 0.5345 (mtm180) cc_final: 0.5073 (mmm-85) REVERT: C 43 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 197 ARG cc_start: 0.6036 (ttt180) cc_final: 0.5130 (ttp80) REVERT: C 233 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7822 (ttt180) REVERT: D 24 ARG cc_start: 0.5253 (mtp180) cc_final: 0.4926 (mmm-85) REVERT: D 43 GLU cc_start: 0.7996 (tt0) cc_final: 0.7372 (mp0) REVERT: D 197 ARG cc_start: 0.5941 (ttm170) cc_final: 0.4761 (ppt170) REVERT: D 233 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7822 (ttt180) REVERT: D 239 GLU cc_start: 0.8495 (tt0) cc_final: 0.8243 (tt0) REVERT: E 24 ARG cc_start: 0.5234 (mtp180) cc_final: 0.4795 (mmm-85) REVERT: E 43 GLU cc_start: 0.8055 (tt0) cc_final: 0.7410 (mp0) REVERT: E 197 ARG cc_start: 0.6101 (ttt180) cc_final: 0.5573 (tpp80) REVERT: E 239 GLU cc_start: 0.8369 (tp30) cc_final: 0.8112 (tt0) REVERT: F 24 ARG cc_start: 0.5269 (mtp180) cc_final: 0.4862 (mmm-85) REVERT: F 43 GLU cc_start: 0.8024 (tt0) cc_final: 0.7423 (mp0) REVERT: F 197 ARG cc_start: 0.6121 (ttt180) cc_final: 0.5582 (tpp80) REVERT: F 233 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7712 (ttt180) REVERT: G 43 GLU cc_start: 0.7988 (tt0) cc_final: 0.7389 (mp0) REVERT: G 85 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8205 (tpp) REVERT: G 197 ARG cc_start: 0.6020 (ttt180) cc_final: 0.5505 (tpp80) REVERT: G 233 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7627 (ttt180) REVERT: G 239 GLU cc_start: 0.8368 (tp30) cc_final: 0.8122 (tt0) REVERT: H 24 ARG cc_start: 0.5302 (mtp180) cc_final: 0.4917 (mmm-85) REVERT: H 43 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: H 86 VAL cc_start: 0.7770 (t) cc_final: 0.7420 (m) REVERT: H 197 ARG cc_start: 0.6082 (ttt180) cc_final: 0.5066 (ttp80) REVERT: H 233 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7836 (ttt180) REVERT: H 239 GLU cc_start: 0.8417 (tp30) cc_final: 0.8124 (tt0) REVERT: H 268 ASN cc_start: 0.8020 (m-40) cc_final: 0.7767 (m110) REVERT: I 43 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: I 86 VAL cc_start: 0.7774 (t) cc_final: 0.7435 (m) REVERT: I 100 GLN cc_start: 0.4637 (OUTLIER) cc_final: 0.4228 (tt0) REVERT: I 197 ARG cc_start: 0.6078 (ttt180) cc_final: 0.5581 (tpp80) REVERT: I 233 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7818 (ttt180) REVERT: J 24 ARG cc_start: 0.5365 (mtp180) cc_final: 0.5030 (mmm-85) REVERT: J 43 GLU cc_start: 0.7937 (tp30) cc_final: 0.7308 (mp0) REVERT: J 85 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8274 (tpp) REVERT: J 86 VAL cc_start: 0.7745 (t) cc_final: 0.7411 (m) REVERT: J 197 ARG cc_start: 0.6124 (ttt180) cc_final: 0.5575 (tpp80) REVERT: J 233 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7869 (ttt180) REVERT: J 278 ARG cc_start: 0.3873 (OUTLIER) cc_final: 0.3626 (ttp-110) REVERT: K 24 ARG cc_start: 0.5105 (mtp180) cc_final: 0.4673 (mmm-85) REVERT: K 43 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: K 86 VAL cc_start: 0.7703 (t) cc_final: 0.7312 (m) REVERT: K 197 ARG cc_start: 0.5975 (ttt180) cc_final: 0.4967 (ttp80) REVERT: K 233 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7840 (ttt180) REVERT: K 268 ASN cc_start: 0.8057 (m-40) cc_final: 0.7785 (m110) outliers start: 22 outliers final: 5 residues processed: 237 average time/residue: 1.7009 time to fit residues: 440.8249 Evaluate side-chains 241 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 233 ARG Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 