Starting phenix.real_space_refine on Sat Jul 4 14:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqh_23947/07_2026/7mqh_23947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqh_23947/07_2026/7mqh_23947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mqh_23947/07_2026/7mqh_23947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqh_23947/07_2026/7mqh_23947.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqh_23947/07_2026/7mqh_23947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqh_23947/07_2026/7mqh_23947.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mqh_23947/07_2026/7mqh_23947.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqh_23947/07_2026/7mqh_23947.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11504 atoms to isotropic. 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 P 16 5.49 5 S 48 5.16 5 C 8040 2.51 5 N 2312 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12736 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Restraints were copied for chains: C, E, G, I, K, M, O, D, F, H, J, L, N, P Time building chain proxies: 1.81, per 1000 atoms: 0.14 Number of scatterers: 12736 At special positions: 0 Unit cell: (105.4, 105.4, 88.04, 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 48 16.00 P 16 15.00 O 2320 8.00 N 2312 7.00 C 8040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 590.8 milliseconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 45.4% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 4.007A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.606A pdb=" N ASP A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 4.007A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 155 removed outlier: 3.606A pdb=" N ASP C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 4.007A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.606A pdb=" N ASP E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 175 through 196 Proline residue: E 187 - end of helix Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 80 through 93 removed outlier: 4.007A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.606A pdb=" N ASP G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 71 Processing helix chain 'I' and resid 80 through 93 removed outlier: 4.007A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 145 through 155 removed outlier: 3.606A pdb=" N ASP I 155 " --> pdb=" O TYR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 4.007A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 removed outlier: 3.606A pdb=" N ASP K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 4.008A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 117 through 127 Processing helix chain 'M' and resid 145 through 155 removed outlier: 3.605A pdb=" N ASP M 155 " --> pdb=" O TYR M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 4.007A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 117 through 127 Processing helix chain 'O' and resid 145 through 155 removed outlier: 3.606A pdb=" N ASP O 155 " --> pdb=" O TYR O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 173 Processing helix chain 'O' and resid 175 through 196 Proline residue: O 187 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.163A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 23 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.163A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA C 23 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.162A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA E 23 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.162A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.162A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA I 23 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.163A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA K 23 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.161A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU M 27 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL M 41 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP M 25 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU M 43 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA M 23 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 8 removed outlier: 6.163A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1656 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: 1.95 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4237 1.34 - 1.46: 2332 1.46 - 1.58: 6343 1.58 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 13000 Sorted by residual: bond pdb=" N ASP M 47 " pdb=" CA ASP M 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 6.05e+00 bond pdb=" N ASP O 47 " pdb=" CA ASP O 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" N ASP C 47 " pdb=" CA ASP C 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" N ASP E 47 " pdb=" CA ASP E 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" N ASP G 47 " pdb=" CA ASP G 47 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 5.99e+00 ... (remaining 12995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 15951 1.22 - 2.45: 1440 2.45 - 3.67: 289 3.67 - 4.89: 64 4.89 - 