Starting phenix.real_space_refine on Sun Sep 29 06:20:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/09_2024/7mqh_23947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/09_2024/7mqh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/09_2024/7mqh_23947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/09_2024/7mqh_23947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/09_2024/7mqh_23947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqh_23947/09_2024/7mqh_23947.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP: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: 4.22, per 1000 atoms: 0.33 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: 3.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.27 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: 3.31 Time building geometry restraints manager: 3.55 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: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 26.210 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- 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= 0.478 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.017 0.004 TRP O 139 HIS 0.007 0.002 HIS E 7 PHE 0.017 0.002 PHE E 78 TYR 0.012 0.003 TYR I 17 ARG 0.008 0.001 ARG M 37 *********************** 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 fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.483 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: 0.2638 time to fit residues: 51.6308 Evaluate side-chains 112 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1295 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= 0.169 Angle : 0.449 4.556 17760 Z= 0.247 Chirality : 0.042 0.127 2136 Planarity : 0.003 0.023 2216 Dihedral : 10.663 63.749 2040 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1624 helix: 1.89 (0.20), residues: 704 sheet: 0.89 (0.23), residues: 248 loop : 0.57 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 197 HIS 0.002 0.001 HIS M 7 PHE 0.014 0.001 PHE G 78 TYR 0.007 0.001 TYR C 17 ARG 0.002 0.000 ARG M 175 *********************** 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 160 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.422 Fit side-chains REVERT: A 27 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7891 (mm-30) REVERT: A 120 GLU cc_start: 0.7908 (mp0) cc_final: 0.7535 (mp0) REVERT: C 27 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7867 (mm-30) REVERT: C 120 GLU cc_start: 0.7910 (mp0) cc_final: 0.7538 (mp0) REVERT: E 27 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7890 (mm-30) REVERT: E 120 GLU cc_start: 0.7901 (mp0) cc_final: 0.7532 (mp0) REVERT: G 27 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7892 (mm-30) REVERT: G 120 GLU cc_start: 0.7906 (mp0) cc_final: 0.7555 (mp0) REVERT: I 27 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7845 (mm-30) REVERT: I 120 GLU cc_start: 0.7909 (mp0) cc_final: 0.7553 (mp0) REVERT: K 27 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7885 (mm-30) REVERT: K 120 GLU cc_start: 0.7920 (mp0) cc_final: 0.7543 (mp0) REVERT: M 27 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7725 (mm-30) REVERT: O 27 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7902 (mm-30) REVERT: O 120 GLU cc_start: 0.7902 (mp0) cc_final: 0.7532 (mp0) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2755 time to fit residues: 62.4414 Evaluate side-chains 159 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 13000 Z= 0.506 Angle : 0.587 4.485 17760 Z= 0.308 Chirality : 0.049 0.135 2136 Planarity : 0.005 0.046 2216 Dihedral : 10.691 63.775 2040 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.66 % Allowed : 5.92 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1624 helix: 1.41 (0.20), residues: 704 sheet: 0.65 (0.24), residues: 240 loop : -0.25 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP M 197 HIS 0.005 0.002 HIS M 7 PHE 0.015 0.003 PHE O 78 TYR 0.012 0.003 TYR C 151 ARG 0.003 0.001 ARG A 82 *********************** 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 145 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.419 Fit side-chains REVERT: A 27 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 120 GLU cc_start: 0.7787 (mp0) cc_final: 0.7583 (mp0) REVERT: C 120 GLU cc_start: 0.7790 (mp0) cc_final: 0.7541 (mp0) REVERT: G 27 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7991 (mm-30) REVERT: I 27 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7962 (mm-30) REVERT: K 27 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7988 (mm-30) REVERT: K 120 GLU cc_start: 0.7792 (mp0) cc_final: 0.7591 (mp0) REVERT: M 27 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7850 (mm-30) REVERT: O 120 GLU cc_start: 0.7783 (mp0) cc_final: 0.7537 (mp0) outliers start: 8 outliers final: 8 residues processed: 137 average time/residue: 0.3087 time to fit residues: 59.2080 Evaluate side-chains 144 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain O residue 143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1861 