Starting phenix.real_space_refine on Sat Jun 28 16:36:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7p_18987/06_2025/8r7p_18987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7p_18987/06_2025/8r7p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r7p_18987/06_2025/8r7p_18987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7p_18987/06_2025/8r7p_18987.map" model { file = "/net/cci-nas-00/data/ceres_data/8r7p_18987/06_2025/8r7p_18987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7p_18987/06_2025/8r7p_18987.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.33, per 1000 atoms: 0.51 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: 9.34 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.46 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: 12.79 Time building geometry restraints manager: 11.36 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: 0.02 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: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.590 Extract box with map and model: 1.310 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 72.580 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP J 277 HIS 0.002 0.000 HIS I 99 PHE 0.009 0.001 PHE F 213 TYR 0.011 0.001 TYR K 243 ARG 0.002 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.11188 ( 1295) hydrogen bonds : angle 4.00227 ( 3813) SS BOND : bond 0.00051 ( 36) SS BOND : angle 0.71395 ( 72) covalent geometry : bond 0.00287 (17136) covalent geometry : angle 0.46153 (23280) *********************** 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 : 2.454 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: 0.3921 (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: 0.6587 (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: 0.5741 (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: 0.6246 (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: 0.6780 (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: 0.5709 (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: 0.6129 (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 207 ASN cc_start: 0.5765 (t0) cc_final: 0.5508 (t0) REVERT: D 230 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6666 (mt-10) REVERT: D 233 ARG cc_start: 0.6524 (ttm170) cc_final: 0.5878 (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: 0.6082 (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: 0.6810 (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: 0.6714 (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: 0.5103 (ttt180) REVERT: H 230 GLU cc_start: 0.6891 (mt-10) cc_final: 0.5338 (mp0) REVERT: H 233 ARG cc_start: 0.6317 (ttm170) cc_final: 0.5545 (ttt180) REVERT: H 239 GLU cc_start: 0.7007 (tp30) cc_final: 0.6037 (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: 0.6738 (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: 0.5709 (mttm) REVERT: I 239 GLU cc_start: 0.7104 (tt0) cc_final: 0.6114 (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: 0.6117 (tp30) outliers start: 11 outliers final: 1 residues processed: 308 average time/residue: 3.3132 time to fit residues: 1116.7062 Evaluate side-chains 246 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 239 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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 172 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 232 ASN L 273 ASN A 273 ASN B 273 ASN C 207 ASN C 273 ASN D 273 ASN E 207 ASN F 273 ASN H 207 ASN H 273 ASN I 273 ASN K 232 ASN K 273 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.168838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.125507 restraints weight = 39706.882| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.44 r_work: 0.2877 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17172 Z= 0.221 Angle : 0.595 7.890 23352 Z= 0.329 Chirality : 0.042 0.187 2712 Planarity : 0.005 0.047 2856 Dihedral : 4.570 58.486 2296 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.28 % Allowed : 14.64 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.18), residues: 2028 helix: 3.29 (0.12), residues: 1560 sheet: -0.33 (0.34), residues: 204 loop : 0.25 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 79 HIS 0.005 0.001 HIS I 75 PHE 0.015 0.002 PHE E 53 TYR 0.025 0.004 TYR J 67 ARG 0.005 0.001 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.05509 ( 1295) hydrogen bonds : angle 3.90653 ( 3813) SS BOND : bond 0.00550 ( 36) SS BOND : angle 1.39562 ( 72) covalent geometry : bond 0.00493 (17136) covalent geometry : angle 0.59060 (23280) *********************** 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 279 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 2.418 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 43 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7111 (mp0) REVERT: L 197 ARG cc_start: 0.5148 (tpt170) cc_final: 0.4760 (tpt170) REVERT: L 233 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7784 (ttt180) REVERT: L 239 GLU cc_start: 0.8498 (tt0) cc_final: 0.8042 (tp30) REVERT: A 24 ARG cc_start: 0.5337 (mtp180) cc_final: 0.4026 (mtp-110) REVERT: A 43 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7470 (mm-30) REVERT: A 85 MET cc_start: 0.8694 (tpp) cc_final: 0.8435 (tpt) REVERT: A 99 HIS cc_start: 0.4674 (OUTLIER) cc_final: 0.4432 (m90) REVERT: A 197 ARG cc_start: 0.6003 (ttt180) cc_final: 0.5647 (ttt180) REVERT: A 233 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7855 (ttt180) REVERT: A 238 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7573 (mttm) REVERT: A 239 GLU cc_start: 0.8607 (tt0) cc_final: 0.8142 (tp30) REVERT: B 24 ARG cc_start: 0.5383 (mtp180) cc_final: 0.4928 (mmm-85) REVERT: B 43 GLU cc_start: 0.8053 (tt0) cc_final: 0.7336 (mp0) REVERT: B 86 VAL cc_start: 0.7817 (t) cc_final: 0.7543 (m) REVERT: B 197 ARG cc_start: 0.5787 (ttt180) cc_final: 0.4862 (ppt170) REVERT: B 233 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7836 (ttp-170) REVERT: B 238 LYS cc_start: 0.8086 (mtmp) cc_final: 0.7642 (mttm) REVERT: B 239 GLU cc_start: 0.8510 (tt0) cc_final: 0.8110 (tp30) REVERT: C 24 ARG cc_start: 0.5360 (mtm180) cc_final: 0.5033 (mmm-85) REVERT: C 43 GLU cc_start: 0.7936 (tp30) cc_final: 0.7237 (mp0) REVERT: C 85 MET cc_start: 0.8704 (tpp) cc_final: 0.8480 (tpt) REVERT: C 197 ARG cc_start: 0.5921 (ttt180) cc_final: 0.5603 (ttt180) REVERT: C 233 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7833 (ttt180) REVERT: C 239 GLU cc_start: 0.8497 (tt0) cc_final: 0.8048 (tp30) REVERT: D 24 ARG cc_start: 0.5315 (mtp180) cc_final: 0.4988 (mmm-85) REVERT: D 43 GLU cc_start: 0.7995 (tt0) cc_final: 0.7668 (mm-30) REVERT: D 85 MET cc_start: 0.8669 (tpp) cc_final: 0.8461 (tpt) REVERT: D 197 ARG cc_start: 0.5828 (ttm170) cc_final: 0.5506 (ttt180) REVERT: D 233 ARG cc_start: 0.8229 (ttm170) cc_final: 0.7846 (ttt180) REVERT: D 238 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7615 (mttm) REVERT: D 239 GLU cc_start: 0.8511 (tt0) cc_final: 0.7930 (tp30) REVERT: E 24 ARG cc_start: 0.5280 (mtp180) cc_final: 0.4901 (mmm-85) REVERT: E 43 GLU cc_start: 0.8029 (tt0) cc_final: 0.7356 (mp0) REVERT: E 197 ARG cc_start: 0.5949 (ttt180) cc_final: 0.4983 (ppt170) REVERT: E 239 GLU cc_start: 0.8372 (tp30) cc_final: 0.7851 (tp30) REVERT: F 24 ARG cc_start: 0.5241 (mtp180) cc_final: 0.4018 (mtp-110) REVERT: F 43 GLU cc_start: 0.8015 (tt0) cc_final: 0.7687 (mm-30) REVERT: F 85 MET cc_start: 0.8650 (tpp) cc_final: 0.8429 (tpt) REVERT: F 197 ARG cc_start: 0.5995 (ttt180) cc_final: 0.5066 (tpt170) REVERT: F 233 ARG cc_start: 0.8284 (ttm170) cc_final: 0.7877 (ttt180) REVERT: G 24 ARG cc_start: 0.5205 (mtm180) cc_final: 0.4784 (mmm-85) REVERT: G 43 GLU cc_start: 0.7992 (tp30) cc_final: 0.7333 (mp0) REVERT: G 85 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8309 (tpp) REVERT: G 197 ARG cc_start: 0.5810 (ttt180) cc_final: 0.4920 (tpt170) REVERT: G 233 ARG cc_start: 0.8151 (ttm170) cc_final: 0.7735 (ttt180) REVERT: G 239 GLU cc_start: 0.8306 (tp30) cc_final: 0.7823 (tp30) REVERT: H 24 ARG cc_start: 0.5274 (mtp180) cc_final: 0.4939 (mmm-85) REVERT: H 43 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: H 85 MET cc_start: 0.8740 (mmm) cc_final: 0.8446 (tpt) REVERT: H 86 VAL cc_start: 0.7903 (t) cc_final: 0.7603 (m) REVERT: H 