43 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 200 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 273 ASN B 268 ASN B 273 ASN C 273 ASN D 273 ASN E 268 ASN E 273 ASN F 207 ASN F 273 ASN H 273 ASN I 207 ASN I 273 ASN J 273 ASN K 273 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.169501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.126100 restraints weight = 39649.152| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.47 r_work: 0.2873 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17172 Z= 0.122 Angle : 0.488 4.409 23352 Z= 0.269 Chirality : 0.040 0.135 2712 Planarity : 0.004 0.040 2856 Dihedral : 3.533 11.678 2280 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.96 % Allowed : 13.30 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.55 (0.18), residues: 2028 helix: 3.09 (0.12), residues: 1560 sheet: -0.67 (0.34), residues: 204 loop : 0.06 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 278 TYR 0.017 0.002 TYR C 67 PHE 0.011 0.001 PHE D 53 TRP 0.004 0.001 TRP J 277 HIS 0.002 0.001 HIS J 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17136) covalent geometry : angle 0.48706 / 0.27 (23280) SS BOND : bond 0.00233 / 0.16 ( 36) SS BOND : angle 0.75481 / 0.57 ( 72) hydrogen bonds : bond 0.04436 / 2.96 ( 1295) hydrogen bonds : angle 3.68029 / 2.69 ( 3813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5275 (mtp180) cc_final: 0.4937 (mmm-85) REVERT: L 43 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7104 (mm-30) REVERT: L 197 ARG cc_start: 0.4985 (tpt170) cc_final: 0.4111 (ppt170) REVERT: L 207 ASN cc_start: 0.7874 (t0) cc_final: 0.7372 (m-40) REVERT: L 233 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7834 (ttt180) REVERT: L 271 GLU cc_start: 0.6960 (tt0) cc_final: 0.6401 (tp30) REVERT: L 278 ARG cc_start: 0.3900 (OUTLIER) cc_final: 0.3687 (ttp-110) REVERT: A 24 ARG cc_start: 0.5294 (mtp180) cc_final: 0.4902 (mmm-85) REVERT: A 43 GLU cc_start: 0.7933 (mt-10) cc_final: 0.6944 (pm20) REVERT: A 86 VAL cc_start: 0.7658 (t) cc_final: 0.7287 (m) REVERT: A 197 ARG cc_start: 0.6031 (ttt180) cc_final: 0.5534 (tpp80) REVERT: A 233 ARG cc_start: 0.8256 (ttm170) cc_final: 0.7862 (ttt180) REVERT: A 238 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7689 (mttm) REVERT: A 279 LYS cc_start: 0.4343 (OUTLIER) cc_final: 0.4102 (mppt) REVERT: B 24 ARG cc_start: 0.5302 (mtp180) cc_final: 0.4869 (mmm-85) REVERT: B 43 GLU cc_start: 0.8000 (tt0) cc_final: 0.7431 (mp0) REVERT: B 86 VAL cc_start: 0.7774 (t) cc_final: 0.7468 (m) REVERT: B 197 ARG cc_start: 0.6028 (ttt180) cc_final: 0.5521 (tpp80) REVERT: B 233 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7647 (ttt180) REVERT: B 239 GLU cc_start: 0.8386 (tt0) cc_final: 0.7912 (tp30) REVERT: C 24 ARG cc_start: 0.5359 (mtm180) cc_final: 0.5094 (mmm-85) REVERT: C 43 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: C 197 ARG cc_start: 0.6061 (ttt180) cc_final: 0.5180 (ttp80) REVERT: C 233 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7860 (ttt180) REVERT: D 24 ARG cc_start: 0.5313 (mtp180) cc_final: 0.4984 (mmm-85) REVERT: D 43 GLU cc_start: 0.8023 (tt0) cc_final: 0.7420 (mp0) REVERT: D 197 ARG cc_start: 0.5959 (ttm170) cc_final: 0.4830 (ppt170) REVERT: D 233 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7863 (ttt180) REVERT: D 239 GLU cc_start: 0.8509 (tt0) cc_final: 0.8268 (tt0) REVERT: E 24 ARG cc_start: 0.5226 (mtp180) cc_final: 0.4805 (mmm-85) REVERT: E 43 GLU cc_start: 