6.11: 16 Bond angle restraints: 17760 Sorted by residual: angle pdb=" C SER M 136 " pdb=" N SER M 137 " pdb=" CA SER M 137 " ideal model delta sigma weight residual 121.87 115.76 6.11 1.64e+00 3.72e-01 1.39e+01 angle pdb=" C SER K 136 " pdb=" N SER K 137 " pdb=" CA SER K 137 " ideal model delta sigma weight residual 121.87 115.80 6.07 1.64e+00 3.72e-01 1.37e+01 angle pdb=" C SER A 136 " pdb=" N SER A 137 " pdb=" CA SER A 137 " ideal model delta sigma weight residual 121.87 115.80 6.07 1.64e+00 3.72e-01 1.37e+01 angle pdb=" C SER C 136 " pdb=" N SER C 137 " pdb=" CA SER C 137 " ideal model delta sigma weight residual 121.87 115.80 6.07 1.64e+00 3.72e-01 1.37e+01 angle pdb=" C SER O 136 " pdb=" N SER O 137 " pdb=" CA SER O 137 " ideal model delta sigma weight residual 121.87 115.80 6.07 1.64e+00 3.72e-01 1.37e+01 ... (remaining 17755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 7023 15.41 - 30.81: 489 30.81 - 46.22: 112 46.22 - 61.62: 40 61.62 - 77.03: 8 Dihedral angle restraints: 7672 sinusoidal: 2888 harmonic: 4784 Sorted by residual: dihedral pdb=" CA PHE M 78 " pdb=" C PHE M 78 " pdb=" N HIS M 79 " pdb=" CA HIS M 79 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA PHE O 78 " pdb=" C PHE O 78 " pdb=" N HIS O 79 " pdb=" CA HIS O 79 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 804 0.030 - 0.059: 680 0.059 - 0.089: 390 0.089 - 0.119: 205 0.119 - 0.148: 57 Chirality restraints: 2136 Sorted by residual: chirality pdb=" CA ILE E 53 " pdb=" N ILE E 53 " pdb=" C ILE E 53 " pdb=" CB ILE E 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE I 53 " pdb=" N ILE I 53 " pdb=" C ILE I 53 " pdb=" CB ILE I 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE G 53 " pdb=" N ILE G 53 " pdb=" C ILE G 53 " pdb=" CB ILE G 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 2133 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 48 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C GLY O 48 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY O 48 " -0.011 2.00e-02 2.50e+03 pdb=" N THR O 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 48 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C GLY I 48 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY I 48 " -0.011 2.00e-02 2.50e+03 pdb=" N THR I 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 48 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C GLY E 48 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY E 48 " 0.011 2.00e-02 2.50e+03 pdb=" N THR E 49 " 0.010 2.00e-02 2.50e+03 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4221 2.86 - 3.37: 11685 3.37 - 3.88: 21260 3.88 - 4.39: 25670 4.39 - 4.90: 42210 Nonbonded interactions: 105046 Sorted by model distance: nonbonded pdb=" OH TYR K 112 " pdb=" OE2 GLU K 124 " model vdw 2.350 3.040 nonbonded pdb=" OH TYR A 112 " pdb=" OE2 GLU A 124 " model vdw 2.350 3.040 nonbonded pdb=" OH TYR G 112 " pdb=" OE2 GLU G 124 " model vdw 2.350 3.040 nonbonded pdb=" OH TYR O 112 " pdb=" OE2 GLU O 124 " model vdw 2.350 3.040 nonbonded pdb=" OH TYR C 112 " pdb=" OE2 GLU C 124 " model vdw 2.350 3.040 ... (remaining 105041 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.540 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 13000 Z= 0.315 Angle : 0.808 6.114 17760 Z= 0.499 Chirality : 0.056 0.148 2136 Planarity : 0.005 0.023 2216 Dihedral : 12.351 77.028 4552 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1624 helix: 0.78 (0.19), residues: 704 sheet: 0.48 (0.21), residues: 248 loop : 0.78 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 37 TYR 0.012 0.003 TYR I 17 PHE 0.017 0.002 PHE E 78 TRP 0.017 0.004 TRP O 139 HIS 0.007 0.002 HIS E 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.31 (13000) covalent geometry : angle 0.80796 / 0.50 (17760) hydrogen bonds : bond 0.10308 / 7.08 ( 552) hydrogen bonds : angle 7.63973 / 5.57 ( 1656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.426 Fit side-chains REVERT: A 27 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7920 (mm-30) REVERT: C 27 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7860 (mm-30) REVERT: E 27 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7827 (mm-30) REVERT: G 27 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7903 (mm-30) REVERT: I 27 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7867 (mm-30) REVERT: K 27 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7903 (mm-30) REVERT: O 27 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7842 (mm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1145 time to fit residues: 22.5617 Evaluate side-chains 112 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.089739 restraints weight = 15337.266| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 0.90 r_work: 0.2826 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 13000 Z= 0.151 Angle : 0.482 4.527 17760 Z= 0.263 Chirality : 0.044 0.130 2136 Planarity : 0.004 0.025 2216 Dihedral : 5.524 39.753 1944 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.21), residues: 1624 helix: 1.82 (0.20), residues: 704 sheet: 0.84 (0.24), residues: 248 loop : 0.44 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 