197 ARG cc_start: 0.5962 (ttt180) cc_final: 0.5648 (ttt180) REVERT: H 233 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7802 (ttt180) REVERT: H 239 GLU cc_start: 0.8342 (tp30) cc_final: 0.7756 (tp30) REVERT: H 268 ASN cc_start: 0.8185 (m-40) cc_final: 0.7880 (m110) REVERT: I 24 ARG cc_start: 0.5296 (mtp180) cc_final: 0.5076 (mmm-85) REVERT: I 43 GLU cc_start: 0.7962 (tp30) cc_final: 0.7654 (mm-30) REVERT: I 85 MET cc_start: 0.8776 (mmm) cc_final: 0.8472 (tpt) REVERT: I 197 ARG cc_start: 0.5961 (ttt180) cc_final: 0.5640 (ttt180) REVERT: I 233 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7817 (ttt180) REVERT: I 238 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7648 (mttm) REVERT: I 239 GLU cc_start: 0.8481 (tt0) cc_final: 0.7922 (tp30) REVERT: J 24 ARG cc_start: 0.5329 (mtp180) cc_final: 0.4921 (mmm-85) REVERT: J 43 GLU cc_start: 0.7887 (tp30) cc_final: 0.7591 (mm-30) REVERT: J 85 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8336 (tpp) REVERT: J 86 VAL cc_start: 0.7873 (t) cc_final: 0.7543 (m) REVERT: J 197 ARG cc_start: 0.5947 (ttt180) cc_final: 0.4972 (ppt170) REVERT: J 233 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7781 (ttt180) REVERT: J 238 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7640 (mttm) REVERT: J 239 GLU cc_start: 0.8606 (tt0) cc_final: 0.8148 (tp30) REVERT: J 278 ARG cc_start: 0.3996 (OUTLIER) cc_final: 0.3646 (ttp-110) REVERT: K 24 ARG cc_start: 0.5212 (mtp180) cc_final: 0.4853 (mmm-85) REVERT: K 43 GLU cc_start: 0.7904 (tp30) cc_final: 0.7187 (mp0) REVERT: K 85 MET cc_start: 0.8777 (tpp) cc_final: 0.8541 (tpt) REVERT: K 86 VAL cc_start: 0.7880 (t) cc_final: 0.7526 (m) REVERT: K 197 ARG cc_start: 0.5948 (ttt180) cc_final: 0.5106 (ttp80) REVERT: K 233 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7785 (ttt180) REVERT: K 239 GLU cc_start: 0.8595 (tt0) cc_final: 0.8013 (tp30) REVERT: K 278 ARG cc_start: 0.3962 (OUTLIER) cc_final: 0.3702 (ttp-110) outliers start: 24 outliers final: 2 residues processed: 270 average time/residue: 3.7169 time to fit residues: 1092.6866 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 : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain B 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 278 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 159 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 GLN A 50 GLN A 273 ASN B 50 GLN B 273 ASN C 50 GLN C 273 ASN D 50 GLN E 50 GLN E 273 ASN F 50 GLN F 268 ASN F 273 ASN G 50 GLN H 50 GLN H 273 ASN I 50 GLN I 273 ASN K 50 GLN K 273 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.170710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.128287 restraints weight = 40164.854| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.32 r_work: 0.3044 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17172 Z= 0.108 Angle : 0.474 5.060 23352 Z= 0.258 Chirality : 0.039 0.137 2712 Planarity : 0.003 0.034 2856 Dihedral : 3.447 46.379 2282 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.48 % Allowed : 14.80 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.18), residues: 2028 helix: 3.42 (0.12), residues: 1560 sheet: -0.19 (0.34), residues: 204 loop : 0.25 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 277 HIS 0.002 0.000 HIS L 274 PHE 0.010 0.001 PHE K 53 TYR 0.015 0.002 TYR C 67 ARG 0.003 0.000 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 1295) hydrogen bonds : angle 3.57016 ( 3813) SS BOND : bond 0.00182 ( 36) SS BOND : angle 0.70531 ( 72) covalent geometry : bond 0.00222 (17136) covalent geometry : angle 0.47317 (23280) *********************** 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 256 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 247 time to evaluate : 2.363 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: L 24 ARG cc_start: 0.5372 (mtp180) cc_final: 0.5026 (mmm-85) REVERT: L 43 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7236 (mp0) REVERT: L 197 ARG cc_start: 0.5192 (tpt170) cc_final: 0.4809 (tpt170) REVERT: L 233 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7798 (ttt180) REVERT: L 239 GLU cc_start: 0.8373 (tt0) cc_final: 0.7952 (tp30) REVERT: A 24 ARG cc_start: 0.5295 (mtp180) cc_final: 0.4098 (mtp-110) REVERT: A 43 GLU cc_start: 0.7814 (mt-10) cc_final: 0.6996 (pm20) REVERT: A 85 MET cc_start: 0.8671 (tpp) cc_final: 0.8452 (tpt) REVERT: A 99 HIS cc_start: 0.4887 (OUTLIER) cc_final: 0.4682 (m90) REVERT: A 197 ARG cc_start: 0.6071 (ttt180) cc_final: 0.5714 (ttt180) REVERT: A 233 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7873 (ttt180) REVERT: A 238 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7565 (mttm) REVERT: A 239 GLU cc_start: 0.8431 (tt0) cc_final: 0.7956 (tp30) REVERT: B 24 ARG cc_start: 0.5488 (mtp180) cc_final: 0.5112 (mmm-85) REVERT: B 43 GLU cc_start: 0.7893 (tt0) cc_final: 0.7363 (mp0) REVERT: B 86 VAL cc_start: 0.7884 (t) cc_final: 0.7619 (m) REVERT: B 197 ARG cc_start: 0.5863 (ttt180) cc_final: 0.5035 (ppt170) REVERT: B 233 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7830 (ttt180) REVERT: B 238 LYS cc_start: 0.7980 (mtmp) cc_final: 0.7550 (mttm) REVERT: B 239 GLU cc_start: 0.8435 (tt0) cc_final: 0.8044 (tp30) REVERT: C 24 ARG cc_start: 0.5496 (mtm180) cc_final: 0.5223 (mmm-85) REVERT: C 43 GLU cc_start: 0.7849 (tp30) cc_final: 0.7327 (mp0) REVERT: C 197 ARG cc_start: 0.5961 (ttt180) cc_final: 0.5655 (ttt180) REVERT: C 233 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7824 (ttt180) REVERT: C 239 GLU cc_start: 0.8313 (tt0) cc_final: 0.7919 (tp30) REVERT: D 24 ARG cc_start: 0.5311 (mtp180) cc_final: 0.5061 (mmm-85) REVERT: D 43 GLU cc_start: 0.7932 (tt0) cc_final: 0.7526 (mp0) REVERT: D 197 ARG cc_start: 0.5973 (ttm170) cc_final: 0.5689 (ttt180) REVERT: D 233 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7860 (ttt180) REVERT: D 238 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7553 (mttm) REVERT: D 239 GLU cc_start: 0.8361 (tt0) cc_final: 0.7768 (tp30) REVERT: E 24 ARG cc_start: 0.5347 (mtp180) cc_final: 0.5060 (mmm-85) REVERT: E 43 GLU cc_start: 0.7946 (tt0) cc_final: 0.7428 (mp0) REVERT: E 197 ARG cc_start: 0.5911 (ttt180) cc_final: 0.5017 (ppt170) REVERT: E 239 GLU cc_start: 0.8275 (tp30) cc_final: 0.7790 (tp30) REVERT: F 24 ARG cc_start: 0.5316 (mtp180) cc_final: 0.4842 (ptp90) REVERT: F 43 GLU cc_start: 0.7921 (tt0) cc_final: 0.7655 (mm-30) REVERT: F 197 ARG cc_start: 0.6110 (ttt180) cc_final: 0.5261 (tpt170) REVERT: F 233 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7866 (ttt180) REVERT: G 24 ARG cc_start: 0.5281 (mtm180) cc_final: 0.4967 (mmm-85) REVERT: G 43 GLU cc_start: 0.7916 (tp30) cc_final: 0.7405 (mp0) REVERT: G 85 MET cc_start: 0.8761 (mmm) cc_final: 0.8375 (tpp) REVERT: G 197 ARG cc_start: 0.5893 (ttt180) cc_final: 0.5041 (tpt170) REVERT: G 233 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7768 (ttt180) REVERT: G 239 GLU cc_start: 0.8125 (tp30) cc_final: 0.7669 (tp30) REVERT: H 24 ARG cc_start: 0.5374 (mtp180) cc_final: 0.5122 (mmm-85) REVERT: H 43 GLU cc_start: 0.7714 (tp30) cc_final: 0.7319 (mp0) REVERT: H 85 MET cc_start: 0.8803 (mmm) cc_final: 0.8557 (tpt) REVERT: H 86 VAL cc_start: 0.7979 (t) cc_final: 0.7694 (m) REVERT: H 197 ARG cc_start: 0.6000 (ttt180) cc_final: 0.5712 (ttt180) REVERT: H 233 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7788 (ttt180) REVERT: H 239 GLU cc_start: 0.8008 (tp30) cc_final: 0.7460 (tp30) REVERT: H 268 ASN cc_start: 0.8269 (m-40) cc_final: 0.8048 (m110) REVERT: I 43 GLU cc_start: 0.7906 (tp30) cc_final: 0.7598 (mm-30) REVERT: I 85 MET cc_start: 0.8823 (mmm) cc_final: 0.8554 (tpt) REVERT: I 86 VAL cc_start: 0.7941 (t) cc_final: 0.7662 (m) REVERT: I 197 ARG cc_start: 0.6056 (ttt180) cc_final: 0.5742 (ttt180) REVERT: I 233 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7837 (ttt180) REVERT: I 238 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7668 (mttm) REVERT: I 239 GLU cc_start: 0.8322 (tt0) cc_final: 0.7726 (tp30) REVERT: J 24 ARG cc_start: 0.5444 (mtp180) cc_final: 0.5190 (mmm-85) REVERT: J 43 GLU cc_start: 0.7725 (tp30) cc_final: 0.7515 (mm-30) REVERT: J 85 MET cc_start: 0.8745 (mmm) cc_final: 0.8402 (tpp) REVERT: J 86 VAL cc_start: 0.7911 (t) cc_final: 0.7607 (m) REVERT: J 197 ARG cc_start: 0.5884 (ttt180) cc_final: 