0.8037 (tt0) cc_final: 0.7424 (mp0) REVERT: E 197 ARG cc_start: 0.6046 (ttt180) cc_final: 0.5526 (tpp80) REVERT: E 239 GLU cc_start: 0.8384 (tp30) cc_final: 0.8144 (tt0) REVERT: F 24 ARG cc_start: 0.5294 (mtp180) cc_final: 0.4038 (mtp-110) REVERT: F 43 GLU cc_start: 0.8036 (tt0) cc_final: 0.7453 (mp0) REVERT: F 197 ARG cc_start: 0.6115 (ttt180) cc_final: 0.5595 (tpp80) REVERT: F 233 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7789 (ttt180) REVERT: G 43 GLU cc_start: 0.7961 (tt0) cc_final: 0.7414 (mp0) REVERT: G 85 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8249 (tpp) REVERT: G 197 ARG cc_start: 0.6045 (ttt180) cc_final: 0.5543 (tpp80) REVERT: G 233 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7744 (ttt180) REVERT: G 239 GLU cc_start: 0.8371 (tp30) cc_final: 0.8143 (tt0) REVERT: H 24 ARG cc_start: 0.5335 (mtp180) cc_final: 0.4983 (mmm-85) REVERT: H 43 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: H 86 VAL cc_start: 0.7798 (t) cc_final: 0.7449 (m) REVERT: H 197 ARG cc_start: 0.6105 (ttt180) cc_final: 0.5133 (ttp80) REVERT: H 233 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7876 (ttt180) REVERT: H 239 GLU cc_start: 0.8435 (tp30) cc_final: 0.8146 (tt0) REVERT: I 43 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: I 86 VAL cc_start: 0.7794 (t) cc_final: 0.7462 (m) REVERT: I 100 GLN cc_start: 0.4655 (OUTLIER) cc_final: 0.4212 (tt0) REVERT: I 197 ARG cc_start: 0.6091 (ttt180) cc_final: 0.5598 (tpp80) REVERT: I 233 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7857 (ttt180) REVERT: J 24 ARG cc_start: 0.5391 (mtp180) cc_final: 0.5061 (mmm-85) REVERT: J 43 GLU cc_start: 0.7868 (tp30) cc_final: 0.7324 (mp0) REVERT: J 85 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8330 (tpp) REVERT: J 86 VAL cc_start: 0.7753 (t) cc_final: 0.7447 (m) REVERT: J 197 ARG cc_start: 0.6138 (ttt180) cc_final: 0.5592 (tpp80) REVERT: J 233 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7784 (ttt180) REVERT: J 269 LEU cc_start: 0.8038 (mt) cc_final: 0.7795 (mm) REVERT: J 278 ARG cc_start: 0.3813 (OUTLIER) cc_final: 0.3585 (ttp-110) REVERT: K 24 ARG cc_start: 0.5099 (mtp180) cc_final: 0.4679 (mmm-85) REVERT: K 43 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: K 86 VAL cc_start: 0.7749 (t) cc_final: 0.7380 (m) REVERT: K 197 ARG cc_start: 0.5987 (ttt180) cc_final: 0.4996 (ttp80) REVERT: K 233 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7753 (ttt180) REVERT: K 268 ASN cc_start: 0.8103 (m-40) cc_final: 0.7837 (m110) outliers start: 18 outliers final: 5 residues processed: 242 average time/residue: 1.6773 time to fit residues: 444.5545 Evaluate side-chains 252 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 233 ARG Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 43 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 70 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 268 ASN B 273 ASN C 273 ASN D 273 ASN E 268 ASN E 273 ASN F 207 ASN F 273 ASN H 268 ASN H 273 ASN I 207 ASN I 273 ASN J 268 ASN J 273 ASN K 273 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.168417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.123451 restraints weight = 39606.508| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.70 r_work: 0.2878 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17172 Z= 0.166 Angle : 0.534 4.327 23352 Z= 0.294 Chirality : 0.041 0.137 2712 Planarity : 0.004 0.040 2856 Dihedral : 3.649 12.203 2280 