Starting phenix.real_space_refine on Thu Mar 5 10:34:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqh_23947/03_2026/7mqh_23947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqh_23947/03_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_23947/03_2026/7mqh_23947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqh_23947/03_2026/7mqh_23947.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqh_23947/03_2026/7mqh_23947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqh_23947/03_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-5986/lib/python3.9/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: 1.61, per 1000 atoms: 0.13 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: 0.94 Conformation dependent library (CDL) restraints added in 473.1 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: 0.29 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: 1.76 Time building geometry restraints manager: 1.30 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: 7055 15.41 - 30.81: 497 30.81 - 46.22: 128 46.22 - 61.62: 48 61.62 - 77.03: 40 Dihedral angle restraints: 7768 sinusoidal: 2984 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 7765 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: 0.04 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.990 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 13.706 77.028 4648 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 covalent geometry : bond 0.00719 (13000) covalent geometry : angle 0.80796 (17760) hydrogen bonds : bond 0.10308 ( 552) hydrogen bonds : angle 7.63973 ( 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 : 0.463 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: 0.1191 time to fit residues: 23.3765 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 : 0.438 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3066 r_free = 0.3066 target = 0.100505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.088746 restraints weight = 15343.924| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 0.97 r_work: 0.2801 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1244 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= 0.152 Angle : 0.482 4.454 17760 Z= 0.263 Chirality : 0.044 0.130 2136 Planarity : 0.004 0.025 2216 Dihedral : 10.771 63.792 2040 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 1.81 (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 G 17 PHE 0.015 0.002 PHE K 78 TRP 0.004 0.001 TRP C 197 HIS 0.003 0.001 HIS M 7 Details of bonding type rmsd covalent geometry : bond 0.00359 (13000) covalent geometry : angle 0.48209 (17760) hydrogen bonds : bond 0.04334 ( 552) hydrogen bonds : angle 6.40817 ( 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 : 0.459 Fit side-chains REVERT: A 27 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 120 GLU cc_start: 0.8129 (mp0) cc_final: 0.7676 (mp0) REVERT: C 27 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8281 (mm-30) REVERT: C 120 GLU cc_start: 0.8113 (mp0) cc_final: 0.7655 (mp0) REVERT: E 27 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8296 (mm-30) REVERT: E 120 GLU cc_start: 0.8122 (mp0) cc_final: 0.7672 (mp0) REVERT: G 27 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8313 (mm-30) REVERT: G 120 GLU cc_start: 0.8135 (mp0) cc_final: 0.7683 (mp0) REVERT: I 27 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8298 (mm-30) REVERT: I 120 GLU cc_start: 0.8120 (mp0) cc_final: 0.7674 (mp0) REVERT: K 27 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8315 (mm-30) REVERT: K 120 GLU cc_start: 0.8141 (mp0) cc_final: 0.7692 (mp0) REVERT: M 8 GLN cc_start: 0.9257 (mm-40) cc_final: 0.9023 (mp10) REVERT: M 27 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8206 (mm-30) REVERT: O 27 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8294 (mm-30) REVERT: O 120 GLU cc_start: 0.8123 (mp0) cc_final: 0.7681 (mp0) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1273 time to fit residues: 25.6601 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 : 0.320 ------------------------------------------------------------------------------- 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: 0.9990 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3058 r_free = 0.3058 target = 0.100235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.086706 restraints weight = 15415.894| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.03 r_work: 0.2782 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13000 Z= 0.181 Angle : 0.475 4.458 17760 Z= 0.256 Chirality : 0.045 0.127 2136 Planarity : 0.004 0.027 2216 Dihedral : 10.481 63.728 2040 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % 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: 1.20 (0.21), residues: 1624 helix: 1.63 (0.20), residues: 704 sheet: 0.94 (0.23), residues: 248 loop : -0.08 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 82 TYR 0.010 0.002 TYR G 17 PHE 0.014 0.002 PHE C 78 TRP 0.003 0.001 TRP A 197 HIS 0.003 0.001 HIS M 7 Details of bonding type rmsd covalent geometry : bond 0.00438 (13000) covalent geometry : angle 0.47476 (17760) hydrogen bonds : bond 0.04461 ( 552) hydrogen bonds : angle 6.43775 ( 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 144 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.484 Fit side-chains REVERT: A 27 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 67 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8212 (ttp-170) REVERT: C 27 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8368 (mm-30) REVERT: C 67 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8205 (ttp-170) REVERT: E 27 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8228 (mm-30) REVERT: E 67 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8203 (ttp-170) REVERT: G 27 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8408 (mm-30) REVERT: G 67 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8205 (ttp-170) REVERT: I 27 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8386 (mm-30) REVERT: I 67 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: K 27 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8405 (mm-30) REVERT: K 67 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8220 (ttp-170) REVERT: M 8 GLN cc_start: 0.9321 (mm-40) cc_final: 0.8918 (mp10) REVERT: M 27 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8214 (mm-30) REVERT: O 27 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8368 (mm-30) REVERT: O 67 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8222 (ttp-170) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1365 time to fit residues: 27.2930 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 : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 97 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.088742 restraints weight = 15484.206| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.00 r_work: 0.2800 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1790 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= 0.131 Angle : 0.417 4.418 17760 Z= 0.229 Chirality : 0.043 0.125 2136 Planarity : 0.003 0.027 2216 Dihedral : 10.409 63.702 2040 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.82 % Allowed : 5.51 % Favored : 93.67 % 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: 1.13 (0.21), residues: 1624 helix: 1.63 (0.20), residues: 704 sheet: 1.17 (0.25), residues: 248 loop : -0.32 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 82 TYR 0.008 0.001 TYR G 17 PHE 0.013 0.001 PHE K 78 TRP 0.002 0.001 TRP A 197 HIS 0.002 0.001 HIS K 7 Details of bonding type rmsd covalent geometry : bond 0.00308 (13000) covalent geometry : angle 0.41686 (17760) hydrogen bonds : bond 0.03849 ( 552) hydrogen bonds : angle 6.14361 ( 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 153 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.426 Fit side-chains REVERT: A 27 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8255 (mm-30) REVERT: A 67 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: A 120 GLU cc_start: 0.8135 (mp0) cc_final: 0.7743 (mp0) REVERT: C 27 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8222 (mm-30) REVERT: C 67 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8213 (ttp-170) REVERT: C 120 GLU cc_start: 0.8127 (mp0) cc_final: 0.7790 (mp0) REVERT: E 27 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8256 (mm-30) REVERT: E 67 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8206 (ttp-170) REVERT: E 120 GLU cc_start: 0.8150 (mp0) cc_final: 0.7760 (mp0) REVERT: G 27 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8269 (mm-30) REVERT: G 67 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8211 (ttp-170) REVERT: G 120 GLU cc_start: 0.8140 (mp0) cc_final: 0.7748 (mp0) REVERT: I 27 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8250 (mm-30) REVERT: I 67 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8219 (ttp-170) REVERT: I 120 GLU cc_start: 0.8141 (mp0) cc_final: 0.7755 (mp0) REVERT: K 27 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8258 (mm-30) REVERT: K 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8216 (ttp-170) REVERT: K 120 GLU cc_start: 0.8165 (mp0) cc_final: 0.7778 (mp0) REVERT: M 27 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8080 (mm-30) REVERT: M 120 GLU cc_start: 0.8136 (mp0) cc_final: 0.7754 (mp0) REVERT: O 27 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8229 (mm-30) REVERT: O 67 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8201 (ttp-170) REVERT: O 120 GLU cc_start: 0.8268 (mp0) cc_final: 0.7958 (mp0) outliers start: 10 outliers final: 0 residues processed: 147 average time/residue: 0.1277 time to fit residues: 26.0037 Evaluate side-chains 142 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 20.0000 chunk 22 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3059 r_free = 0.3059 target = 0.099314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.087098 restraints weight = 15358.331| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 0.99 r_work: 0.2779 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1866 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= 