Starting phenix.real_space_refine on Sun Sep 13 06:57:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqh_23947/09_2026/7mqh_23947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqh_23947/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mqh_23947/09_2026/7mqh_23947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqh_23947/09_2026/7mqh_23947.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mqh_23947/09_2026/7mqh_23947.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqh_23947/09_2026/7mqh_23947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqh_23947/09_2026/7mqh_23947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqh_23947/09_2026/7mqh_23947.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: 1.87, per 1000 atoms: 0.15 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: 1.08 Conformation dependent library (CDL) restraints added in 596.8 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: 0.35 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: 1.94 Time building geometry restraints manager: 1.45 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 - 1.26: 15978 1.26 - 2.52: 1383 2.52 - 3.78: 302 3.78 - 5.04: 81 5.04 - 6.30: 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: 6983 15.41 - 30.81: 489 30.81 - 46.22: 120 46.22 - 61.62: 56 61.62 - 77.03: 24 Dihedral angle restraints: 7672 sinusoidal: 2888 harmonic: 4784 Sorted by residual: dihedral pdb=" C4' G F 603 " pdb=" C3' G F 603 " pdb=" C2' G F 603 " pdb=" C1' G F 603 " ideal model delta sinusoidal sigma weight residual 36.34 -33.30 69.65 1 3.10e+00 1.04e-01 6.52e+02 dihedral pdb=" C4' G H 603 " pdb=" C3' G H 603 " pdb=" C2' G H 603 " pdb=" C1' G H 603 " ideal model delta sinusoidal sigma weight residual 36.34 -33.28 69.63 1 3.10e+00 1.04e-01 6.51e+02 dihedral pdb=" C4' G N 603 " pdb=" C3' G N 603 " pdb=" C2' G N 603 " pdb=" C1' G N 603 " ideal model delta sinusoidal sigma weight residual 36.35 -33.27 69.61 1 3.10e+00 1.04e-01 6.51e+02 ... (remaining 7669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1800 0.078 - 0.156: 312 0.156 - 0.234: 0 0.234 - 0.313: 16 0.313 - 0.391: 8 Chirality restraints: 2136 Sorted by residual: chirality pdb=" C2' G L 603 " pdb=" C3' G L 603 " pdb=" O2' G L 603 " pdb=" C1' G L 603 " both_signs ideal model delta sigma weight residual False -2.79 -2.40 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C2' G J 603 " pdb=" C3' G J 603 " pdb=" O2' G J 603 " pdb=" C1' G J 603 " both_signs ideal model delta sigma weight residual False -2.79 -2.40 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C2' G P 603 " pdb=" C3' G P 603 " pdb=" O2' G P 603 " pdb=" C1' G P 603 " both_signs ideal model delta sigma weight residual False -2.79 -2.40 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.930 Find NCS groups from input model: 0.150 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- 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= 0.316 Angle : 0.835 6.304 17760 Z= 0.501 Chirality : 0.064 0.391 2136 Planarity : 0.005 0.023 2216 Dihedral : 13.384 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 0.00722 / 0.32 (13000) covalent geometry : angle 0.83465 / 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 : 0.613 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: 0.1275 time to fit residues: 25.3118 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 : 0.514 ------------------------------------------------------------------------------- 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 = 0.100780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.090842 restraints weight = 15348.566| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 0.84 r_work: 0.2830 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1389 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= 0.157 Angle : 0.559 5.306 17760 Z= 0.287 Chirality : 0.049 0.254 2136 Planarity : 0.004 0.025 2216 Dihedral : 5.220 33.807 1944 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: 1.83 (0.20), residues: 704 sheet: 0.84 (0.24), residues: 248 loop : 0.43 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.009 0.002 TYR E 17 PHE 0.014 0.002 PHE A 78 TRP 0.003 0.001 TRP M 197 HIS 0.003 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (13000) covalent geometry : angle 0.55948 / 0.29 (17760) hydrogen bonds : bond 0.04276 / 2.95 ( 552) hydrogen bonds : angle 6.39040 / 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 : 0.482 Fit side-chains REVERT: A 27 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8358 (mm-30) REVERT: A 120 GLU cc_start: 0.8077 (mp0) cc_final: 0.7691 (mp0) REVERT: C 27 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8313 (mm-30) REVERT: C 120 GLU cc_start: 0.8072 (mp0) cc_final: 0.7678 (mp0) REVERT: E 27 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8377 (mm-30) REVERT: E 120 GLU cc_start: 0.8072 (mp0) cc_final: 0.7677 (mp0) REVERT: G 27 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8352 (mm-30) REVERT: G 120 GLU cc_start: 0.8076 (mp0) cc_final: 0.7691 (mp0) REVERT: I 27 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8340 (mm-30) REVERT: I 120 GLU cc_start: 0.8081 (mp0) cc_final: 0.7700 (mp0) REVERT: K 27 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8350 (mm-30) REVERT: K 120 GLU cc_start: 0.8087 (mp0) cc_final: 0.7707 (mp0) REVERT: M 8 GLN cc_start: 0.9267 (mm-40) cc_final: 0.9020 (mp10) REVERT: M 27 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8208 (mm-30) REVERT: O 27 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8358 (mm-30) REVERT: O 120 GLU cc_start: 0.8070 (mp0) cc_final: 0.7690 (mp0) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1400 time to fit residues: 28.2900 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 : 0.407 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.101224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.088757 restraints weight = 15322.291| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 0.97 r_work: 0.2804 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 13000 Z= 0.133 Angle : 0.448 4.489 17760 Z= 0.241 Chirality : 0.045 0.141 2136 Planarity : 0.003 0.025 2216 Dihedral : 5.235 36.683 1944 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.74 % Allowed : 5.43 % 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: 1.47 (0.21), residues: 1624 helix: 1.82 (0.20), residues: 704 sheet: 1.22 (0.24), residues: 248 loop : 0.04 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 82 TYR 0.008 0.002 TYR A 17 PHE 0.013 0.001 PHE M 78 TRP 0.003 0.001 TRP C 197 HIS 0.002 0.001 HIS G 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (13000) covalent geometry : angle 0.44822 / 0.24 (17760) hydrogen bonds : bond 0.03895 / 2.69 ( 552) hydrogen bonds : angle 6.13407 / 4.48 ( 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 153 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.553 Fit side-chains REVERT: A 27 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 67 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8220 (ttp-170) REVERT: A 120 GLU cc_start: 0.8382 (mp0) cc_final: 0.7913 (mp0) REVERT: C 27 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8463 (mm-30) REVERT: C 67 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8212 (ttp-170) REVERT: C 120 GLU cc_start: 0.8359 (mp0) cc_final: 0.7894 (mp0) REVERT: E 27 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8454 (mm-30) REVERT: E 67 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8224 (ttp-170) REVERT: E 120 GLU cc_start: 0.8241 (mp0) cc_final: 0.7744 (mp0) REVERT: G 27 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8433 (mm-30) REVERT: G 67 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8211 (ttp-170) REVERT: G 120 GLU cc_start: 0.8251 (mp0) cc_final: 0.7758 (mp0) REVERT: I 27 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8426 (mm-30) REVERT: I 67 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8222 (ttp-170) REVERT: K 27 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8440 (mm-30) REVERT: K 67 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8224 (ttp-170) REVERT: K 120 GLU cc_start: 0.8382 (mp0) cc_final: 0.7920 (mp0) REVERT: M 27 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8235 (mm-30) REVERT: M 120 GLU cc_start: 0.8259 (mp0) cc_final: 0.7800 (mp0) REVERT: O 27 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8457 (mm-30) REVERT: O 67 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8228 (ttp-170) REVERT: O 120 GLU cc_start: 0.8367 (mp0) cc_final: 0.7904 (mp0) outliers start: 9 outliers final: 0 residues processed: 144 average time/residue: 0.1421 time to fit residues: 28.6954 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 : 0.590 ------------------------------------------------------------------------------- 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: 8.