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.01 % Allowed : 13.51 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.37 (0.18), residues: 2028 helix: 2.96 (0.12), residues: 1560 sheet: -0.74 (0.33), residues: 204 loop : 0.03 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 278 TYR 0.022 0.003 TYR B 67 PHE 0.014 0.002 PHE A 53 TRP 0.006 0.001 TRP B 277 HIS 0.003 0.001 HIS L 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (17136) covalent geometry : angle 0.53230 / 0.29 (23280) SS BOND : bond 0.00312 / 0.21 ( 36) SS BOND : angle 0.94590 / 0.70 ( 72) hydrogen bonds : bond 0.04883 / 3.26 ( 1295) hydrogen bonds : angle 3.81661 / 2.78 ( 3813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5303 (mtp180) cc_final: 0.4988 (mmm-85) REVERT: L 43 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7056 (mm-30) REVERT: L 197 ARG cc_start: 0.5044 (tpt170) cc_final: 0.4120 (ppt170) REVERT: L 233 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7786 (ttt180) REVERT: L 268 ASN cc_start: 0.8017 (m-40) cc_final: 0.7759 (m110) REVERT: L 271 GLU cc_start: 0.6940 (tt0) cc_final: 0.6332 (tp30) REVERT: L 278 ARG cc_start: 0.3918 (OUTLIER) cc_final: 0.3714 (ttp-110) REVERT: A 24 ARG cc_start: 0.5316 (mtp180) cc_final: 0.4932 (mmm-85) REVERT: A 43 GLU cc_start: 0.7875 (mt-10) cc_final: 0.6891 (pm20) REVERT: A 86 VAL cc_start: 0.7634 (t) cc_final: 0.7273 (m) REVERT: A 197 ARG cc_start: 0.6043 (ttt180) cc_final: 0.5557 (tpp80) REVERT: A 233 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7810 (ttt180) REVERT: A 279 LYS cc_start: 0.4484 (OUTLIER) cc_final: 0.4153 (ttmt) REVERT: B 24 ARG cc_start: 0.5367 (mtp180) cc_final: 0.4962 (mmm-85) REVERT: B 43 GLU cc_start: 0.8030 (tt0) cc_final: 0.7419 (mp0) REVERT: B 86 VAL cc_start: 0.7779 (t) cc_final: 0.7456 (m) REVERT: B 197 ARG cc_start: 0.6167 (ttt180) cc_final: 0.5611 (tpp80) REVERT: B 233 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7790 (ttt180) REVERT: B 239 GLU cc_start: 0.8329 (tt0) cc_final: 0.7891 (tp30) REVERT: C 24 ARG cc_start: 0.5400 (mtm180) cc_final: 0.5143 (mmm-85) REVERT: C 43 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: C 197 ARG cc_start: 0.6076 (ttt180) cc_final: 0.5207 (ttp80) REVERT: C 233 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7797 (ttt180) REVERT: D 24 ARG cc_start: 0.5279 (mtp180) cc_final: 0.4974 (mmm-85) REVERT: D 43 GLU cc_start: 0.7982 (tt0) cc_final: 0.7382 (mp0) REVERT: D 197 ARG cc_start: 0.5973 (ttm170) cc_final: 0.4835 (ppt170) REVERT: D 233 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7793 (ttt180) REVERT: D 239 GLU cc_start: 0.8440 (tt0) cc_final: 0.8196 (tt0) REVERT: E 24 ARG cc_start: 0.5243 (mtp180) cc_final: 0.4847 (mmm-85) REVERT: E 43 GLU cc_start: 0.8034 (tt0) cc_final: 0.7403 (mp0) REVERT: E 197 ARG cc_start: 0.6191 (ttt180) cc_final: 0.5637 (tpp80) REVERT: E 239 GLU cc_start: 0.8320 (tp30) cc_final: 0.8089 (tt0) REVERT: F 24 ARG cc_start: 0.5260 (mtp180) cc_final: 0.4040 (mtp-110) REVERT: F 43 GLU cc_start: 0.7995 (tt0) cc_final: 0.7428 (mp0) REVERT: F 197 ARG cc_start: 0.6237 (ttt180) cc_final: 0.5715 (tpp80) REVERT: F 233 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7688 (ttt180) REVERT: F 238 LYS cc_start: 0.8149 (mttp) cc_final: 0.7740 (mttm) REVERT: G 43 GLU cc_start: 0.7956 (tt0) cc_final: 0.7416 (mp0) REVERT: G 85 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8167 (tpp) REVERT: G 197 ARG cc_start: 0.6116 (ttt180) cc_final: 0.5580 (tpp80) REVERT: G 233 