175 TYR 0.009 0.002 TYR O 17 PHE 0.015 0.002 PHE K 78 TRP 0.004 0.001 TRP M 197 HIS 0.003 0.001 HIS E 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (13000) covalent geometry : angle 0.48165 / 0.26 (17760) hydrogen bonds : bond 0.04308 / 2.98 ( 552) hydrogen bonds : angle 6.39200 / 4.68 ( 1656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.483 Fit side-chains REVERT: A 27 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 120 GLU cc_start: 0.8218 (mp0) cc_final: 0.7824 (mp0) REVERT: C 27 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 120 GLU cc_start: 0.8201 (mp0) cc_final: 0.7801 (mp0) REVERT: E 27 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8376 (mm-30) REVERT: E 120 GLU cc_start: 0.8210 (mp0) cc_final: 0.7821 (mp0) REVERT: G 27 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8365 (mm-30) REVERT: G 120 GLU cc_start: 0.8225 (mp0) cc_final: 0.7837 (mp0) REVERT: I 27 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8342 (mm-30) REVERT: I 120 GLU cc_start: 0.8205 (mp0) cc_final: 0.7819 (mp0) REVERT: K 27 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8362 (mm-30) REVERT: K 120 GLU cc_start: 0.8227 (mp0) cc_final: 0.7837 (mp0) REVERT: M 8 GLN cc_start: 0.9269 (mm-40) cc_final: 0.9020 (mp10) REVERT: M 27 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8278 (mm-30) REVERT: O 27 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8332 (mm-30) REVERT: O 120 GLU cc_start: 0.8205 (mp0) cc_final: 0.7821 (mp0) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1240 time to fit residues: 24.9353 Evaluate side-chains 143 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.099167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.085818 restraints weight = 15518.818| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.02 r_work: 0.2770 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 13000 Z= 0.232 Angle : 0.518 4.462 17760 Z= 0.276 Chirality : 0.046 0.130 2136 Planarity : 0.004 0.036 2216 Dihedral : 5.974 43.986 1944 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.82 % Allowed : 5.67 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1624 helix: 1.54 (0.20), residues: 704 sheet: 0.77 (0.24), residues: 240 loop : -0.22 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 82 TYR 0.011 0.002 TYR I 17 PHE 0.015 0.002 PHE O 78 TRP 0.003 0.001 TRP K 197 HIS 0.004 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 (13000) covalent geometry : angle 0.51798 / 0.28 (17760) hydrogen bonds : bond 0.04970 / 3.42 ( 552) hydrogen bonds : angle 6.64257 / 4.85 ( 1656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.381 Fit side-chains REVERT: A 27 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8440 (mm-30) REVERT: A 67 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8192 (ttp-170) REVERT: C 27 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8285 (mm-30) REVERT: C 67 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8179 (ttp-170) REVERT: E 27 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8286 (mm-30) REVERT: E 67 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8186 (ttp-170) REVERT: G 27 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8436 (mm-30) REVERT: G 67 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8192 (ttp-170) REVERT: I 27 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8293 (mm-30) REVERT: I 67 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8201 (ttp-170) REVERT: K 27 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8446 (mm-30) REVERT: K 67 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: M 8 GLN cc_start: 0.9333 (mm-40) cc_final: 0.8912 (mp10) REVERT: M 27 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8311 (mm-30) REVERT: O 27 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8288 (mm-30) REVERT: O 67 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8192 (ttp-170) outliers start: 10 outliers final: 3 residues processed: 136 average time/residue: 0.1239 time to fit residues: 23.6174 Evaluate side-chains 139 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 97 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.090980 restraints weight = 15301.148| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.03 r_work: 0.2827 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 13000 Z= 0.094 Angle : 0.387 4.449 17760 Z= 0.216 Chirality : 0.042 0.125 2136 Planarity : 0.003 0.026 2216 Dihedral : 5.375 42.487 1944 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.25 % Allowed : 5.92 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1624 helix: 1.60 (0.20), residues: 712 sheet: 1.09 (0.24), residues: 248 loop : -0.34 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 189 TYR 0.006 0.001 TYR E 17 PHE 0.012 0.001 PHE A 78 TRP 0.002 0.001 TRP M 139 HIS 0.002 0.000 HIS G 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (13000) covalent geometry : angle 0.38707 / 0.22 (17760) hydrogen bonds : bond 0.03358 / 2.32 ( 552) hydrogen bonds : angle 5.87932 / 4.30 ( 1656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.455 Fit side-chains REVERT: A 27 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8494 (mm-30) REVERT: A 67 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8165 (ttp-170) REVERT: A 120 GLU cc_start: 0.8209 (mp0) cc_final: 0.7892 (mp0) REVERT: C 27 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8402 (mm-30) REVERT: C 67 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8162 (ttp-170) REVERT: C 120 GLU cc_start: 0.8195 (mp0) cc_final: 0.7881 (mp0) REVERT: E 27 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8225 (mm-30) REVERT: E 67 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8164 (ttp-170) REVERT: E 120 GLU cc_start: 0.8187 (mp0) cc_final: 0.7871 (mp0) REVERT: G 27 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8475 (mm-30) REVERT: G 67 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8155 (ttp-170) REVERT: G 120 GLU cc_start: 0.8199 (mp0) cc_final: 0.7879 (mp0) REVERT: I 27 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8488 (mm-30) REVERT: I 67 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8172 (ttp-170) REVERT: I 120 GLU cc_start: 0.8199 (mp0) cc_final: 0.7884 (mp0) REVERT: K 27 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8484 (mm-30) REVERT: K 67 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8167 (ttp-170) REVERT: K 120 GLU cc_start: 0.8217 (mp0) cc_final: 0.7907 (mp0) REVERT: M 27 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8101 (mm-30) REVERT: M 120 GLU cc_start: 0.8267 (mp0) cc_final: 0.7970 (mp0) REVERT: O 27 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8247 (mm-30) REVERT: O 67 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8169 (ttp-170) REVERT: O 120 GLU cc_start: 0.8190 (mp0) cc_final: 0.7880 (mp0) outliers start: 3 outliers final: 0 residues processed: 145 average time/residue: 0.1219 time to fit residues: 24.7040 Evaluate side-chains 143 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 42 GLN E 42 GLN G 42 GLN I 42 GLN K 42 GLN M 42 GLN O 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.087930 restraints weight = 15358.642| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 0.98 r_work: 0.2795 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 13000 Z= 0.171 Angle : 0.446 4.453 17760 Z= 0.240 Chirality : 0.044 0.127 2136 Planarity : 0.003 0.028 2216 Dihedral : 5.682 43.377 1944 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.74 % Allowed : 7.89 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1624 helix: 1.62 (0.20), residues: 696 sheet: 1.01 (0.26), residues: 240 loop : -0.55 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 169 TYR 0.009 0.002 TYR A 17 PHE 0.013 0.002 PHE A 78 TRP 0.002 0.001 TRP K 197 HIS 0.003 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (13000) covalent geometry : angle 0.44614 / 0.24 (17760) hydrogen bonds : bond 0.04290 / 2.96 ( 552) hydrogen bonds : angle 6.27969 / 4.59 ( 1656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.523 Fit side-chains REVERT: A 27 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 67 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: A 120 GLU cc_start: 0.8275 (mp0) cc_final: 0.7892 (mp0) REVERT: C 27 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8239 (mm-30) REVERT: C 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8210 (ttp-170) REVERT: C 120 GLU cc_start: 0.8270 (mp0) cc_final: 0.7884 (mp0) REVERT: E 27 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8166 (mm-30) REVERT: E 67 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8215 (ttp-170) REVERT: E 120 GLU cc_start: 0.8272 (mp0) cc_final: 0.7891 (mp0) REVERT: G 27 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8263 (mm-30) REVERT: G 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8211 (ttp-170) REVERT: G 120 GLU cc_start: 0.8280 (mp0) cc_final: 0.7898 (mp0) REVERT: I 27 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8270 (mm-30) REVERT: I 67 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8210 (ttp-170) REVERT: I 120 GLU cc_start: 0.8272 (mp0) cc_final: 0.7893 (mp0) REVERT: K 27 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8269 (mm-30) REVERT: K 67 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8217 (ttp-170) REVERT: K 120 GLU cc_start: 0.8281 (mp0) cc_final: 0.7900 (mp0) REVERT: M 27 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8155 (mm-30) REVERT: M 120 GLU cc_start: 0.8155 (mp0) cc_final: 0.7704 (mp0) REVERT: O 27 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8244 (mm-30) REVERT: O 67 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: O 120 GLU cc_start: 0.8273 (mp0) cc_final: 0.7899 (mp0) outliers start: 9 outliers final: 1 residues processed: 150 average time/residue: 0.1169 time to fit residues: 24.8090 Evaluate side-chains 143 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 173 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 42 GLN E 42 GLN G 42 GLN I 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.100651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.088853 restraints weight = 15308.398| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 0.95 r_work: 0.2809 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 13000 Z= 0.144 Angle : 0.421 4.411 17760 