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 41 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN ** 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.088479 restraints weight = 15504.005| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 0.95 r_work: 0.2795 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 13000 Z= 0.184 Angle : 0.488 4.459 17760 Z= 0.257 Chirality : 0.047 0.132 2136 Planarity : 0.004 0.028 2216 Dihedral : 5.542 39.009 1944 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.90 % Allowed : 6.09 % Favored : 93.01 % 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: 1.00 (0.21), residues: 1624 helix: 1.58 (0.20), residues: 704 sheet: 1.06 (0.25), residues: 240 loop : -0.42 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 82 TYR 0.009 0.002 TYR E 17 PHE 0.014 0.002 PHE E 78 TRP 0.002 0.001 TRP K 197 HIS 0.003 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (13000) covalent geometry : angle 0.48845 / 0.26 (17760) hydrogen bonds : bond 0.04505 / 3.10 ( 552) hydrogen bonds : angle 6.40292 / 4.68 ( 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: 11 poor density : 142 time to evaluate : 0.527 Fit side-chains REVERT: A 27 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8405 (mm-30) REVERT: A 67 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8253 (ttp-170) REVERT: A 120 GLU cc_start: 0.8060 (mp0) cc_final: 0.7804 (mp0) REVERT: C 27 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8335 (mm-30) REVERT: C 67 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8241 (ttp-170) REVERT: C 120 GLU cc_start: 0.8039 (mp0) cc_final: 0.7784 (mp0) REVERT: E 27 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8350 (mm-30) REVERT: E 67 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8242 (ttp-170) REVERT: E 120 GLU cc_start: 0.8047 (mp0) cc_final: 0.7790 (mp0) REVERT: G 27 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8412 (mm-30) REVERT: G 67 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8239 (ttp-170) REVERT: G 120 GLU cc_start: 0.8063 (mp0) cc_final: 0.7808 (mp0) REVERT: I 27 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8387 (mm-30) REVERT: I 67 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8255 (ttp-170) REVERT: I 120 GLU cc_start: 0.8145 (mp0) cc_final: 0.7762 (mp0) REVERT: K 27 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8414 (mm-30) REVERT: K 67 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8256 (ttp-170) REVERT: K 120 GLU cc_start: 0.8051 (mp0) cc_final: 0.7797 (mp0) REVERT: M 27 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8231 (mm-30) REVERT: M 67 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8275 (ttp-170) REVERT: O 27 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8350 (mm-30) REVERT: O 67 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8244 (ttp-170) REVERT: O 120 GLU cc_start: 0.8040 (mp0) cc_final: 0.7783 (mp0) outliers start: 11 outliers final: 8 residues processed: 145 average time/residue: 0.1333 time to fit residues: 27.1801 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 : 0.439 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3058 r_free = 0.3058 target = 0.100162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.087980 restraints weight = 15256.126| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 0.98 r_work: 0.2790 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2026 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= 0.172 Angle : 0.464 4.411 17760 Z= 0.246 Chirality : 0.046 0.127 2136 Planarity : 0.003 0.028 2216 Dihedral : 5.457 38.066 1944 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.89 % Allowed : 6.17 % Favored : 91.94 % 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: 0.85 (0.20), residues: 1624 helix: 1.55 (0.20), residues: 696 sheet: 1.00 (0.26), residues: 240 loop : -0.61 (0.24), 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 0.013 0.002 PHE K 78 TRP 0.002 0.001 TRP K 197 HIS 0.003 0.001 HIS I 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (13000) covalent geometry : angle 0.46374 / 0.25 (17760) hydrogen bonds : bond 0.04243 / 2.92 ( 552) hydrogen bonds : angle 6.29276 / 4.60 ( 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 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.514 Fit side-chains REVERT: A 27 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 67 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8220 (ttp-170) REVERT: A 120 GLU cc_start: 0.8213 (mp0) cc_final: 0.7861 (mp0) REVERT: C 27 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8282 (mm-30) REVERT: C 67 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8216 (ttp-170) REVERT: C 120 GLU cc_start: 0.8132 (mp0) cc_final: 0.7770 (mp0) REVERT: E 27 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8291 (mm-30) REVERT: E 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8210 (ttp-170) REVERT: E 120 GLU cc_start: 0.8202 (mp0) cc_final: 0.7850 (mp0) REVERT: G 27 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8329 (mm-30) REVERT: G 67 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8215 (ttp-170) REVERT: G 120 GLU cc_start: 0.8214 (mp0) cc_final: 0.7858 (mp0) REVERT: I 27 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8410 (mm-30) REVERT: I 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8210 (ttp-170) REVERT: I 120 GLU cc_start: 