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7599 (ttt180) REVERT: G 239 GLU cc_start: 0.8306 (tp30) cc_final: 0.8077 (tt0) REVERT: H 24 ARG cc_start: 0.5329 (mtp180) cc_final: 0.4981 (mmm-85) REVERT: H 43 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: H 86 VAL cc_start: 0.7776 (t) cc_final: 0.7415 (m) REVERT: H 197 ARG cc_start: 0.6172 (ttt180) cc_final: 0.5165 (ttp80) REVERT: H 233 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7811 (ttt180) REVERT: H 239 GLU cc_start: 0.8382 (tp30) cc_final: 0.8087 (tt0) REVERT: I 43 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: I 86 VAL cc_start: 0.7789 (t) cc_final: 0.7444 (m) REVERT: I 100 GLN cc_start: 0.4743 (OUTLIER) cc_final: 0.4296 (tt0) REVERT: I 197 ARG cc_start: 0.6175 (ttt180) cc_final: 0.5666 (tpp80) REVERT: I 233 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7788 (ttt180) REVERT: J 24 ARG cc_start: 0.5410 (mtp180) cc_final: 0.5093 (mmm-85) REVERT: J 43 GLU cc_start: 0.7906 (tp30) cc_final: 0.7340 (mp0) REVERT: J 85 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8254 (tpp) REVERT: J 86 VAL cc_start: 0.7724 (t) cc_final: 0.7408 (m) REVERT: J 197 ARG cc_start: 0.6226 (ttt180) cc_final: 0.5153 (ttp80) REVERT: J 233 ARG cc_start: 0.8177 (ttm170) cc_final: 0.7841 (ttt180) REVERT: J 269 LEU cc_start: 0.7998 (mt) cc_final: 0.7760 (mm) REVERT: K 24 ARG cc_start: 0.5153 (mtp180) cc_final: 0.4758 (mmm-85) REVERT: K 43 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: K 86 VAL cc_start: 0.7696 (t) cc_final: 0.7314 (m) REVERT: K 197 ARG cc_start: 0.6024 (ttt180) cc_final: 0.4995 (ttp80) REVERT: K 233 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7814 (ttt180) REVERT: K 268 ASN cc_start: 0.8055 (m-40) cc_final: 0.7796 (m110) outliers start: 19 outliers final: 5 residues processed: 230 average time/residue: 1.7076 time to fit residues: 428.3106 Evaluate side-chains 240 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 233 ARG Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 43 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 91 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 273 ASN B 273 ASN C 273 ASN D 273 ASN E 273 ASN F 207 ASN F 273 ASN H 268 ASN H 273 ASN I 207 ASN I 273 ASN J 268 ASN J 273 ASN K 273 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.168230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.123915 restraints weight = 39297.544| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.61 r_work: 0.3004 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17172 Z= 0.175 Angle : 0.546 4.310 23352 Z= 0.301 Chirality : 0.041 0.137 2712 Planarity : 0.004 0.040 2856 Dihedral : 3.738 12.383 2280 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.91 % Allowed : 13.84 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.23 (0.18), residues: 2028 helix: 2.87 (0.12), residues: 1560 sheet: -0.79 (0.33), residues: 204 loop : -0.05 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 206 TYR 0.022 0.003 TYR E 67 PHE 0.013 0.002 PHE F 53 TRP 0.006 0.001 TRP B 277 HIS 0.003 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (17136) covalent geometry : angle 0.54382 / 0.30 (23280) SS BOND : bond 0.00335 / 0.23 ( 36) SS BOND : angle 0.97885 / 0.72 ( 72) hydrogen bonds : bond 0.05019 / 3.35 ( 1295) hydrogen bonds : angle 3.87344 / 2.82 ( 3813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12447.78 seconds wall clock time: 210 minutes 42.46 seconds (12642.46 seconds total)