Z= 0.229 Chirality : 0.043 0.125 2136 Planarity : 0.003 0.027 2216 Dihedral : 5.624 43.513 1944 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.32 % Allowed : 7.24 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1624 helix: 1.57 (0.20), residues: 704 sheet: 1.10 (0.27), residues: 240 loop : -0.62 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 82 TYR 0.008 0.002 TYR C 17 PHE 0.012 0.002 PHE I 78 TRP 0.002 0.001 TRP M 197 HIS 0.002 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (13000) covalent geometry : angle 0.42124 / 0.23 (17760) hydrogen bonds : bond 0.03963 / 2.73 ( 552) hydrogen bonds : angle 6.12519 / 4.47 ( 1656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.319 Fit side-chains REVERT: A 27 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8320 (mm-30) REVERT: A 67 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8225 (ttp-170) REVERT: A 120 GLU cc_start: 0.8131 (mp0) cc_final: 0.7758 (mp0) REVERT: C 27 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8315 (mm-30) REVERT: C 67 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: C 120 GLU cc_start: 0.8125 (mp0) cc_final: 0.7749 (mp0) REVERT: E 27 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 67 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8220 (ttp-170) REVERT: E 120 GLU cc_start: 0.8127 (mp0) cc_final: 0.7753 (mp0) REVERT: G 27 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8332 (mm-30) REVERT: G 67 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8221 (ttp-170) REVERT: G 120 GLU cc_start: 0.8142 (mp0) cc_final: 0.7768 (mp0) REVERT: I 27 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8312 (mm-30) REVERT: I 67 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8214 (ttp-170) REVERT: I 120 GLU cc_start: 0.8126 (mp0) cc_final: 0.7758 (mp0) REVERT: K 27 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8318 (mm-30) REVERT: K 67 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8224 (ttp-170) REVERT: K 120 GLU cc_start: 0.8137 (mp0) cc_final: 0.7765 (mp0) REVERT: M 27 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8148 (mm-30) REVERT: M 120 GLU cc_start: 0.8131 (mp0) cc_final: 0.7695 (mp0) REVERT: O 27 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8311 (mm-30) REVERT: O 67 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: O 120 GLU cc_start: 0.8127 (mp0) cc_final: 0.7758 (mp0) outliers start: 16 outliers final: 8 residues processed: 150 average time/residue: 0.1191 time to fit residues: 24.9891 Evaluate side-chains 150 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 42 GLN E 42 GLN G 42 GLN I 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.089018 restraints weight = 15219.147| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 0.99 r_work: 0.2810 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 13000 Z= 0.127 Angle : 0.405 4.409 17760 Z= 0.222 Chirality : 0.043 0.124 2136 Planarity : 0.003 0.027 2216 Dihedral : 5.558 43.179 1944 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.23 % Allowed : 6.74 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1624 helix: 1.66 (0.20), residues: 704 sheet: 1.11 (0.28), residues: 240 loop : -0.65 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 82 TYR 0.008 0.001 TYR E 17 PHE 0.012 0.001 PHE G 78 TRP 0.002 0.001 TRP M 197 HIS 0.002 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13000) covalent geometry : angle 0.40519 / 0.22 (17760) hydrogen bonds : bond 0.03775 / 2.60 ( 552) hydrogen bonds : angle 6.00072 / 4.39 ( 1656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.316 Fit side-chains REVERT: A 27 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8282 (mm-30) REVERT: A 67 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8221 (ttp-170) REVERT: A 120 GLU cc_start: 0.8142 (mp0) cc_final: 0.7763 (mp0) REVERT: C 27 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8280 (mm-30) REVERT: C 67 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8206 (ttp-170) REVERT: C 120 GLU cc_start: 0.8135 (mp0) cc_final: 0.7751 (mp0) REVERT: E 27 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8277 (mm-30) REVERT: E 67 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8212 (ttp-170) REVERT: E 120 GLU cc_start: 0.8147 (mp0) cc_final: 0.7771 (mp0) REVERT: G 27 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8282 (mm-30) REVERT: G 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8210 (ttp-170) REVERT: G 120 GLU cc_start: 0.8160 (mp0) cc_final: 0.7780 (mp0) REVERT: I 27 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8271 (mm-30) REVERT: I 67 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8206 (ttp-170) REVERT: I 120 GLU cc_start: 0.8146 (mp0) cc_final: 0.7772 (mp0) REVERT: K 27 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8273 (mm-30) REVERT: K 67 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: K 120 GLU cc_start: 0.8149 (mp0) cc_final: 0.7775 (mp0) REVERT: M 27 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8190 (mm-30) REVERT: M 120 GLU cc_start: 0.8146 (mp0) cc_final: 0.7768 (mp0) REVERT: O 27 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8271 (mm-30) REVERT: O 67 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: O 120 GLU cc_start: 0.8142 (mp0) cc_final: 0.7767 (mp0) outliers start: 15 outliers final: 8 residues processed: 149 average time/residue: 0.1178 time to fit residues: 24.8103 Evaluate side-chains 150 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 42 GLN E 42 GLN G 42 GLN I 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.099287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.087028 restraints weight = 15253.705| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.00 r_work: 0.2776 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 13000 Z= 0.211 Angle : 0.478 4.426 17760 Z= 0.254 Chirality : 0.045 0.130 2136 Planarity : 0.004 0.029 2216 Dihedral : 5.837 44.068 1944 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 6.74 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1624 helix: 1.51 (0.20), residues: 696 sheet: 0.61 (0.29), residues: 240 loop : -0.81 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 169 TYR 0.010 0.002 TYR A 17 PHE 0.013 0.002 PHE C 78 TRP 0.002 0.001 TRP M 139 HIS 0.003 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (13000) covalent geometry : angle 0.47838 / 0.25 (17760) hydrogen bonds : bond 0.04681 / 3.22 ( 552) hydrogen bonds : angle 6.42982 / 4.70 ( 1656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.496 Fit side-chains REVERT: A 27 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8334 (mm-30) REVERT: A 67 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8205 (ttp-170) REVERT: C 27 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 67 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8187 (ttp-170) REVERT: E 27 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8226 (mm-30) REVERT: E 67 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8196 (ttp-170) REVERT: G 27 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8326 (mm-30) REVERT: G 67 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8198 (ttp-170) REVERT: I 27 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8308 (mm-30) REVERT: I 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8194 (ttp-170) REVERT: K 27 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8322 (mm-30) REVERT: K 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8197 (ttp-170) REVERT: M 27 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8210 (mm-30) REVERT: M 67 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8220 (ttp-170) REVERT: O 27 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8182 (mm-30) REVERT: O 67 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8184 (ttp-170) outliers start: 22 outliers final: 15 residues processed: 149 average time/residue: 0.1158 time to fit residues: 24.3255 Evaluate side-chains 157 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 173 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 19 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 42 GLN E 42 GLN G 42 GLN I 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.087922 restraints weight = 15266.041| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.00 r_work: 0.2791 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 13000 Z= 0.154 Angle : 0.428 4.421 17760 Z= 0.233 Chirality : 0.043 0.127 2136 Planarity : 0.003 0.028 2216 Dihedral : 5.726 44.079 1944 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.48 % Allowed : 7.07 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1624 helix: 1.50 (0.20), residues: 704 sheet: 0.54 (0.28), residues: 240 loop : -0.81 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 82 TYR 0.008 0.002 TYR C 17 PHE 0.013 0.002 PHE I 78 TRP 0.002 0.001 TRP M 197 HIS 0.002 0.001 HIS M 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (13000) covalent geometry : angle 0.42783 / 0.23 (17760) hydrogen bonds : bond 0.04081 / 2.81 ( 552) hydrogen bonds : angle 6.19620 / 4.53 ( 1656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.447 Fit side-chains REVERT: A 27 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8268 (mm-30) REVERT: A 67 ARG cc_start: 0.8474 (ttp80) cc_final: 0.8224 (ttp-170) REVERT: A 120 GLU cc_start: 0.8241 (mp0) cc_final: 0.7938 (mp0) REVERT: C 27 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8066 (mm-30) REVERT: C 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: C 120 GLU cc_start: 0.8237 (mp0) cc_final: 0.7932 (mp0) REVERT: E 27 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8055 (mm-30) REVERT: E 67 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8219 (ttp-170) REVERT: E 120 GLU cc_start: 0.8238 (mp0) cc_final: 0.7937 (mp0) REVERT: G 27 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8260 (mm-30) REVERT: G 67 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8213 (ttp-170) REVERT: G 120 GLU cc_start: 0.8255 (mp0) cc_final: 0.7953 (mp0) REVERT: I 27 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8068 (mm-30) REVERT: I 67 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8208 (ttp-170) REVERT: I 120 GLU cc_start: 0.8243 (mp0) cc_final: 0.7945 (mp0) REVERT: K 27 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8260 (mm-30) REVERT: K 67 