0.214 Angle : 0.485 4.385 17760 Z= 0.259 Chirality : 0.046 0.130 2136 Planarity : 0.004 0.031 2216 Dihedral : 10.505 63.726 2040 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.66 % Allowed : 7.32 % 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: 0.77 (0.21), residues: 1624 helix: 1.49 (0.20), residues: 696 sheet: 0.92 (0.27), residues: 240 loop : -0.64 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 82 TYR 0.010 0.002 TYR G 17 PHE 0.014 0.002 PHE M 78 TRP 0.003 0.001 TRP A 197 HIS 0.003 0.001 HIS M 7 Details of bonding type rmsd covalent geometry : bond 0.00520 (13000) covalent geometry : angle 0.48517 (17760) hydrogen bonds : bond 0.04734 ( 552) hydrogen bonds : angle 6.48374 ( 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 150 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.488 Fit side-chains REVERT: A 27 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 67 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8217 (ttp-170) REVERT: C 27 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8200 (mm-30) REVERT: C 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8207 (ttp-170) REVERT: E 27 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8317 (mm-30) REVERT: E 67 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8216 (ttp-170) REVERT: G 27 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8327 (mm-30) REVERT: G 67 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: I 27 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8330 (mm-30) REVERT: I 67 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8213 (ttp-170) REVERT: K 27 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8324 (mm-30) REVERT: K 67 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8215 (ttp-170) REVERT: M 27 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8193 (mm-30) REVERT: O 27 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8222 (mm-30) REVERT: O 67 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8208 (ttp-170) outliers start: 8 outliers final: 1 residues processed: 150 average time/residue: 0.1327 time to fit residues: 27.9585 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 : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN G 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.102054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.089863 restraints weight = 15167.728| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.00 r_work: 0.2825 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1980 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= 0.099 Angle : 0.386 4.412 17760 Z= 0.214 Chirality : 0.042 0.122 2136 Planarity : 0.003 0.026 2216 Dihedral : 10.330 63.715 2040 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.15 % Allowed : 7.32 % Favored : 91.53 % 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: 0.92 (0.21), residues: 1624 helix: 1.60 (0.20), residues: 712 sheet: 1.07 (0.27), residues: 240 loop : -0.63 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 189 TYR 0.007 0.001 TYR K 17 PHE 0.012 0.001 PHE M 78 TRP 0.002 0.001 TRP G 139 HIS 0.001 0.001 HIS E 116 Details of bonding type rmsd covalent geometry : bond 0.00219 (13000) covalent geometry : angle 0.38649 (17760) hydrogen bonds : bond 0.03462 ( 552) hydrogen bonds : angle 5.88844 ( 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 156 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.477 Fit side-chains REVERT: A 27 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8370 (mm-30) REVERT: A 67 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8204 (ttp-170) REVERT: A 120 GLU cc_start: 0.8293 (mp0) cc_final: 0.8015 (mp0) REVERT: C 27 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8348 (mm-30) REVERT: C 67 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8198 (ttp-170) REVERT: C 120 GLU cc_start: 0.8285 (mp0) cc_final: 0.8006 (mp0) REVERT: E 27 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8342 (mm-30) REVERT: E 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8207 (ttp-170) REVERT: E 120 GLU cc_start: 0.8299 (mp0) cc_final: 0.8018 (mp0) REVERT: G 27 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8372 (mm-30) REVERT: G 67 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8197 (ttp-170) REVERT: G 120 GLU cc_start: 0.8305 (mp0) cc_final: 0.8026 (mp0) REVERT: I 27 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8359 (mm-30) REVERT: I 67 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8201 (ttp-170) REVERT: I 120 GLU cc_start: 0.8294 (mp0) cc_final: 0.8020 (mp0) REVERT: K 27 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8370 (mm-30) REVERT: K 67 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8202 (ttp-170) REVERT: K 120 GLU cc_start: 0.8305 (mp0) cc_final: 0.8030 (mp0) REVERT: M 27 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8077 (mm-30) REVERT: M 120 GLU cc_start: 0.8298 (mp0) cc_final: 0.8025 (mp0) REVERT: O 27 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8346 (mm-30) REVERT: O 67 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8194 (ttp-170) REVERT: O 120 GLU cc_start: 0.8296 (mp0) cc_final: 0.8018 (mp0) outliers start: 14 outliers final: 7 residues processed: 149 average time/residue: 0.1343 time to fit residues: 27.8609 Evaluate side-chains 149 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain O residue 61 SER 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: 0.6980 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: 0.6980 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN G 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.087398 restraints weight = 15216.213| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 0.99 r_work: 0.2783 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 13000 Z= 0.199 Angle : 0.466 4.421 17760 Z= 0.249 Chirality : 0.045 0.130 2136 Planarity : 0.004 0.028 2216 Dihedral : 10.453 63.719 2040 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.89 % Allowed : 6.74 % 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: 0.66 (0.21), residues: 1624 helix: 1.55 (0.20), residues: 696 sheet: 0.70 (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 A 82 TYR 0.010 0.002 TYR A 17 PHE 0.013 0.002 PHE M 78 TRP 0.002 0.001 TRP M 139 HIS 0.003 0.001 HIS M 7 Details of bonding type rmsd covalent geometry : bond 0.00483 (13000) covalent geometry : angle 0.46620 (17760) hydrogen bonds : bond 0.04552 ( 552) hydrogen bonds : angle 6.36839 ( 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 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.432 Fit side-chains REVERT: A 27 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8358 (mm-30) REVERT: A 67 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8219 (ttp-170) REVERT: A 120 GLU cc_start: 0.8280 (mp0) cc_final: 0.7896 (mp0) REVERT: C 27 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8288 (mm-30) REVERT: C 67 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8220 (ttp-170) REVERT: C 120 GLU cc_start: 0.8270 (mp0) cc_final: 0.7882 (mp0) REVERT: E 27 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8346 (mm-30) REVERT: E 67 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8217 (ttp-170) REVERT: E 120 GLU cc_start: 0.8268 (mp0) cc_final: 0.7887 (mp0) REVERT: G 27 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8305 (mm-30) REVERT: G 67 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8216 (ttp-170) REVERT: G 120 GLU cc_start: 0.8280 (mp0) cc_final: 0.7899 (mp0) REVERT: I 27 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8350 (mm-30) REVERT: I 67 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8208 (ttp-170) REVERT: I 120 GLU cc_start: 0.8272 (mp0) cc_final: 0.7894 (mp0) REVERT: K 27 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8305 (mm-30) REVERT: K 67 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8214 (ttp-170) REVERT: K 120 GLU cc_start: 0.8286 (mp0) cc_final: 0.7909 (mp0) REVERT: M 27 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8165 (mm-30) REVERT: M 67 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8249 (ttp-170) REVERT: M 120 GLU cc_start: 0.8276 (mp0) cc_final: 0.7896 (mp0) REVERT: O 27 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8293 (mm-30) REVERT: O 67 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8198 (ttp-170) REVERT: O 120 GLU cc_start: 0.8276 (mp0) cc_final: 0.7897 (mp0) outliers start: 23 outliers final: 19 residues processed: 150 average time/residue: 0.1255 time to fit residues: 26.2170 Evaluate side-chains 161 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN 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 42 GLN 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 42 GLN 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 42 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN G 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.089129 restraints weight = 15075.281| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 0.98 r_work: 0.2809 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2011 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= 0.125 Angle : 0.405 4.365 17760 Z= 0.222 Chirality : 0.043 0.125 2136 Planarity : 0.003 0.027 2216 Dihedral : 10.359 63.695 2040 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.81 % Allowed : 6.83 % 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: 0.74 (0.21), residues: 1624 helix: 1.59 (0.20), residues: 704 sheet: 0.77 (0.28), residues: 240 loop : -0.79 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 82 TYR 0.008 0.001 TYR C 17 PHE 0.012 0.001 PHE I 78 TRP 0.002 0.001 TRP O 139 HIS 0.002 0.001 HIS M 7 Details of bonding type rmsd covalent geometry : bond 0.00291 (13000) covalent geometry : angle 0.40527 (17760) hydrogen bonds : bond 0.03752 ( 552) hydrogen bonds : angle 6.01630 ( 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 : 0.492 Fit side-chains REVERT: A 27 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8240 (mm-30) REVERT: A 67 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8198 (ttp-170) REVERT: A 120 GLU cc_start: 0.8094 (mp0) cc_final: 0.7716 (mp0) REVERT: C 27 