0.5019 (ppt170) REVERT: J 233 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7802 (ttt180) REVERT: J 238 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7620 (mttm) REVERT: J 239 GLU cc_start: 0.8449 (tt0) cc_final: 0.8015 (tp30) REVERT: J 268 ASN cc_start: 0.8232 (m-40) cc_final: 0.7988 (m110) REVERT: J 278 ARG cc_start: 0.3836 (OUTLIER) cc_final: 0.3554 (ttp-110) REVERT: K 24 ARG cc_start: 0.5318 (mtp180) cc_final: 0.5039 (mmm-85) REVERT: K 43 GLU cc_start: 0.7840 (tp30) cc_final: 0.7287 (mp0) REVERT: K 85 MET cc_start: 0.8728 (tpp) cc_final: 0.8512 (tpt) REVERT: K 86 VAL cc_start: 0.7964 (t) cc_final: 0.7599 (m) REVERT: K 197 ARG cc_start: 0.5967 (ttt180) cc_final: 0.5250 (ttp80) REVERT: K 233 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7799 (ttt180) REVERT: K 239 GLU cc_start: 0.8358 (tt0) cc_final: 0.7858 (tp30) outliers start: 9 outliers final: 1 residues processed: 255 average time/residue: 3.6708 time to fit residues: 1017.1728 Evaluate side-chains 242 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain K residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 156 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 273 ASN B 273 ASN C 273 ASN F 273 ASN H 273 ASN I 268 ASN I 273 ASN J 50 GLN K 273 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.168367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123185 restraints weight = 39787.847| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.62 r_work: 0.2996 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1864 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= 0.176 Angle : 0.543 5.159 23352 Z= 0.298 Chirality : 0.041 0.139 2712 Planarity : 0.004 0.061 2856 Dihedral : 3.704 46.150 2282 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.18), residues: 2028 helix: 3.18 (0.12), residues: 1560 sheet: -0.51 (0.34), residues: 204 loop : 0.33 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 277 HIS 0.004 0.001 HIS I 75 PHE 0.013 0.002 PHE F 53 TYR 0.021 0.003 TYR B 67 ARG 0.004 0.001 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 1295) hydrogen bonds : angle 3.80508 ( 3813) SS BOND : bond 0.00324 ( 36) SS BOND : angle 1.02951 ( 72) covalent geometry : bond 0.00390 (17136) covalent geometry : angle 0.54097 (23280) *********************** 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 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 2.823 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: 0.5343 (mtp180) cc_final: 0.4931 (mmm-85) REVERT: L 43 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7188 (mp0) REVERT: L 197 ARG cc_start: 0.5123 (tpt170) cc_final: 0.4223 (ppt170) REVERT: L 233 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7856 (ttt180) REVERT: L 278 ARG cc_start: 0.4187 (OUTLIER) cc_final: 0.3862 (ttp-110) REVERT: A 24 ARG cc_start: 0.5281 (mtp180) cc_final: 0.4043 (mtp-110) REVERT: A 85 MET cc_start: 0.8661 (tpp) cc_final: 0.8460 (tpt) REVERT: A 86 VAL cc_start: 0.7671 (t) cc_final: 0.7348 (m) REVERT: A 99 HIS cc_start: 0.4829 (OUTLIER) cc_final: 0.4605 (m90) REVERT: A 197 ARG cc_start: 0.6036 (ttt180) cc_final: 0.5148 (tpt170) REVERT: A 233 ARG cc_start: 0.8243 (ttm170) cc_final: 0.7753 (ttt180) REVERT: A 238 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7630 (mttm) REVERT: A 239 GLU cc_start: 0.8467 (tt0) cc_final: 0.7947 (tp30) REVERT: A 279 LYS cc_start: 0.4425 (OUTLIER) cc_final: 0.4105 (mppt) REVERT: B 24 ARG cc_start: 0.5444 (mtp180) cc_final: 0.5022 (mmm-85) REVERT: B 43 GLU cc_start: 0.7948 (tt0) cc_final: 0.7385 (mp0) REVERT: B 86 VAL cc_start: 0.7840 (t) cc_final: 0.7521 (m) REVERT: B 197 ARG cc_start: 0.5838 (ttt180) cc_final: 0.4920 (tpt170) REVERT: B 233 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7844 (ttt180) REVERT: B 238 LYS cc_start: 0.8078 (mtmp) cc_final: 0.7631 (mttm) REVERT: B 239 GLU cc_start: 0.8449 (tt0) cc_final: 0.7991 (tp30) REVERT: C 24 ARG cc_start: 0.5396 (mtm180) cc_final: 0.5109 (mmm-85) REVERT: C 43 GLU cc_start: 0.7873 (tp30) cc_final: 0.7251 (mp0) REVERT: C 197 ARG cc_start: 0.5991 (ttt180) cc_final: 0.5214 (ttp80) REVERT: C 233 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7879 (ttt180) REVERT: C 239 GLU cc_start: 0.8341 (tt0) cc_final: 0.8129 (tt0) REVERT: D 24 ARG cc_start: 0.5348 (mtp180) cc_final: 0.5049 (mmm-85) REVERT: D 43 GLU cc_start: 0.7935 (tt0) cc_final: 0.7419 (mp0) REVERT: D 197 ARG cc_start: 0.5942 (ttm170) cc_final: 0.4833 (ppt170) REVERT: D 233 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7724 (ttt180) REVERT: D 238 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7535 (mttm) REVERT: D 239 GLU cc_start: 0.8401 (tt0) cc_final: 0.8153 (tt0) REVERT: E 24 ARG cc_start: 0.5325 (mtp180) cc_final: 0.4946 (mmm-85) REVERT: E 43 GLU cc_start: 0.7953 (tt0) cc_final: 0.7426 (mp0) REVERT: E 197 ARG cc_start: 0.5880 (ttt180) cc_final: 0.4954 (tpt170) REVERT: E 239 GLU cc_start: 0.8315 (tp30) cc_final: 0.7792 (tp30) REVERT: F 24 ARG cc_start: 0.5417 (mtp180) cc_final: 0.4198 (mtp-110) REVERT: F 43 GLU cc_start: 0.7929 (tt0) cc_final: 0.7631 (mm-30) REVERT: F 197 ARG cc_start: 0.6050 (ttt180) cc_final: 0.5151 (tpt170) REVERT: F 233 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7690 (ttt180) REVERT: G 24 ARG cc_start: 0.5294 (mtm180) cc_final: 0.4945 (mmm-85) REVERT: G 43 GLU cc_start: 0.7904 (tt0) cc_final: 0.7367 (mp0) REVERT: G 85 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8257 (tpp) REVERT: G 197 ARG cc_start: 0.5936 (ttt180) cc_final: 0.5003 (tpt170) REVERT: G 233 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7744 (ttt180) REVERT: G 239 GLU cc_start: 0.8238 (tp30) cc_final: 0.7708 (tp30) REVERT: H 24 ARG cc_start: 0.5348 (mtp180) cc_final: 0.5022 (mmm-85) REVERT: H 43 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: H 85 MET cc_start: 0.8685 (mmm) cc_final: 0.8449 (tpt) REVERT: H 86 VAL cc_start: 0.7878 (t) cc_final: 0.7579 (m) REVERT: H 197 ARG cc_start: 0.6086 (ttt180) cc_final: 0.5261 (ttp80) REVERT: H 233 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7684 (ttt180) REVERT: H 239 GLU cc_start: 0.8203 (tp30) cc_final: 0.7943 (tt0) REVERT: H 268 ASN cc_start: 0.8203 (m-40) cc_final: 0.7940 (m110) REVERT: I 43 GLU cc_start: 0.7906 (tp30) cc_final: 0.7592 (mm-30) REVERT: I 85 MET cc_start: 0.8723 (mmm) cc_final: 0.8481 (tpt) REVERT: I 86 VAL cc_start: 0.7854 (t) cc_final: 0.7553 (m) REVERT: I 197 ARG cc_start: 0.6053 (ttt180) cc_final: 0.5140 (tpt170) REVERT: I 233 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7697 (ttt180) REVERT: I 238 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7574 (mttm) REVERT: I 239 GLU cc_start: 0.8369 (tt0) cc_final: 0.7753 (tp30) REVERT: J 24 ARG cc_start: 0.5412 (mtp180) cc_final: 0.5129 (mmm-85) REVERT: J 43 GLU cc_start: 0.7854 (tp30) cc_final: 0.7354 (mp0) REVERT: J 85 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8302 (tpp) REVERT: J 86 VAL cc_start: 0.7821 (t) cc_final: 0.7487 (m) REVERT: J 197 ARG cc_start: 0.5970 (ttt180) cc_final: 0.4953 (ppt170) REVERT: J 233 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7789 (ttt180) REVERT: J 238 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7641 (mttm) REVERT: J 239 GLU cc_start: 0.8480 (tt0) cc_final: 0.7970 (tp30) REVERT: J 268 ASN cc_start: 0.8128 (m-40) cc_final: 0.7857 (m110) REVERT: J 278 ARG cc_start: 0.3877 (OUTLIER) cc_final: 0.3494 (ttp-110) REVERT: K 24 ARG cc_start: 0.5281 (mtp180) cc_final: 0.4938 (mmm-85) REVERT: K 43 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: K 85 MET cc_start: 0.8691 (tpp) cc_final: 0.8446 (tpt) REVERT: K 86 VAL cc_start: 0.7819 (t) cc_final: 0.7406 (m) REVERT: K 197 ARG cc_start: 0.5974 (ttt180) cc_final: 0.5148 (ttp80) REVERT: K 233 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7750 (ttt180) REVERT: K 239 GLU cc_start: 0.8435 (tt0) cc_final: 0.7867 (tp30) outliers start: 17 outliers final: 3 residues processed: 240 average time/residue: 3.7405 time to fit residues: 976.2676 Evaluate side-chains 233 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 2.495 ------------------------------------------------------------------------------- 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 99 HIS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 207 ASN C 273 ASN D 273 ASN E 273 ASN F 273 ASN G 207 ASN H 273 ASN I 207 ASN I 273 ASN J 207 ASN J 273 ASN K 273 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.169304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.124175 restraints weight = 39624.023| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.63 r_work: 0.2998 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1990 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= 0.145 Angle : 0.513 4.303 23352 Z= 0.281 Chirality : 0.040 0.137 2712 Planarity : 0.004 0.038 2856 Dihedral : 3.669 45.285 2282 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.91 % Allowed : 13.