0.8147 (mp0) cc_final: 0.7757 (mp0) REVERT: K 27 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8332 (mm-30) REVERT: K 67 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8224 (ttp-170) REVERT: K 120 GLU cc_start: 0.8147 (mp0) cc_final: 0.7787 (mp0) REVERT: M 27 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8196 (mm-30) REVERT: M 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8211 (ttp-170) REVERT: M 120 GLU cc_start: 0.8114 (mp0) cc_final: 0.7773 (mp0) REVERT: O 27 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8295 (mm-30) REVERT: O 67 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8211 (ttp-170) REVERT: O 120 GLU cc_start: 0.8194 (mp0) cc_final: 0.7841 (mp0) outliers start: 23 outliers final: 15 residues processed: 150 average time/residue: 0.1401 time to fit residues: 29.5805 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 : 0.508 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 141 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3071 r_free = 0.3071 target = 0.101041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.088864 restraints weight = 15196.945| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 0.99 r_work: 0.2803 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2105 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= 0.134 Angle : 0.425 4.407 17760 Z= 0.229 Chirality : 0.044 0.125 2136 Planarity : 0.003 0.027 2216 Dihedral : 5.221 35.920 1944 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.48 % Allowed : 6.58 % Favored : 91.94 % 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 (0.20), residues: 1624 helix: 1.64 (0.20), residues: 704 sheet: 0.93 (0.27), residues: 240 loop : -0.65 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 82 TYR 0.008 0.001 TYR G 17 PHE 0.012 0.001 PHE M 78 TRP 0.002 0.001 TRP G 197 HIS 0.002 0.001 HIS G 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (13000) covalent geometry : angle 0.42476 / 0.23 (17760) hydrogen bonds : bond 0.03793 / 2.61 ( 552) hydrogen bonds : angle 6.06255 / 4.43 ( 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 160 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.518 Fit side-chains REVERT: A 27 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8358 (mm-30) REVERT: A 67 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8219 (ttp-170) REVERT: A 120 GLU cc_start: 0.8150 (mp0) cc_final: 0.7597 (mp0) REVERT: C 27 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8360 (mm-30) REVERT: C 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8210 (ttp-170) REVERT: C 120 GLU cc_start: 0.8126 (mp0) cc_final: 0.7575 (mp0) REVERT: E 27 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8364 (mm-30) REVERT: E 67 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: E 120 GLU cc_start: 0.8146 (mp0) cc_final: 0.7602 (mp0) REVERT: G 27 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8377 (mm-30) REVERT: G 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8212 (ttp-170) REVERT: G 120 GLU cc_start: 0.8153 (mp0) cc_final: 0.7606 (mp0) REVERT: I 27 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8346 (mm-30) REVERT: I 67 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8216 (ttp-170) REVERT: I 120 GLU cc_start: 0.8122 (mp0) cc_final: 0.7742 (mp0) REVERT: K 27 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8376 (mm-30) REVERT: K 67 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8218 (ttp-170) REVERT: K 120 GLU cc_start: 0.8154 (mp0) cc_final: 0.7607 (mp0) REVERT: M 27 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8178 (mm-30) REVERT: M 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8209 (ttp-170) REVERT: M 120 GLU cc_start: 0.8241 (mp0) cc_final: 0.7892 (mp0) REVERT: O 27 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8371 (mm-30) REVERT: O 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8210 (ttp-170) REVERT: O 120 GLU cc_start: 0.8142 (mp0) cc_final: 0.7599 (mp0) outliers start: 18 outliers final: 10 residues processed: 150 average time/residue: 0.1408 time to fit residues: 29.5914 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 : 0.502 ------------------------------------------------------------------------------- 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 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 61 SER 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: 10.0000 chunk 82 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- 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 = 0.3050 r_free = 0.3050 target = 0.099451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.087225 restraints weight = 15204.764| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 0.98 r_work: 0.2778 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 