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8257 (mm-30) REVERT: C 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8207 (ttp-170) REVERT: C 120 GLU cc_start: 0.8077 (mp0) cc_final: 0.7683 (mp0) REVERT: E 27 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8222 (mm-30) REVERT: E 67 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8202 (ttp-170) REVERT: E 120 GLU cc_start: 0.8081 (mp0) cc_final: 0.7709 (mp0) REVERT: G 27 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8225 (mm-30) REVERT: G 67 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8193 (ttp-170) REVERT: G 120 GLU cc_start: 0.8103 (mp0) cc_final: 0.7727 (mp0) REVERT: I 27 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8229 (mm-30) REVERT: I 67 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8192 (ttp-170) REVERT: I 120 GLU cc_start: 0.8084 (mp0) cc_final: 0.7715 (mp0) REVERT: K 27 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8264 (mm-30) REVERT: K 67 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8202 (ttp-170) REVERT: K 120 GLU cc_start: 0.8108 (mp0) cc_final: 0.7738 (mp0) REVERT: M 27 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8171 (mm-30) REVERT: M 67 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8205 (ttp-170) REVERT: M 120 GLU cc_start: 0.8079 (mp0) cc_final: 0.7713 (mp0) REVERT: O 27 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8259 (mm-30) REVERT: O 67 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8184 (ttp-170) REVERT: O 120 GLU cc_start: 0.8093 (mp0) cc_final: 0.7710 (mp0) outliers start: 22 outliers final: 18 residues processed: 150 average time/residue: 0.1301 time to fit residues: 27.1941 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 : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN 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 42 GLN 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 42 GLN 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 42 GLN 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: 7.9990 chunk 149 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN G 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.100266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.088028 restraints weight = 15152.254| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 0.99 r_work: 0.2792 rms_B_bonded: 1.52 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: 0.8564 moved from start: 0.2009 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= 0.161 Angle : 0.436 4.407 17760 Z= 0.235 Chirality : 0.044 0.127 2136 Planarity : 0.003 0.028 2216 Dihedral : 10.380 63.704 2040 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.81 % Allowed : 6.91 % Favored : 91.28 % 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: 1.58 (0.20), residues: 696 sheet: 0.57 (0.29), residues: 240 loop : -0.88 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 82 TYR 0.009 0.002 TYR G 17 PHE 0.013 0.002 PHE G 78 TRP 0.002 0.001 TRP A 197 HIS 0.002 0.001 HIS M 7 Details of bonding type rmsd covalent geometry : bond 0.00386 (13000) covalent geometry : angle 0.43607 (17760) hydrogen bonds : bond 0.04195 ( 552) hydrogen bonds : angle 6.20321 ( 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 164 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.390 Fit side-chains REVERT: A 27 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 67 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8213 (ttp-170) REVERT: A 120 GLU cc_start: 0.8157 (mp0) cc_final: 0.7758 (mp0) REVERT: C 27 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8307 (mm-30) REVERT: C 67 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8215 (ttp-170) REVERT: C 120 GLU cc_start: 0.8140 (mp0) cc_final: 0.7737 (mp0) REVERT: E 27 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8268 (mm-30) REVERT: E 67 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8217 (ttp-170) REVERT: E 120 GLU cc_start: 0.8145 (mp0) cc_final: 0.7750 (mp0) REVERT: G 27 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8234 (mm-30) REVERT: G 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8208 (ttp-170) REVERT: G 120 GLU cc_start: 0.8161 (mp0) cc_final: 0.7761 (mp0) REVERT: I 27 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8285 (mm-30) REVERT: I 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8207 (ttp-170) REVERT: I 120 GLU cc_start: 0.8151 (mp0) cc_final: 0.7757 (mp0) REVERT: K 27 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8269 (mm-30) REVERT: K 67 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: K 120 GLU cc_start: 0.8156 (mp0) cc_final: 0.7761 (mp0) REVERT: M 27 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8251 (mm-30) REVERT: M 67 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8214 (ttp-170) REVERT: M 120 GLU cc_start: 0.8140 (mp0) cc_final: 0.7700 (mp0) REVERT: O 27 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8308 (mm-30) REVERT: O 67 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8199 (ttp-170) REVERT: O 120 GLU cc_start: 0.8148 (mp0) cc_final: 0.7755 (mp0) outliers start: 