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.18), residues: 2028 helix: 3.15 (0.12), residues: 1560 sheet: -0.61 (0.33), residues: 204 loop : 0.15 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 277 HIS 0.002 0.001 HIS C 99 PHE 0.012 0.001 PHE F 53 TYR 0.020 0.003 TYR B 67 ARG 0.004 0.000 ARG K 278 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 1295) hydrogen bonds : angle 3.71754 ( 3813) SS BOND : bond 0.00303 ( 36) SS BOND : angle 0.89823 ( 72) covalent geometry : bond 0.00310 (17136) covalent geometry : angle 0.51147 (23280) *********************** 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 251 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 2.408 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: L 24 ARG cc_start: 0.5381 (mtp180) cc_final: 0.4989 (mmm-85) REVERT: L 43 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7073 (mm-30) REVERT: L 197 ARG cc_start: 0.5110 (tpt170) cc_final: 0.4219 (ppt170) REVERT: L 233 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7729 (ttt180) REVERT: L 278 ARG cc_start: 0.4107 (OUTLIER) cc_final: 0.3831 (ttp-110) REVERT: A 86 VAL cc_start: 0.7702 (t) cc_final: 0.7363 (m) REVERT: A 197 ARG cc_start: 0.6096 (ttt180) cc_final: 0.5202 (tpt170) REVERT: A 233 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7722 (ttt180) REVERT: A 238 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7599 (mttm) REVERT: A 239 GLU cc_start: 0.8350 (tt0) cc_final: 0.7811 (tp30) REVERT: A 279 LYS cc_start: 0.4389 (OUTLIER) cc_final: 0.4054 (mppt) REVERT: B 24 ARG cc_start: 0.5423 (mtp180) cc_final: 0.5007 (mmm-85) REVERT: B 43 GLU cc_start: 0.7944 (tt0) cc_final: 0.7431 (mp0) REVERT: B 86 VAL cc_start: 0.7862 (t) cc_final: 0.7549 (m) REVERT: B 197 ARG cc_start: 0.5984 (ttt180) cc_final: 0.5044 (tpt170) REVERT: B 233 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7727 (ttt180) REVERT: B 238 LYS cc_start: 0.8131 (mtmp) cc_final: 0.7672 (mttm) REVERT: B 239 GLU cc_start: 0.8320 (tt0) cc_final: 0.7830 (tp30) REVERT: C 24 ARG cc_start: 0.5412 (mtm180) cc_final: 0.5130 (mmm-85) REVERT: C 43 GLU cc_start: 0.7833 (tp30) cc_final: 0.7299 (mp0) REVERT: C 197 ARG cc_start: 0.6021 (ttt180) cc_final: 0.5234 (ttp80) REVERT: C 233 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7746 (ttt180) REVERT: D 24 ARG cc_start: 0.5299 (mtp180) cc_final: 0.4994 (mmm-85) REVERT: D 43 GLU cc_start: 0.7940 (tt0) cc_final: 0.7475 (mp0) REVERT: D 197 ARG cc_start: 0.6000 (ttm170) cc_final: 0.4885 (ppt170) REVERT: D 233 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7707 (ttt180) REVERT: D 238 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7592 (mttm) REVERT: D 239 GLU cc_start: 0.8325 (tt0) cc_final: 0.8108 (tt0) REVERT: E 24 ARG cc_start: 0.5312 (mtp180) cc_final: 0.4928 (mmm-85) REVERT: E 43 GLU cc_start: 0.7950 (tt0) cc_final: 0.7457 (mp0) REVERT: E 197 ARG cc_start: 0.6011 (ttt180) cc_final: 0.5063 (tpt170) REVERT: E 239 GLU cc_start: 0.8188 (tp30) cc_final: 0.7649 (tp30) REVERT: F 24 ARG cc_start: 0.5393 (mtp180) cc_final: 0.4152 (mtp-110) REVERT: F 43 GLU cc_start: 0.7934 (tt0) cc_final: 0.7483 (mp0) REVERT: F 197 ARG cc_start: 0.6075 (ttt180) cc_final: 0.5182 (tpt170) REVERT: F 233 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7731 (ttt180) REVERT: G 24 ARG cc_start: 0.5338 (mtm180) cc_final: 0.5135 (mmm-85) REVERT: G 43 GLU cc_start: 0.7874 (tt0) cc_final: 0.7411 (mp0) REVERT: G 85 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8270 (tpp) REVERT: G 197 ARG cc_start: 0.5972 (ttt180) cc_final: 0.5029 (tpt170) REVERT: G 233 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7734 (ttt180) REVERT: G 239 GLU cc_start: 0.8183 (tp30) cc_final: 0.7628 (tp30) REVERT: H 24 ARG cc_start: 0.5384 (mtp180) cc_final: 0.5050 (mmm-85) REVERT: H 43 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: H 85 MET cc_start: 0.8666 (mmm) cc_final: 0.8465 (tpt) REVERT: H 86 VAL cc_start: 0.7870 (t) cc_final: 0.7566 (m) REVERT: H 197 ARG cc_start: 0.6033 (ttt180) cc_final: 0.5207 (ttp80) REVERT: H 233 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7691 (ttt180) REVERT: H 239 GLU cc_start: 0.8221 (tp30) cc_final: 0.7974 (tt0) REVERT: H 268 ASN cc_start: 0.8251 (m-40) cc_final: 0.7961 (m110) REVERT: I 43 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7604 (mm-30) REVERT: I 86 VAL cc_start: 0.7873 (t) cc_final: 0.7558 (m) REVERT: I 100 GLN cc_start: 0.4591 (OUTLIER) cc_final: 0.4135 (tt0) REVERT: I 197 ARG cc_start: 0.6115 (ttt180) cc_final: 0.5193 (tpt170) REVERT: I 233 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7672 (ttt180) REVERT: I 268 ASN cc_start: 0.8120 (m-40) cc_final: 0.7870 (m110) REVERT: J 24 ARG cc_start: 0.5426 (mtp180) cc_final: 0.5127 (mmm-85) REVERT: J 43 GLU cc_start: 0.7809 (tp30) cc_final: 0.7392 (mp0) REVERT: J 85 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8311 (tpp) REVERT: J 86 VAL cc_start: 0.7841 (t) cc_final: 0.7509 (m) REVERT: J 197 ARG cc_start: 0.6016 (ttt180) cc_final: 0.5119 (tpt170) REVERT: J 233 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7754 (ttt180) REVERT: J 238 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7663 (mttm) REVERT: J 239 GLU cc_start: 0.8398 (tt0) cc_final: 0.7870 (tp30) REVERT: J 268 ASN cc_start: 0.8130 (m-40) cc_final: 0.7845 (m110) REVERT: J 278 ARG cc_start: 0.3880 (OUTLIER) cc_final: 0.3601 (ttp-110) REVERT: K 24 ARG cc_start: 0.5258 (mtp180) cc_final: 0.4853 (mmm-85) REVERT: K 43 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: K 85 MET cc_start: 0.8709 (tpp) cc_final: 0.8488 (tpt) REVERT: K 86 VAL cc_start: 0.7800 (t) cc_final: 0.7409 (m) REVERT: K 197 ARG cc_start: 0.5986 (ttt180) cc_final: 0.5121 (ttp80) REVERT: K 233 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7736 (ttt180) REVERT: K 239 GLU cc_start: 0.8315 (tt0) cc_final: 0.8114 (tt0) outliers start: 17 outliers final: 4 residues processed: 240 average time/residue: 3.7468 time to fit residues: 981.2183 Evaluate side-chains 240 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 2.768 ------------------------------------------------------------------------------- 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 D 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 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 69 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 153 optimal weight: 0.0000 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN F 273 ASN G 207 ASN H 273 ASN I 207 ASN I 273 ASN J 273 ASN K 268 ASN K 273 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.169382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.126956 restraints weight = 39780.196| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.53 r_work: 0.2873 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17172 Z= 0.136 Angle : 0.499 4.178 23352 Z= 0.274 Chirality : 0.040 0.137 2712 Planarity : 0.004 0.037 2856 Dihedral : 3.502 11.474 2280 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.85 % Allowed : 13.30 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.18), residues: 2028 helix: 3.19 (0.12), residues: 1560 sheet: -0.56 (0.34), residues: 204 loop : 0.12 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 277 HIS 0.002 0.001 HIS C 99 PHE 0.012 0.001 PHE F 53 TYR 0.019 0.002 TYR B 67 ARG 0.004 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 1295) hydrogen bonds : angle 3.68088 ( 3813) SS BOND : bond 0.00266 ( 36) SS BOND : angle 0.83232 ( 72) covalent geometry : bond 0.00290 (17136) covalent geometry : angle 0.49749 (23280) *********************** 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 258 