13000 Z= 0.208 Angle : 0.494 4.387 17760 Z= 0.259 Chirality : 0.047 0.130 2136 Planarity : 0.004 0.029 2216 Dihedral : 5.581 38.728 1944 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.49 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: 0.61 (0.21), residues: 1624 helix: 1.52 (0.20), residues: 696 sheet: 0.55 (0.28), residues: 240 loop : -0.79 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 169 TYR 0.010 0.002 TYR E 17 PHE 0.014 0.002 PHE C 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 0.00506 / 0.21 (13000) covalent geometry : angle 0.49426 / 0.26 (17760) hydrogen bonds : bond 0.04646 / 3.20 ( 552) hydrogen bonds : angle 6.42501 / 4.69 ( 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 : 0.521 Fit side-chains REVERT: A 27 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8373 (mm-30) REVERT: A 67 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8222 (ttp-170) REVERT: A 120 GLU cc_start: 0.8117 (mp0) cc_final: 0.7587 (mp0) REVERT: C 27 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8260 (mm-30) REVERT: C 67 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8206 (ttp-170) REVERT: C 120 GLU cc_start: 0.8090 (mp0) cc_final: 0.7559 (mp0) REVERT: E 27 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8258 (mm-30) REVERT: E 67 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8205 (ttp-170) REVERT: E 120 GLU cc_start: 0.8101 (mp0) cc_final: 0.7574 (mp0) REVERT: G 27 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8365 (mm-30) REVERT: G 67 ARG cc_start: 0.8474 (ttp80) cc_final: 0.8214 (ttp-170) REVERT: G 120 GLU cc_start: 0.8127 (mp0) cc_final: 0.7600 (mp0) REVERT: I 27 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8362 (mm-30) REVERT: I 67 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8214 (ttp-170) REVERT: K 27 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8362 (mm-30) REVERT: K 67 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8220 (ttp-170) REVERT: K 120 GLU cc_start: 0.8106 (mp0) cc_final: 0.7585 (mp0) REVERT: M 27 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8269 (mm-30) REVERT: M 67 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8217 (ttp-170) REVERT: M 120 GLU cc_start: 0.8079 (mp0) cc_final: 0.7663 (mp0) REVERT: O 27 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8261 (mm-30) REVERT: O 67 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8204 (ttp-170) REVERT: O 120 GLU cc_start: 0.8073 (mp0) cc_final: 0.7554 (mp0) outliers start: 23 outliers final: 9 residues processed: 150 average time/residue: 0.1402 time to fit residues: 29.5137 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 : 0.514 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 41 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 157 optimal weight: 0.0370 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.3125 r_free = 0.3125 target = 0.104217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.093272 restraints weight = 14972.697| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 0.85 r_work: 0.2883 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 13000 Z= 0.074 Angle : 0.368 4.453 17760 Z= 0.204 Chirality : 0.042 0.120 2136 Planarity : 0.003 0.025 2216 Dihedral : 4.637 29.932 1944 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.40 % Allowed : 6.58 % 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: 0.95 (0.21), residues: 1624 helix: 1.81 (0.20), residues: 704 sheet: 0.92 (0.28), residues: 240 loop : -0.74 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 189 TYR 0.005 0.001 TYR M 17 PHE 0.010 0.001 PHE G 78 TRP 0.004 0.001 TRP K 139 HIS 0.001 0.000 HIS G 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00146 / 0.07 (13000) covalent geometry : angle 0.36783 / 0.20 (17760) hydrogen bonds : bond 0.02914 / 2.01 ( 552) hydrogen bonds : angle 5.50593 / 4.02 ( 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 173 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.613 Fit side-chains REVERT: A 27 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 61 SER cc_start: 0.8761 (p) cc_final: 0.8436 (t) REVERT: A 67 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8194 (ttp-170) REVERT: A 120 GLU cc_start: 0.8242 (mp0) cc_final: 0.7843 (mp0) REVERT: C 27 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8352 (mm-30) REVERT: C 61 SER cc_start: 0.8758 (p) cc_final: 0.8404 (t) REVERT: C 67 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8179 (ttp-170) REVERT: C 120 GLU cc_start: 0.8228 (mp0) cc_final: 0.7832 (mp0) REVERT: E 27 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8330 (mm-30) REVERT: E 61 SER cc_start: 0.8760 (p) cc_final: 0.8410 (t) REVERT: E 67 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8191 (ttp-170) REVERT: E 120 GLU cc_start: 0.8256 (mp0) cc_final: 0.7851 (mp0) REVERT: G 27 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8410 (mm-30) REVERT: G 61 SER cc_start: 0.8774 (p) cc_final: 0.8427 (t) REVERT: G 67 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8182 (ttp-170) REVERT: G 120 GLU cc_start: 0.8256 (mp0) cc_final: 0.7858 (mp0) REVERT: I 27 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8382 (mm-30) REVERT: I 61 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8460 (t) REVERT: I 67 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8190 (ttp-170) REVERT: I 119 LYS cc_start: 0.8625 (tttp) cc_final: 0.8400 (tttp) REVERT: I 120 GLU cc_start: 0.8126 (mp0) cc_final: 0.7766 (mp0) REVERT: K 27 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8403 (mm-30) REVERT: K 61 SER cc_start: 0.8765 (p) cc_final: 0.8410 (t) REVERT: K 67 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8191 (ttp-170) REVERT: K 120 GLU cc_start: 0.8274 (mp0) cc_final: 0.7880 (mp0) REVERT: M 27 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8072 (mm-30) REVERT: M 61 SER cc_start: 0.8750 (p) cc_final: 0.8428 (t) REVERT: M 67 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8189 (ttp-170) REVERT: M 120 GLU cc_start: 0.8110 (mp0) cc_final: 0.7839 (mp0) REVERT: O 27 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8354 (mm-30) REVERT: O 61 SER cc_start: 0.8757 (p) cc_final: 0.8404 (t) REVERT: O 67 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8193 (ttp-170) REVERT: O 120 GLU cc_start: 0.8262 (mp0) cc_final: 0.7858 (mp0) outliers start: 17 outliers final: 8 residues processed: 164 average time/residue: 0.1347 time to fit residues: 31.3530 Evaluate side-chains 158 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 19 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 50 optimal weight: 0.0040 overall best weight: 2.1996 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.101935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.089751 restraints weight = 15094.892| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 0.98 r_work: 0.2821 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2228 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= 0.124 Angle : 0.413 4.422 17760 Z= 0.222 Chirality : 0.044 0.124 2136 Planarity : 0.003 0.026 2216 Dihedral : 4.968 33.205 1944 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.90 % Allowed : 6.50 % Favored : 92.60 % 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: 1.91 (0.20), residues: 696 sheet: 0.97 (0.29), residues: 240 loop : -0.75 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 82 TYR 0.008 0.001 TYR C 17 PHE 0.012 0.001 PHE I 78 TRP 0.002 0.001 TRP I 197 HIS 0.002 0.001 HIS O 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (13000) covalent geometry : angle 0.41280 / 0.22 (17760) hydrogen bonds : bond 0.03711 / 2.56 ( 552) hydrogen bonds : angle 5.88658 / 4.30 ( 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 146 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.542 Fit side-chains REVERT: A 27 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8315 (mm-30) REVERT: A 67 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8191 (ttp-170) REVERT: A 120 GLU cc_start: 0.8045 (mp0) cc_final: 0.7547 (mp0) REVERT: C 27 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8305 (mm-30) REVERT: C 67 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8188 (ttp-170) REVERT: C 120 GLU cc_start: 0.8051 (mp0) cc_final: 0.7573 (mp0) REVERT: E 27 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8299 (mm-30) REVERT: E 67 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8193 (ttp-170) REVERT: E 120 GLU cc_start: 0.8135 (mp0) cc_final: 0.7609 (mp0) REVERT: G 27 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8310 (mm-30) REVERT: G 67 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8179 (ttp-170) REVERT: G 120 GLU cc_start: 0.8044 (mp0) cc_final: 0.7569 (mp0) REVERT: I 27 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8305 (mm-30) REVERT: I 67 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8191 (ttp-170) REVERT: I 120 GLU cc_start: 0.8248 (mp0) cc_final: 0.7986 (mp0) REVERT: K 27 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8310 (mm-30) REVERT: K 67 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8196 (ttp-170) REVERT: K 120 GLU cc_start: 0.8162 (mp0) cc_final: 0.7634 (mp0) REVERT: M 27 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8089 (mm-30) REVERT: M 67 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8186 (ttp-170) REVERT: M 120 GLU cc_start: 0.8183 (mp0) cc_final: 0.7785 (mp0) REVERT: O 27 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8307 (mm-30) REVERT: O 67 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8192 (ttp-170) REVERT: O 120 GLU cc_start: 0.8070 (mp0) cc_final: 0.7594 (mp0) outliers start: 11 outliers final: 9 residues processed: 137 average time/residue: 0.1401 time to fit residues: 26.7817 Evaluate side-chains 144 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 85 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 GLN M 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.100899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.088656 restraints weight = 15205.622| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 0.98 r_work: 0.2798 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2191 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= 0.153 Angle : 0.443 4.421 17760 Z= 0.236 Chirality : 0.045 0.126 2136 Planarity : 0.003 0.027 2216 Dihedral : 5.294 36.730 1944 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.90 % Allowed : 6.50 % Favored : 92.60 % 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: 0.87 (0.21), residues: 1624 helix: 1.71 (0.20), residues: 704 sheet: 0.90 (0.30), residues: 240 loop : -0.76 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 82 TYR 0.009 0.002 TYR A 17 PHE 0.013 0.002 PHE C 78 TRP 0.002 0.001 TRP E 197 HIS 0.002 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (13000) covalent geometry : angle 0.44306 / 0.24 (17760) hydrogen bonds : bond 0.04071 / 2.80 ( 552) hydrogen bonds : angle 6.12377 / 4.47 ( 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 139 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.386 Fit side-chains REVERT: A 27 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8417 (mm-30) REVERT: A 67 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8194 (ttp-170) REVERT: A 120 GLU cc_start: 0.8069 (mp0) cc_final: 0.7568 (mp0) REVERT: C 27 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8409 (mm-30) REVERT: C 67 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8189 (ttp-170) REVERT: C 120 GLU cc_start: 0.8056 (mp0) cc_final: 0.7501 (mp0) REVERT: E 27 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8333 (mm-30) REVERT: E 67 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8191 (ttp-170) REVERT: E 120 GLU cc_start: 0.8072 (mp0) cc_final: 0.7541 (mp0) REVERT: G 27 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8411 (mm-30) REVERT: G 67 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8189 (ttp-170) REVERT: G 120 GLU cc_start: 0.8079 (mp0) cc_final: 0.7580 (mp0) REVERT: I 27 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8416 (mm-30) REVERT: I 67 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8196 (ttp-170) REVERT: I 120 GLU cc_start: 0.8215 (mp0) cc_final: 0.7886 (mp0) REVERT: K 27 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8410 (mm-30) REVERT: K 67 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8204 (ttp-170) REVERT: K 120 GLU cc_start: 0.8067 (mp0) cc_final: 0.7518 (mp0) REVERT: M 27 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8204 (mm-30) REVERT: M 67 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8199 (ttp-170) REVERT: M 120 GLU cc_start: 0.8223 (mp0) cc_final: 0.7820 (mp0) REVERT: O 27 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8414 (mm-30) REVERT: O 67 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8195 (ttp-170) REVERT: O 120 GLU cc_start: 0.8066 (mp0) cc_final: 0.7529 (mp0) outliers start: 11 outliers final: 9 residues processed: 130 average time/residue: 0.1402 time to fit residues: 25.4207 Evaluate side-chains 137 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 GLN M 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.090171 restraints weight = 15067.113| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 0.98 r_work: 0.2825 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2265 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= 0.108 Angle : 0.399 4.424 17760 Z= 0.217 Chirality : 0.043 0.123 2136 Planarity : 0.003 0.026 2216 Dihedral : 4.978 33.303 1944 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.90 % Allowed : 6.50 % Favored : 92.60 % 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: 0.96 (0.21), residues: 1624 helix: 1.89 (0.20), residues: 696 sheet: 0.96 (0.30), residues: 240 loop : -0.81 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 189 TYR 0.007 0.001 TYR G 17 PHE 0.012 0.001 PHE A 78 TRP 0.002 0.001 TRP M 139 HIS 0.001 0.000 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (13000) covalent geometry : angle 0.39944 / 0.22 (17760) hydrogen bonds : bond 0.03491 / 2.40 ( 552) hydrogen bonds : angle 5.80923 / 4.24 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.10 seconds wall clock time: 44 minutes 53.63 seconds (2693.63 seconds total)