22 outliers final: 18 residues processed: 150 average time/residue: 0.1347 time to fit residues: 28.1025 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 : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN 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 42 GLN 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 42 GLN 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 42 GLN Chi-restraints excluded: chain O residue 61 SER 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: 6.9990 chunk 85 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN G 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.090298 restraints weight = 15105.235| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 0.99 r_work: 0.2831 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2112 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= 0.097 Angle : 0.379 4.403 17760 Z= 0.210 Chirality : 0.042 0.122 2136 Planarity : 0.003 0.026 2216 Dihedral : 10.218 63.720 2040 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.73 % Allowed : 7.07 % Favored : 91.20 % 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: 0.80 (0.21), residues: 1624 helix: 1.73 (0.20), residues: 704 sheet: 0.80 (0.29), residues: 240 loop : -0.85 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 175 TYR 0.007 0.001 TYR G 17 PHE 0.012 0.001 PHE I 78 TRP 0.003 0.001 TRP M 139 HIS 0.001 0.000 HIS M 7 Details of bonding type rmsd covalent geometry : bond 0.00214 (13000) covalent geometry : angle 0.37883 (17760) hydrogen bonds : bond 0.03356 ( 552) hydrogen bonds : angle 5.75718 ( 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 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.354 Fit side-chains REVERT: A 27 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8324 (mm-30) REVERT: A 67 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8195 (ttp-170) REVERT: A 120 GLU cc_start: 0.8168 (mp0) cc_final: 0.7785 (mp0) REVERT: C 27 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8334 (mm-30) REVERT: C 67 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8196 (ttp-170) REVERT: C 120 GLU cc_start: 0.8154 (mp0) cc_final: 0.7818 (mp0) REVERT: E 27 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8308 (mm-30) REVERT: E 67 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8195 (ttp-170) REVERT: E 120 GLU cc_start: 0.8164 (mp0) cc_final: 0.7784 (mp0) REVERT: G 27 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8349 (mm-30) REVERT: G 67 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8185 (ttp-170) REVERT: G 120 GLU cc_start: 0.8173 (mp0) cc_final: 0.7789 (mp0) REVERT: I 27 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8320 (mm-30) REVERT: I 67 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8192 (ttp-170) REVERT: I 120 GLU cc_start: 0.8164 (mp0) cc_final: 0.7789 (mp0) REVERT: K 27 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8340 (mm-30) REVERT: K 67 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8193 (ttp-170) REVERT: K 120 GLU cc_start: 0.8181 (mp0) cc_final: 0.7806 (mp0) REVERT: M 27 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8032 (mm-30) REVERT: M 67 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8204 (ttp-170) REVERT: M 120 GLU cc_start: 0.8167 (mp0) cc_final: 0.7793 (mp0) REVERT: O 27 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8325 (mm-30) REVERT: O 67 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8177 (ttp-170) REVERT: O 120 GLU cc_start: 0.8165 (mp0) cc_final: 0.7837 (mp0) outliers start: 21 outliers final: 14 residues processed: 151 average time/residue: 0.1278 time to fit residues: 26.9144 Evaluate side-chains 157 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 O residue 61 SER 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: 6.9990 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 49 optimal weight: 0.3980 chunk 92 optimal weight: 0.0020 chunk 145 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN G 42 GLN K 42 GLN O 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.091671 restraints weight = 15070.929| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 0.93 r_work: 0.2856 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 13000 Z= 0.096 Angle : 0.376 4.413 17760 Z= 0.208 Chirality : 0.042 0.122 2136 Planarity : 0.003 0.026 2216 Dihedral : 10.128 63.713 2040 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.99 % Allowed : 7.73 % Favored : 91.28 % 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 (0.21), residues: 1624 helix: 1.90 (0.20), residues: 696 sheet: 0.90 (0.29), residues: 240 loop : -0.82 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 189 TYR 0.007 0.001 TYR G 17 PHE 0.012 0.001 PHE I 78 TRP 0.003 0.001 TRP O 139 HIS 0.001 0.000 HIS M 7 Details of bonding type rmsd covalent geometry : bond 0.00213 (13000) covalent geometry : angle 0.37595 (17760) hydrogen bonds : bond 0.03336 ( 552) hydrogen bonds : angle 5.65832 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2402.20 seconds wall clock time: 41 minutes 48.88 seconds (2508.88 seconds total)