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 2.679 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: 0.5288 (mtp180) cc_final: 0.4934 (mmm-85) REVERT: L 43 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7107 (mm-30) REVERT: L 197 ARG cc_start: 0.5032 (tpt170) cc_final: 0.4130 (ppt170) REVERT: L 233 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7855 (ttt180) REVERT: L 271 GLU cc_start: 0.6971 (tt0) cc_final: 0.6338 (tp30) REVERT: L 278 ARG cc_start: 0.4086 (OUTLIER) cc_final: 0.3833 (ttp-110) REVERT: A 24 ARG cc_start: 0.5279 (mtp180) cc_final: 0.4023 (mtp-110) REVERT: A 86 VAL cc_start: 0.7662 (OUTLIER) cc_final: 0.7284 (m) REVERT: A 197 ARG cc_start: 0.6059 (ttt180) cc_final: 0.5111 (tpt170) REVERT: A 233 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7764 (ttt180) REVERT: A 238 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7609 (mttm) REVERT: A 239 GLU cc_start: 0.8520 (tt0) cc_final: 0.7943 (tp30) REVERT: A 279 LYS cc_start: 0.4286 (OUTLIER) cc_final: 0.3948 (mppt) REVERT: B 24 ARG cc_start: 0.5391 (mtp180) cc_final: 0.4948 (mmm-85) REVERT: B 43 GLU cc_start: 0.8035 (tt0) cc_final: 0.7417 (mp0) REVERT: B 86 VAL cc_start: 0.7787 (t) cc_final: 0.7463 (m) REVERT: B 197 ARG cc_start: 0.5953 (ttt180) cc_final: 0.4972 (tpt170) REVERT: B 233 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7735 (ttt180) REVERT: B 238 LYS cc_start: 0.8172 (mtmp) cc_final: 0.7702 (mttm) REVERT: B 239 GLU cc_start: 0.8460 (tt0) cc_final: 0.7914 (tp30) REVERT: C 24 ARG cc_start: 0.5359 (mtm180) cc_final: 0.5082 (mmm-85) REVERT: C 43 GLU cc_start: 0.7910 (tt0) cc_final: 0.7331 (mp0) REVERT: C 197 ARG cc_start: 0.6022 (ttt180) cc_final: 0.5172 (ttp80) REVERT: C 233 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7866 (ttt180) REVERT: D 24 ARG cc_start: 0.5312 (mtp180) cc_final: 0.4982 (mmm-85) REVERT: D 43 GLU cc_start: 0.8016 (tt0) cc_final: 0.7449 (mp0) REVERT: D 197 ARG cc_start: 0.5978 (ttm170) cc_final: 0.4808 (ppt170) REVERT: D 233 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7745 (ttt180) REVERT: D 238 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7605 (mttm) REVERT: D 239 GLU cc_start: 0.8492 (tt0) cc_final: 0.8254 (tt0) REVERT: E 24 ARG cc_start: 0.5246 (mtp180) cc_final: 0.4827 (mmm-85) REVERT: E 43 GLU cc_start: 0.8038 (tt0) cc_final: 0.7426 (mp0) REVERT: E 197 ARG cc_start: 0.5953 (ttt180) cc_final: 0.4982 (tpt170) REVERT: E 239 GLU cc_start: 0.8374 (tp30) cc_final: 0.8078 (tt0) REVERT: F 24 ARG cc_start: 0.5344 (mtp180) cc_final: 0.4066 (mtp-110) REVERT: F 43 GLU cc_start: 0.8005 (tt0) cc_final: 0.7438 (mp0) REVERT: F 197 ARG cc_start: 0.6052 (ttt180) cc_final: 0.5531 (tpp80) REVERT: F 233 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7780 (ttt180) REVERT: G 24 ARG cc_start: 0.5251 (mtm180) cc_final: 0.4870 (mmm-85) REVERT: G 43 GLU cc_start: 0.7950 (tt0) cc_final: 0.7391 (mp0) REVERT: G 85 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8281 (tpp) REVERT: G 197 ARG cc_start: 0.5922 (ttt180) cc_final: 0.4936 (tpt170) REVERT: G 233 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7763 (ttt180) REVERT: G 239 GLU cc_start: 0.8374 (tp30) cc_final: 0.8097 (tt0) REVERT: H 24 ARG cc_start: 0.5297 (mtp180) cc_final: 0.4956 (mmm-85) REVERT: H 43 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: H 85 MET cc_start: 0.8716 (mmm) cc_final: 0.8509 (tpt) REVERT: H 86 VAL cc_start: 0.7802 (t) cc_final: 0.7483 (m) REVERT: H 197 ARG cc_start: 0.6090 (ttt180) cc_final: 0.5164 (ttp80) REVERT: H 233 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7902 (ttt180) REVERT: H 239 GLU cc_start: 0.8420 (tp30) cc_final: 0.8124 (tt0) REVERT: H 268 ASN cc_start: 0.8209 (m-40) cc_final: 0.7900 (m110) REVERT: I 43 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: I 86 VAL cc_start: 0.7812 (t) cc_final: 0.7482 (m) REVERT: I 100 GLN cc_start: 0.4555 (OUTLIER) cc_final: 0.4076 (tt0) REVERT: I 197 ARG cc_start: 0.6117 (ttt180) cc_final: 0.5128 (tpt170) REVERT: I 233 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7800 (ttt180) REVERT: J 24 ARG cc_start: 0.5382 (mtp180) cc_final: 0.5045 (mmm-85) REVERT: J 43 GLU cc_start: 0.7886 (tp30) cc_final: 0.7369 (mp0) REVERT: J 85 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8328 (tpp) REVERT: J 86 VAL cc_start: 0.7775 (t) cc_final: 0.7439 (m) REVERT: J 197 ARG cc_start: 0.6078 (ttt180) cc_final: 0.5083 (tpt170) REVERT: J 233 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7713 (ttt180) REVERT: J 238 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7679 (mttm) REVERT: J 239 GLU cc_start: 0.8534 (tt0) cc_final: 0.7955 (tp30) REVERT: J 268 ASN cc_start: 0.8108 (m-40) cc_final: 0.7842 (m110) REVERT: J 278 ARG cc_start: 0.3920 (OUTLIER) cc_final: 0.3622 (ttp-110) REVERT: K 24 ARG cc_start: 0.5185 (mtp180) cc_final: 0.4747 (mmm-85) REVERT: K 43 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: K 85 MET cc_start: 0.8733 (tpp) cc_final: 0.8511 (tpt) REVERT: K 86 VAL cc_start: 0.7746 (t) cc_final: 0.7354 (m) REVERT: K 197 ARG cc_start: 0.5952 (ttt180) cc_final: 0.5010 (ttp80) REVERT: K 233 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7777 (ttt180) outliers start: 16 outliers final: 4 residues processed: 246 average time/residue: 3.7321 time to fit residues: 999.6985 Evaluate side-chains 251 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 C residue 51 THR Chi-restraints excluded: chain D 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 73 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 273 ASN A 273 ASN B 273 ASN C 207 ASN C 273 ASN F 273 ASN G 207 ASN H 273 ASN I 207 ASN I 268 ASN I 273 ASN J 207 ASN J 273 ASN K 268 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 = 0.3801 r_free = 0.3801 target = 0.168836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.123935 restraints weight = 39668.115| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.70 r_work: 0.2881 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2186 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= 0.159 Angle : 0.528 5.495 23352 Z= 0.290 Chirality : 0.041 0.138 2712 Planarity : 0.004 0.039 2856 Dihedral : 3.597 12.015 2280 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.18 % Allowed : 13.25 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.18), residues: 2028 helix: 3.07 (0.12), residues: 1560 sheet: -0.67 (0.33), residues: 204 loop : 0.10 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 277 HIS 0.003 0.001 HIS J 99 PHE 0.012 0.002 PHE F 53 TYR 0.021 0.003 TYR B 67 ARG 0.004 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 1295) hydrogen bonds : angle 3.77542 ( 3813) SS BOND : bond 0.00305 ( 36) SS BOND : angle 0.93258 ( 72) covalent geometry : bond 0.00346 (17136) covalent geometry : angle 0.52605 (23280) *********************** 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 256 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5248 (mtp180) cc_final: 0.4906 (mmm-85) REVERT: L 43 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7075 (mm-30) REVERT: L 197 ARG cc_start: 0.5019 (tpt170) cc_final: 0.4096 (ppt170) REVERT: L 233 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7791 (ttt180) REVERT: L 268 ASN cc_start: 0.8141 (m-40) cc_final: 0.7881 (m110) REVERT: L 271 GLU cc_start: 0.6887 (tt0) cc_final: 0.6249 (tp30) REVERT: L 278 ARG cc_start: 0.4051 (OUTLIER) cc_final: 0.3805 (ttp-110) REVERT: A 24 ARG cc_start: 0.5244 (mtp180) cc_final: 0.4026 (mtp-110) REVERT: A 43 GLU cc_start: 0.7883 (mt-10) cc_final: 0.6898 (pm20) REVERT: A 86 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7257 (m) REVERT: A 197 ARG cc_start: 0.6014 (ttt180) cc_final: 0.5523 (tpp80) REVERT: A 233 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7784 (ttt180) REVERT: A 238 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7588 (mttm) REVERT: A 268 ASN cc_start: 0.8024 (m-40) cc_final: 0.7817 (m110) REVERT: A 279 LYS cc_start: 0.4296 (OUTLIER) cc_final: 0.4056 (mppt) REVERT: B 24 ARG cc_start: 0.5368 (mtp180) cc_final: 0.4923 (mmm-85) REVERT: B 43 GLU cc_start: 0.8015 (tt0) cc_final: 0.7396 (mp0) REVERT: B 86 VAL cc_start: 0.7767 (t) cc_final: 0.7430 (m) REVERT: B 197 ARG cc_start: 0.5991 (ttt180) cc_final: 0.5027 (tpt170) REVERT: B 233 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7817 (ttt180) REVERT: B 239 GLU cc_start: 0.8390 (tt0) cc_final: 0.7817 (tp30) REVERT: C 24 ARG cc_start: 0.5268 (mtm180) cc_final: 0.4985 (mmm-85) REVERT: C 43 GLU cc_start: 0.7879 (tt0) cc_final: 0.7294 (mp0) REVERT: C 197 ARG cc_start: 0.6059 (ttt180) cc_final: 0.5149 (ttp80) REVERT: C 233 ARG cc_start: 0.8191 (ttm170) cc_final: 0.7821 (ttt180) REVERT: D 24 ARG cc_start: 0.5284 (mtp180) cc_final: 0.4967 (mmm-85) REVERT: D 43 GLU cc_start: 0.7967 (tt0) cc_final: 0.7370 (mp0) REVERT: D 197 ARG cc_start: 0.5973 (ttm170) cc_final: 0.4804 (ppt170) REVERT: D 233 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7812 (ttt180) REVERT: D 239 GLU cc_start: 0.8429 (tt0) cc_final: 0.8169 (tt0) REVERT: D 268 ASN cc_start: 0.8009 (m-40) cc_final: 0.7681 (m110) REVERT: E 24 ARG cc_start: 0.5230 (mtp180) cc_final: 0.4797 (mmm-85) REVERT: E 43 GLU cc_start: 0.8014 (tt0) cc_final: 0.7389 (mp0) REVERT: E 197 ARG cc_start: 0.6009 (ttt180) cc_final: 0.5038 (tpt170) REVERT: E 239 GLU cc_start: 0.8334 (tp30) cc_final: 0.8078 (tt0) REVERT: F 24 ARG cc_start: 0.5288 (mtp180) cc_final: 0.4030 (mtp-110) REVERT: F 43 GLU cc_start: 0.7990 (tt0) cc_final: 0.7403 (mp0) REVERT: F 197 ARG cc_start: 0.6095 (ttt180) cc_final: 0.5559 (tpp80) REVERT: F 233 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7694 (ttt180) REVERT: G 24 ARG cc_start: 0.5270 (mtm180) cc_final: 0.5056 (mmm-85) REVERT: G 43 GLU cc_start: 0.7918 (tt0) cc_final: 0.7359 (mp0) REVERT: G 85 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8183 (tpp) REVERT: G 197 ARG cc_start: 0.5993 (ttt180) cc_final: 0.4999 (tpt170) REVERT: G 233 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7708 (ttt180) REVERT: G 239 GLU cc_start: 0.8339 (tp30) cc_final: 0.8080 (tt0) REVERT: G 268 ASN cc_start: 0.8075 (m-40) cc_final: 0.7793 (m110) REVERT: H 24 ARG cc_start: 0.5286 (mtp180) cc_final: 0.4907 (mmm-85) REVERT: H 43 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: H 86 VAL cc_start: 0.7757 (t) cc_final: 0.7457 (m) REVERT: H 197 ARG cc_start: 0.6054 (ttt180) cc_final: 0.5120 (ttp80) REVERT: H 233 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7829 (ttt180) REVERT: H 239 GLU cc_start: 0.8373 (tp30) cc_final: 0.8076 (tt0) REVERT: I 43 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: I 86 VAL cc_start: 0.7780 (t) cc_final: 0.7433 (m) REVERT: I 100 GLN cc_start: 0.4641 (OUTLIER) cc_final: 0.4180 (tt0) REVERT: I 197 ARG cc_start: 0.6096 (ttt180) cc_final: 0.5590 (tpp80) REVERT: I 233 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7753 (ttt180) REVERT: I 268 ASN cc_start: 0.8003 (m-40) cc_final: 0.7736 (m110) REVERT: J 24 ARG cc_start: 0.5387 (mtp180) cc_final: 0.5057 (mmm-85) REVERT: J 43 GLU cc_start: 0.7882 (tp30) cc_final: 0.7320 (mp0) REVERT: J 85 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8255 (tpp) REVERT: J 86 VAL cc_start: 0.7725 (t) cc_final: 0.7381 (m) REVERT: J 197 ARG cc_start: 0.6143 (ttt180) cc_final: 0.5597 (tpp80) REVERT: J 233 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7863 (ttt180) REVERT: J 268 ASN cc_start: 0.8060 (m-40) cc_final: 0.7803 (m110) REVERT: J 278 ARG cc_start: 0.3859 (OUTLIER) cc_final: 0.3611 (ttp-110) REVERT: K 24 ARG cc_start: 0.5096 (mtp180) cc_final: 0.4658 (mmm-85) REVERT: K 43 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: K 85 MET cc_start: 0.8671 (tpp) cc_final: 0.8454 (tpt) REVERT: K 86 VAL cc_start: 0.7689 (t) cc_final: 0.7306 (m) REVERT: K 197 ARG cc_start: 0.5960 (ttt180) cc_final: 0.4960 (ttp80) REVERT: K 233 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7835 (ttt180) outliers start: 22 outliers final: 4 residues processed: 241 average time/residue: 3.7107 time to fit residues: 973.1208 Evaluate side-chains 244 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain D 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 72 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN F 273 ASN G 207 ASN G 273 ASN H 273 ASN I 207 ASN I 273 ASN J 207 ASN J 273 ASN K 273 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.170284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.126411 restraints weight = 39901.997| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.60 r_work: 0.2883 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17172 Z= 0.110 Angle : 0.473 4.243 23352 Z= 0.259 Chirality : 0.039 0.134 2712 Planarity : 0.004 0.038 2856 Dihedral : 3.441 11.820 2280 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.80 % Allowed : 13.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.18), residues: 2028 helix: 3.22 (0.12), residues: 1560 sheet: -0.56 (0.34), residues: 204 loop : 0.12 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 277 HIS 0.002 0.001 HIS K 99 PHE 0.010 0.001 PHE F 53 TYR 0.016 0.002 TYR C 67 ARG 0.003 0.000 ARG K 278 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 1295) hydrogen bonds : angle 3.59160 ( 3813) SS BOND : bond 0.00203 ( 36) SS BOND : angle 0.67412 ( 72) covalent geometry : bond 0.00225 (17136) covalent geometry : angle 0.47182 (23280) *********************** 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 255 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.5273 (mtp180) cc_final: 0.4942 (mmm-85) REVERT: L 43 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7095 (mm-30) REVERT: L 197 ARG cc_start: 0.4992 (tpt170) cc_final: 0.4122 (ppt170) REVERT: L 233 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7850 (ttt180) REVERT: L 271 GLU cc_start: 0.6966 (tt0) cc_final: 0.6345 (tp30) REVERT: L 278 ARG cc_start: 0.3997 (OUTLIER) cc_final: 0.3767 (ttp-110) REVERT: A 24 ARG cc_start: 0.5290 (mtp180) cc_final: 0.4913 (mmm-85) REVERT: A 86 VAL cc_start: 0.7642 (t) cc_final: 0.7272 (m) REVERT: A 197 ARG cc_start: 0.6034 (ttt180) cc_final: 0.5545 (tpp80) REVERT: A 233 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7773 (ttt180) REVERT: A 238 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7649 (mttm) REVERT: A 279 LYS cc_start: 0.4341 (OUTLIER) cc_final: 0.4071 (mppt) REVERT: B 24 ARG cc_start: 0.5367 (mtp180) cc_final: 0.4939 (mmm-85) REVERT: B 43 GLU cc_start: 0.8025 (tt0) cc_final: 0.7461 (mp0) REVERT: B 86 VAL cc_start: 0.7762 (t) cc_final: 0.7460 (m) REVERT: B 197 ARG cc_start: 0.6045 (ttt180) cc_final: 0.5095 (tpt170) REVERT: B 233 ARG cc_start: 0.8224 (ttm170) cc_final: 0.7745 (ttt180) REVERT: B 239 GLU cc_start: 0.8433 (tt0) cc_final: 0.7879 (tp30) REVERT: C 21 MET cc_start: 0.4609 (tpt) cc_final: 0.4385 (tpp) REVERT: C 24 ARG cc_start: 0.5358 (mtm180) cc_final: 0.5109 (mmm-85) REVERT: C 43 GLU cc_start: 0.7900 (tt0) cc_final: 0.7315 (mp0) REVERT: C 197 ARG cc_start: 0.6040 (ttt180) cc_final: 0.5188 (ttp80) REVERT: C 233 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7869 (ttt180) REVERT: C 268 ASN cc_start: 0.8180 (m-40) cc_final: 0.7912 (m-40) REVERT: D 24 ARG cc_start: 0.5293 (mtp180) cc_final: 0.4982 (mmm-85) REVERT: D 43 GLU cc_start: 0.8037 (tt0) cc_final: 0.7459 (mp0) REVERT: D 197 ARG cc_start: 0.5948 (ttm170) cc_final: 0.4822 (ppt170) REVERT: D 233 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7768 (ttt180) REVERT: D 239 GLU cc_start: 0.8521 (tt0) cc_final: 0.8281 (tt0) REVERT: D 268 ASN cc_start: 0.8034 (m-40) cc_final: 0.7707 (m110) REVERT: E 24 ARG cc_start: 0.5250 (mtp180) cc_final: 0.4828 (mmm-85) REVERT: E 43 GLU cc_start: 0.7995 (tt0) cc_final: 0.7383 (mp0) REVERT: E 197 ARG cc_start: 0.6086 (ttt180) cc_final: 0.5115 (tpt170) REVERT: E 239 GLU cc_start: 0.8396 (tp30) cc_final: 0.8154 (tt0) REVERT: F 24 ARG cc_start: 0.5303 (mtp180) cc_final: 0.4064 (mtp-110) REVERT: F 43 GLU cc_start: 0.8036 (tt0) cc_final: 0.7488 (mp0) REVERT: F 197 ARG cc_start: 0.6070 (ttt180) cc_final: 0.5548 (tpp80) REVERT: F 233 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7812 (ttt180) REVERT: F 238 LYS cc_start: 0.8190 (mttp) cc_final: 0.7796 (mttm) REVERT: G 24 ARG cc_start: 0.5256 (mtm180) cc_final: 0.4894 (mmm-85) REVERT: G 43 GLU cc_start: 0.7964 (tt0) cc_final: 0.7441 (mp0) REVERT: G 85 MET cc_start: 0.8655 (mmm) cc_final: 0.8293 (tpp) REVERT: G 197 ARG cc_start: 0.6042 (ttt180) cc_final: 0.5046 (tpt170) REVERT: G 233 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7767 (ttt180) REVERT: G 239 GLU cc_start: 0.8404 (tp30) cc_final: 0.8168 (tt0) REVERT: G 268 ASN