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8213 (ttp-170) REVERT: K 120 GLU cc_start: 0.8249 (mp0) cc_final: 0.7950 (mp0) REVERT: M 27 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8110 (mm-30) REVERT: M 67 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8206 (ttp-170) REVERT: M 120 GLU cc_start: 0.8247 (mp0) cc_final: 0.7942 (mp0) REVERT: O 27 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8069 (mm-30) REVERT: O 67 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8203 (ttp-170) REVERT: O 120 GLU cc_start: 0.8242 (mp0) cc_final: 0.7942 (mp0) outliers start: 18 outliers final: 11 residues processed: 149 average time/residue: 0.1182 time to fit residues: 24.7116 Evaluate side-chains 153 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 64 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 42 GLN E 42 GLN G 42 GLN I 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.101629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.089378 restraints weight = 15266.104| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.00 r_work: 0.2813 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 13000 Z= 0.117 Angle : 0.394 4.389 17760 Z= 0.217 Chirality : 0.042 0.124 2136 Planarity : 0.003 0.027 2216 Dihedral : 5.536 43.048 1944 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.40 % Allowed : 7.15 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1624 helix: 1.72 (0.20), residues: 696 sheet: 0.73 (0.29), residues: 240 loop : -0.81 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 189 TYR 0.008 0.001 TYR O 17 PHE 0.012 0.001 PHE A 78 TRP 0.003 0.001 TRP M 139 HIS 0.002 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13000) covalent geometry : angle 0.39433 / 0.22 (17760) hydrogen bonds : bond 0.03614 / 2.49 ( 552) hydrogen bonds : angle 5.92051 / 4.33 ( 1656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.417 Fit side-chains REVERT: A 27 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8248 (mm-30) REVERT: A 67 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8206 (ttp-170) REVERT: A 120 GLU cc_start: 0.8287 (mp0) cc_final: 0.8030 (mp0) REVERT: C 27 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8227 (mm-30) REVERT: C 67 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8196 (ttp-170) REVERT: C 120 GLU cc_start: 0.8287 (mp0) cc_final: 0.8032 (mp0) REVERT: E 27 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8227 (mm-30) REVERT: E 67 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8199 (ttp-170) REVERT: E 120 GLU cc_start: 0.8289 (mp0) cc_final: 0.8038 (mp0) REVERT: G 27 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8241 (mm-30) REVERT: G 67 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8194 (ttp-170) REVERT: G 120 GLU cc_start: 0.8299 (mp0) cc_final: 0.8048 (mp0) REVERT: I 27 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8224 (mm-30) REVERT: I 67 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8194 (ttp-170) REVERT: I 120 GLU cc_start: 0.8294 (mp0) cc_final: 0.8044 (mp0) REVERT: K 27 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8246 (mm-30) REVERT: K 67 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8203 (ttp-170) REVERT: K 120 GLU cc_start: 0.8297 (mp0) cc_final: 0.8051 (mp0) REVERT: M 27 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8136 (mm-30) REVERT: M 67 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8193 (ttp-170) REVERT: M 120 GLU cc_start: 0.8290 (mp0) cc_final: 0.8035 (mp0) REVERT: O 27 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8177 (mm-30) REVERT: O 67 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8185 (ttp-170) REVERT: O 120 GLU cc_start: 0.8290 (mp0) cc_final: 0.8040 (mp0) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 0.1302 time to fit residues: 26.9959 Evaluate side-chains 152 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain K residue 173 GLU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 79 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 42 GLN E 42 GLN G 42 GLN I 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.100517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.089822 restraints weight = 15255.605| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 0.87 r_work: 0.2816 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 13000 Z= 0.156 Angle : 0.431 4.404 17760 Z= 0.233 Chirality : 0.044 0.126 2136 Planarity : 0.003 0.027 2216 Dihedral : 5.670 43.357 1944 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.64 % Allowed : 6.91 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.21), residues: 1624 helix: 1.61 (0.20), residues: 696 sheet: 0.55 (0.29), residues: 240 loop : -0.82 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 82 TYR 0.009 0.002 TYR E 17 PHE 0.012 0.002 PHE M 78 TRP 0.002 0.001 TRP M 197 HIS 0.002 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13000) covalent geometry : angle 0.43077 / 0.23 (17760) hydrogen bonds : bond 0.04147 / 2.86 ( 552) hydrogen bonds : angle 6.16972 / 4.51 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.91 seconds wall clock time: 39 minutes 45.32 seconds (2385.32 seconds total)