cc_start: 0.8143 (m-40) cc_final: 0.7917 (m110) REVERT: H 24 ARG cc_start: 0.5334 (mtp180) cc_final: 0.4987 (mmm-85) REVERT: H 43 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: H 86 VAL cc_start: 0.7785 (t) cc_final: 0.7446 (m) REVERT: H 197 ARG cc_start: 0.6073 (ttt180) cc_final: 0.5116 (ttp80) REVERT: H 233 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7910 (ttt180) REVERT: H 239 GLU cc_start: 0.8442 (tp30) cc_final: 0.8171 (tt0) REVERT: I 43 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: I 86 VAL cc_start: 0.7818 (t) cc_final: 0.7485 (m) REVERT: I 100 GLN cc_start: 0.4565 (OUTLIER) cc_final: 0.4142 (tt0) REVERT: I 197 ARG cc_start: 0.6113 (ttt180) cc_final: 0.5628 (tpp80) REVERT: I 233 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7760 (ttt180) REVERT: I 268 ASN cc_start: 0.8099 (m-40) cc_final: 0.7821 (m110) REVERT: J 24 ARG cc_start: 0.5366 (mtp180) cc_final: 0.5047 (mmm-85) REVERT: J 43 GLU cc_start: 0.7834 (tp30) cc_final: 0.7322 (mp0) REVERT: J 85 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8343 (tpp) REVERT: J 86 VAL cc_start: 0.7737 (t) cc_final: 0.7421 (m) REVERT: J 197 ARG cc_start: 0.6093 (ttt180) cc_final: 0.5562 (tpp80) REVERT: J 233 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7797 (ttt180) REVERT: J 268 ASN cc_start: 0.8116 (m-40) cc_final: 0.7859 (m110) REVERT: J 278 ARG cc_start: 0.3819 (OUTLIER) cc_final: 0.3611 (ttp-110) REVERT: K 24 ARG cc_start: 0.5161 (mtp180) cc_final: 0.4745 (mmm-85) REVERT: K 43 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: K 86 VAL cc_start: 0.7710 (t) cc_final: 0.7340 (m) REVERT: K 197 ARG cc_start: 0.5967 (ttt180) cc_final: 0.4994 (ttp80) REVERT: K 233 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7779 (ttt180) outliers start: 15 outliers final: 3 residues processed: 246 average time/residue: 3.7239 time to fit residues: 997.7881 Evaluate side-chains 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain A residue 279 LYS 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 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 118 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 0.0170 chunk 120 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN F 268 ASN F 273 ASN G 207 ASN G 273 ASN H 273 ASN I 207 ASN I 273 ASN J 207 ASN J 273 ASN K 273 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.170064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127075 restraints weight = 39775.285| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.55 r_work: 0.2861 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17172 Z= 0.125 Angle : 0.485 4.396 23352 Z= 0.266 Chirality : 0.040 0.135 2712 Planarity : 0.004 0.038 2856 Dihedral : 3.450 11.593 2280 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.80 % Allowed : 13.51 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.18), residues: 2028 helix: 3.20 (0.12), residues: 1560 sheet: -0.57 (0.34), residues: 204 loop : 0.16 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 277 HIS 0.002 0.001 HIS K 99 PHE 0.011 0.001 PHE F 53 TYR 0.018 0.002 TYR B 67 ARG 0.003 0.000 ARG K 278 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 1295) hydrogen bonds : angle 3.61949 ( 3813) SS BOND : bond 0.00236 ( 36) SS BOND : angle 0.77235 ( 72) covalent geometry : bond 0.00265 (17136) covalent geometry : angle 0.48347 (23280) *********************** 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 254 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 239 time to evaluate : 2.628 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: 0.5295 (mtp180) cc_final: 0.4963 (mmm-85) REVERT: L 43 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7126 (mm-30) REVERT: L 197 ARG cc_start: 0.5002 (tpt170) cc_final: 0.4118 (ppt170) REVERT: L 233 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7875 (ttt180) REVERT: L 271 GLU cc_start: 0.6994 (tt0) cc_final: 0.6378 (tp30) REVERT: L 278 ARG cc_start: 0.3966 (OUTLIER) cc_final: 0.3749 (ttp-110) REVERT: A 24 ARG cc_start: 0.5299 (mtp180) cc_final: 0.4044 (mtp-110) REVERT: A 43 GLU cc_start: 0.7971 (mt-10) cc_final: 0.6962 (pm20) REVERT: A 86 VAL cc_start: 0.7666 (t) cc_final: 0.7290 (m) REVERT: A 197 ARG cc_start: 0.6040 (ttt180) cc_final: 0.5549 (tpp80) REVERT: A 233 ARG cc_start: 0.8278 (ttm170) cc_final: 0.7792 (ttt180) REVERT: A 238 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7686 (mttm) REVERT: A 268 ASN cc_start: 0.8102 (m-40) cc_final: 0.7893 (m110) REVERT: A 279 LYS cc_start: 0.4397 (OUTLIER) cc_final: 0.4128 (mppt) REVERT: B 24 ARG cc_start: 0.5358 (mtp180) cc_final: 0.4928 (mmm-85) REVERT: B 43 GLU cc_start: 0.8070 (tt0) cc_final: 0.7478 (mp0) REVERT: B 86 VAL cc_start: 0.7775 (t) cc_final: 0.7467 (m) REVERT: B 197 ARG cc_start: 0.6043 (ttt180) cc_final: 0.5537 (tpp80) REVERT: B 233 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7762 (ttt180) REVERT: B 239 GLU cc_start: 0.8493 (tt0) cc_final: 0.7944 (tp30) REVERT: C 24 ARG cc_start: 0.5402 (mtm180) cc_final: 0.5135 (mmm-85) REVERT: C 43 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: C 197 ARG cc_start: 0.6068 (ttt180) cc_final: 0.5205 (ttp80) REVERT: C 233 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7896 (ttt180) REVERT: D 24 ARG cc_start: 0.5349 (mtp180) cc_final: 0.5030 (mmm-85) REVERT: D 43 GLU cc_start: 0.8070 (tt0) cc_final: 0.7444 (mp0) REVERT: D 197 ARG cc_start: 0.5953 (ttm170) cc_final: 0.4820 (ppt170) REVERT: D 233 ARG cc_start: 0.8318 (ttm170) cc_final: 0.7792 (ttt180) REVERT: D 239 GLU cc_start: 0.8560 (tt0) cc_final: 0.8309 (tt0) REVERT: E 24 ARG cc_start: 0.5253 (mtp180) cc_final: 0.4829 (mmm-85) REVERT: E 43 GLU cc_start: 0.8054 (tt0) cc_final: 0.7429 (mp0) REVERT: E 197 ARG cc_start: 0.6074 (ttt180) cc_final: 0.5560 (tpp80) REVERT: E 239 GLU cc_start: 0.8453 (tp30) cc_final: 0.8202 (tt0) REVERT: F 24 ARG cc_start: 0.5323 (mtp180) cc_final: 0.4094 (mtp-110) REVERT: F 43 GLU cc_start: 0.8076 (tt0) cc_final: 0.7469 (mp0) REVERT: F 197 ARG cc_start: 0.6098 (ttt180) cc_final: 0.5580 (tpp80) REVERT: F 233 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7815 (ttt180) REVERT: F 238 LYS cc_start: 0.8199 (mttp) cc_final: 0.7801 (mttm) REVERT: F 268 ASN cc_start: 0.8053 (m-40) cc_final: 0.7769 (m110) REVERT: G 24 ARG cc_start: 0.5268 (mtm180) cc_final: 0.4891 (mmm-85) REVERT: G 43 GLU cc_start: 0.8013 (tt0) cc_final: 0.7454 (mp0) REVERT: G 85 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8325 (tpp) REVERT: G 197 ARG cc_start: 0.6052 (ttt180) cc_final: 0.5055 (tpt170) REVERT: G 233 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7786 (ttt180) REVERT: G 239 GLU cc_start: 0.8444 (tp30) cc_final: 0.8187 (tt0) REVERT: G 268 ASN cc_start: 0.8170 (m-40) cc_final: 0.7888 (m110) REVERT: H 24 ARG cc_start: 0.5338 (mtp180) cc_final: 0.5000 (mmm-85) REVERT: H 43 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: H 86 VAL cc_start: 0.7801 (t) cc_final: 0.7443 (m) REVERT: H 197 ARG cc_start: 0.6107 (ttt180) cc_final: 0.5138 (ttp80) REVERT: H 233 ARG cc_start: 0.8260 (ttm170) cc_final: 0.7934 (ttt180) REVERT: H 239 GLU cc_start: 0.8521 (tp30) cc_final: 0.8229 (tt0) REVERT: H 268 ASN cc_start: 0.8184 (m-40) cc_final: 0.7878 (m110) REVERT: I 43 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7752 (mm-30) REVERT: I 86 VAL cc_start: 0.7832 (t) cc_final: 0.7472 (m) REVERT: I 100 GLN cc_start: 0.4597 (OUTLIER) cc_final: 0.4173 (tt0) REVERT: I 197 ARG cc_start: 0.6113 (ttt180) cc_final: 0.5623 (tpp80) REVERT: I 233 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7842 (ttt180) REVERT: I 268 ASN cc_start: 0.8102 (m-40) cc_final: 0.7824 (m110) REVERT: J 24 ARG cc_start: 0.5393 (mtp180) cc_final: 0.5081 (mmm-85) REVERT: J 43 GLU cc_start: 0.7892 (tp30) cc_final: 0.7366 (mp0) REVERT: J 85 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8361 (tpp) REVERT: J 86 VAL cc_start: 0.7764 (t) cc_final: 0.7448 (m) REVERT: J 197 ARG cc_start: 0.6149 (ttt180) cc_final: 0.5608 (tpp80) REVERT: J 233 ARG cc_start: 0.8242 (ttm170) cc_final: 0.7824 (ttt180) REVERT: J 268 ASN cc_start: 0.8179 (m-40) cc_final: 0.7923 (m110) REVERT: K 24 ARG cc_start: 0.5161 (mtp180) cc_final: 0.4735 (mmm-85) REVERT: K 43 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: K 86 VAL cc_start: 0.7736 (t) cc_final: 0.7356 (m) REVERT: K 197 ARG cc_start: 0.5997 (ttt180) cc_final: 0.5008 (ttp80) REVERT: K 233 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7801 (ttt180) outliers start: 15 outliers final: 3 residues processed: 242 average time/residue: 3.8065 time to fit residues: 1002.0459 Evaluate side-chains 251 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 2.756 ------------------------------------------------------------------------------- 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 43 GLU 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 173 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN E 273 ASN F 273 ASN G 273 ASN H 273 ASN I 207 ASN I 273 ASN J 207 ASN J 273 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 = 0.3823 r_free = 0.3823 target = 0.170787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.127447 restraints weight = 39585.585| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.39 r_work: 0.2893 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17172 Z= 0.109 Angle : 0.467 4.585 23352 Z= 0.256 Chirality : 0.039 0.133 2712 Planarity : 0.003 0.038 2856 Dihedral : 3.391 11.899 2280 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.64 % Allowed : 13.68 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.18), residues: 2028 helix: 3.25 (0.12), residues: 1560 sheet: -0.48 (0.34), residues: 204 loop : 0.18 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 277 HIS 0.002 0.000 HIS J 99 PHE 0.010 0.001 PHE F 53 TYR 0.016 0.002 TYR C 67 ARG 0.003 0.000 ARG K 278 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 1295) hydrogen bonds : angle 3.54496 ( 3813) SS BOND : bond 0.00202 ( 36) SS BOND : angle 0.69116 ( 72) covalent geometry : bond 0.00226 (17136) covalent geometry : angle 0.46569 (23280) ********************** 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 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 2.451 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: L 24 ARG cc_start: 0.5285 (mtp180) cc_final: 0.4974 (mmm-85) REVERT: L 43 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7089 (mm-30) REVERT: L 197 ARG cc_start: 0.5036 (tpt170) cc_final: 0.4149 (ppt170) REVERT: L 233 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7868 (ttt180) REVERT: L 271 GLU cc_start: 0.6991 (tt0) cc_final: 0.6382 (tp30) REVERT: L 278 ARG cc_start: 0.3971 (OUTLIER) cc_final: 0.3750 (ttp-110) REVERT: A 43 GLU cc_start: 0.7948 (mt-10) cc_final: 0.6950 (pm20) REVERT: A 86 VAL cc_start: 0.7678 (t) cc_final: 0.7313 (m) REVERT: A 197 ARG cc_start: 0.6060 (ttt180) cc_final: 0.5579 (tpp80) REVERT: A 233 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7776 (ttt180) REVERT: A 238 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7670 (mttm) REVERT: A 279 LYS cc_start: 0.4474 (OUTLIER) cc_final: 0.4113 (ttmt) REVERT: B 24 ARG cc_start: 0.5357 (mtp180) cc_final: 0.4950 (mmm-85) REVERT: B 43 GLU cc_start: 0.8031 (tt0) cc_final: 0.7466 (mp0) REVERT: B 86 VAL cc_start: 0.7776 (t) cc_final: 0.7485 (m) REVERT: B 197 ARG cc_start: 0.6090 (ttt180) cc_final: 0.5581 (tpp80) REVERT: B 233 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7752 (ttt180) REVERT: B 239 GLU cc_start: 0.8428 (tt0) cc_final: 0.7883 (tp30) REVERT: C 24 ARG cc_start: 0.5469 (mtm180) cc_final: 0.5207 (mmm-85) REVERT: C 43 GLU cc_start: 0.7906 (tt0) cc_final: 0.7335 (mp0) REVERT: C 197 ARG cc_start: 0.6062 (ttt180) cc_final: 0.5225 (ttp80) REVERT: C 233 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7867 (ttt180) REVERT: D 24 ARG cc_start: 0.5374 (mtp180) cc_final: 0.5049 (mmm-85) REVERT: D 43 GLU cc_start: 0.8026 (tt0) cc_final: 0.7471 (mp0) REVERT: D 197 ARG cc_start: 0.5964 (ttm170) cc_final: 0.4857 (ppt170) REVERT: D 233 ARG cc_start: 0.8286 (ttm170) cc_final: 0.7771 (ttt180) REVERT: D 239 GLU cc_start: 0.8492 (tt0) cc_final: 0.8247 (tt0) REVERT: D 268 ASN cc_start: 0.8009 (m-40) cc_final: 0.7678 (m110) REVERT: E 24 ARG cc_start: 0.5241 (mtp180) cc_final: 0.4837 (mmm-85) REVERT: E 43 GLU cc_start: 0.7978 (tt0) cc_final: 0.7383 (mp0) REVERT: E 197 ARG cc_start: 0.6075 (ttt180) cc_final: 0.5563 (tpp80) REVERT: E 239 GLU cc_start: 0.8385 (tp30) cc_final: 0.8164 (tt0) REVERT: F 24 ARG cc_start: 0.5296 (mtp180) cc_final: 0.4081 (mtp-110) REVERT: F 43 GLU cc_start: 0.8037 (tt0) cc_final: 0.7499 (mp0) REVERT: F 197 ARG cc_start: 0.6171 (ttt180) cc_final: 0.5667 (tpp80) REVERT: F 233 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7807 (ttt180) REVERT: F 238 LYS cc_start: 0.8188 (mttp) cc_final: 0.7801 (mttm) REVERT: G 24 ARG cc_start: 0.5311 (mtm180) cc_final: 0.4944 (mmm-85) REVERT: G 43 GLU cc_start: 0.7973 (tt0) cc_final: 0.7436 (mp0) REVERT: G 85 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8282 (tpp) REVERT: G 197 ARG cc_start: 0.6105 (ttt180) cc_final: 0.5612 (tpp80) REVERT: G 233 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7769 (ttt180) REVERT: G 239 GLU cc_start: 0.8377 (tp30) cc_final: 0.7775 (tp30) REVERT: H 24 ARG cc_start: 0.5338 (mtp180) cc_final: 0.5019 (mmm-85) REVERT: H 43 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: H 86 VAL cc_start: 0.7797 (t) cc_final: 0.7446 (m) REVERT: H 197 ARG cc_start: 0.6140 (ttt180) cc_final: 0.5201 (ttp80) REVERT: H 233 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7912 (ttt180) REVERT: H 239 GLU cc_start: 0.8443 (tp30) cc_final: 0.8150 (tt0) REVERT: H 268 ASN cc_start: 0.8187 (m-40) cc_final: 0.7830 (m-40) REVERT: I 43 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: I 86 VAL cc_start: 0.7817 (t) cc_final: 0.7484 (m) REVERT: I 100 GLN cc_start: 0.4628 (OUTLIER) cc_final: 0.4188 (tt0) REVERT: I 197 ARG cc_start: 0.6167 (ttt180) cc_final: 0.5676 (tpp80) REVERT: I 233 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7747 (ttt180) REVERT: J 24 ARG cc_start: 0.5360 (mtp180) cc_final: 0.5065 (mmm-85) REVERT: J 43 GLU cc_start: 0.7827 (tp30) cc_final: 0.7362 (mp0) REVERT: J 85 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: J 86 VAL cc_start: 0.7722 (t) cc_final: 0.7423 (m) REVERT: J 197 ARG cc_start: 0.6132 (ttt180) cc_final: 0.5604 (tpp80) REVERT: J 233 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7796 (ttt180) REVERT: K 24 ARG cc_start: 0.5176 (mtp180) cc_final: 0.4784 (mmm-85) REVERT: K 43 GLU cc_start: 0.7876 (tp30) cc_final: 0.7334 (mp0) REVERT: K 86 VAL cc_start: 0.7722 (t) cc_final: 0.7365 (m) REVERT: K 197 ARG cc_start: 0.5995 (ttt180) cc_final: 0.5020 (ttp80) REVERT: K 233 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7779 (ttt180) outliers start: 12 outliers final: 2 residues processed: 240 average time/residue: 4.0210 time to fit residues: 1053.0843 Evaluate side-chains 245 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 234 time to evaluate : 4.041 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 181 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 179 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 273 ASN B 273 ASN C 273 ASN D 273 ASN E 273 ASN F 268 ASN F 273 ASN H 273 ASN I 207 ASN I 268 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 = 0.3806 r_free = 0.3806 target = 0.169226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127154 restraints weight = 39625.926| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.55 r_work: 0.2849 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2296 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= 0.157 Angle : 0.518 4.292 23352 Z= 0.285 Chirality : 0.040 0.136 2712 Planarity : 0.004 0.038 2856 Dihedral : 3.555 11.998 2280 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.69 % Allowed : 13.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.18), residues: 2028 helix: 3.10 (0.12), residues: 1560 sheet: -0.64 (0.34), residues: 204 loop : 0.11 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 277 HIS 0.003 0.001 HIS L 99 PHE 0.013 0.002 PHE A 53 TYR 0.021 0.003 TYR B 67 ARG 0.003 0.000 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 1295) hydrogen bonds : angle 3.71817 ( 3813) SS BOND : bond 0.00296 ( 36) SS BOND : angle 0.90996 ( 72) covalent geometry : bond 0.00343 (17136) covalent geometry : angle 0.51616 (23280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27246.64 seconds wall clock time: 463 minutes 57.34 seconds (27837.34 seconds total)