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= 0.123 Angle : 0.384 4.384 17760 Z= 0.215 Chirality : 0.041 0.124 2136 Planarity : 0.003 0.026 2216 Dihedral : 10.416 63.724 2040 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1624 helix: 1.59 (0.20), residues: 712 sheet: 1.07 (0.23), residues: 248 loop : -0.38 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 139 HIS 0.002 0.000 HIS E 116 PHE 0.011 0.001 PHE I 78 TYR 0.006 0.001 TYR M 17 ARG 0.001 0.000 ARG A 82 *********************** 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 145 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.490 Fit side-chains REVERT: A 27 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 120 GLU cc_start: 0.7885 (mp0) cc_final: 0.7518 (mp0) REVERT: C 27 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7778 (mm-30) REVERT: C 120 GLU cc_start: 0.7881 (mp0) cc_final: 0.7522 (mp0) REVERT: E 27 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7742 (mm-30) REVERT: E 120 GLU cc_start: 0.7997 (mp0) cc_final: 0.7714 (mp0) REVERT: G 27 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7977 (mm-30) REVERT: G 120 GLU cc_start: 0.7998 (mp0) cc_final: 0.7716 (mp0) REVERT: I 27 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7834 (mm-30) REVERT: I 120 GLU cc_start: 0.7999 (mp0) cc_final: 0.7714 (mp0) REVERT: K 27 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7984 (mm-30) REVERT: K 120 GLU cc_start: 0.7893 (mp0) cc_final: 0.7526 (mp0) REVERT: M 27 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7697 (mm-30) REVERT: M 120 GLU cc_start: 0.7949 (mp0) cc_final: 0.7676 (mp0) REVERT: O 27 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7753 (mm-30) REVERT: O 120 GLU cc_start: 0.7879 (mp0) cc_final: 0.7519 (mp0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2807 time to fit residues: 56.9080 Evaluate side-chains 144 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN O 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 13000 Z= 0.563 Angle : 0.596 4.713 17760 Z= 0.311 Chirality : 0.051 0.139 2136 Planarity : 0.005 0.048 2216 Dihedral : 10.710 63.768 2040 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.82 % Allowed : 7.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1624 helix: 1.20 (0.20), residues: 696 sheet: 0.32 (0.26), residues: 240 loop : -0.81 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP M 197 HIS 0.005 0.002 HIS C 7 PHE 0.015 0.003 PHE C 78 TYR 0.013 0.003 TYR C 17 ARG 0.003 0.001 ARG C 169 *********************** 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 138 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.366 Fit side-chains REVERT: A 67 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7829 (ttp-110) REVERT: A 120 GLU cc_start: 0.7834 (mp0) cc_final: 0.7386 (mp0) REVERT: C 67 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7826 (ttp-110) REVERT: C 120 GLU cc_start: 0.7832 (mp0) cc_final: 0.7392 (mp0) REVERT: E 27 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7861 (mm-30) REVERT: E 67 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7830 (ttp-110) REVERT: G 67 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7827 (ttp-110) REVERT: I 67 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7831 (ttp-110) REVERT: K 67 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7828 (ttp-110) REVERT: K 120 GLU cc_start: 0.7838 (mp0) cc_final: 0.7394 (mp0) REVERT: K 173 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: M 27 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7877 (mm-30) REVERT: M 173 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: O 67 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7827 (ttp-110) REVERT: O 120 GLU cc_start: 0.7830 (mp0) cc_final: 0.7390 (mp0) REVERT: O 173 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7085 (mt-10) outliers start: 10 outliers final: 0 residues processed: 135 average time/residue: 0.2889 time to fit residues: 54.4269 Evaluate side-chains 131 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 M 42 GLN O 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2062 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= 0.113 Angle : 0.372 4.365 17760 Z= 0.209 Chirality : 0.041 0.121 2136 Planarity : 0.003 0.027 2216 Dihedral : 10.384 63.769 2040 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1624 helix: 1.53 (0.20), residues: 712 sheet: 0.84 (0.26), residues: 240 loop : -0.75 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 139 HIS 0.001 0.000 HIS G 116 PHE 0.011 0.001 PHE K 78 TYR 0.006 0.001 TYR E 17 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.482 Fit side-chains REVERT: A 27 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 67 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7820 (ttp-170) REVERT: A 120 GLU cc_start: 0.7870 (mp0) cc_final: 0.7506 (mp0) REVERT: C 27 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7729 (mm-30) REVERT: C 67 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7819 (ttp-170) REVERT: C 120 GLU cc_start: 0.7869 (mp0) cc_final: 0.7511 (mp0) REVERT: E 27 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7721 (mm-30) REVERT: E 67 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7823 (ttp-170) REVERT: E 120 GLU cc_start: 0.7945 (mp0) cc_final: 0.7643 (mp0) REVERT: G 27 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7915 (mm-30) REVERT: G 67 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7817 (ttp-170) REVERT: G 120 GLU cc_start: 0.7944 (mp0) cc_final: 0.7646 (mp0) REVERT: I 27 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7747 (mm-30) REVERT: I 67 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7820 (ttp-170) REVERT: I 120 GLU cc_start: 0.7947 (mp0) cc_final: 0.7644 (mp0) REVERT: K 27 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7915 (mm-30) REVERT: K 67 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7819 (ttp-170) REVERT: K 120 GLU cc_start: 0.7878 (mp0) cc_final: 0.7515 (mp0) REVERT: M 27 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7627 (mm-30) REVERT: M 120 GLU cc_start: 0.7955 (mp0) cc_final: 0.7658 (mp0) REVERT: O 27 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7733 (mm-30) REVERT: O 67 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7819 (ttp-170) REVERT: O 120 GLU cc_start: 0.7867 (mp0) cc_final: 0.7510 (mp0) outliers start: 14 outliers final: 3 residues processed: 152 average time/residue: 0.2830 time to fit residues: 60.1259 Evaluate side-chains 147 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain O residue 42 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 M 42 GLN O 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.005 0.025 13000 Z= 0.333 Angle : 0.475 4.383 17760 Z= 0.253 Chirality : 0.045 0.131 2136 Planarity : 0.004 0.030 2216 Dihedral : 10.511 63.728 2040 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.89 % Allowed : 6.66 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1624 helix: 1.55 (0.20), residues: 696 sheet: 0.51 (0.27), residues: 240 loop : -0.84 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 197 HIS 0.003 0.001 HIS O 7 PHE 0.014 0.002 PHE I 78 TYR 0.010 0.002 TYR I 17 ARG 0.002 0.000 ARG M 82 *********************** 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 fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.487 Fit side-chains REVERT: A 27 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 120 GLU cc_start: 0.7838 (mp0) cc_final: 0.7346 (mp0) REVERT: C 27 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7914 (mm-30) REVERT: C 120 GLU cc_start: 0.7836 (mp0) cc_final: 0.7349 (mp0) REVERT: E 27 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7907 (mm-30) REVERT: E 120 GLU cc_start: 0.8046 (mp0) cc_final: 0.7656 (mp0) REVERT: G 27 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7884 (mm-30) REVERT: G 120 GLU cc_start: 0.8044 (mp0) cc_final: 0.7654 (mp0) REVERT: I 27 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7868 (mm-30) REVERT: I 120 GLU cc_start: 0.8056 (mp0) cc_final: 0.7680 (mp0) REVERT: K 27 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7882 (mm-30) REVERT: K 120 GLU cc_start: 0.7846 (mp0) cc_final: 0.7355 (mp0) REVERT: M 27 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7741 (mm-30) REVERT: M 120 GLU cc_start: 0.8062 (mp0) cc_final: 0.7689 (mp0) REVERT: O 27 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7929 (mm-30) REVERT: O 120 GLU cc_start: 0.7836 (mp0) cc_final: 0.7348 (mp0) outliers start: 23 outliers final: 15 residues processed: 150 average time/residue: 0.2966 time to fit residues: 62.2040 Evaluate side-chains 157 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 0.0470 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN G 42 GLN I 42 GLN K 42 GLN M 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2127 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= 0.119 Angle : 0.369 4.377 17760 Z= 0.206 Chirality : 0.041 0.121 2136 Planarity : 0.003 0.026 2216 Dihedral : 10.260 63.752 2040 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.81 % Allowed : 6.74 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1624 helix: 1.76 (0.20), residues: 704 sheet: 0.85 (0.28), residues: 240 loop : -0.80 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 139 HIS 0.001 0.000 HIS M 90 PHE 0.011 0.001 PHE I 78 TYR 0.006 0.001 TYR M 17 ARG 0.001 0.000 ARG O 189 *********************** 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 171 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.385 Fit side-chains REVERT: A 27 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 67 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7823 (ttp-170) REVERT: A 120 GLU cc_start: 0.7846 (mp0) cc_final: 0.7501 (mp0) REVERT: C 27 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7912 (mm-30) REVERT: C 67 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7822 (ttp-170) REVERT: C 120 GLU cc_start: 0.7875 (mp0) cc_final: 0.7522 (mp0) REVERT: E 27 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7899 (mm-30) REVERT: E 67 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7822 (ttp-170) REVERT: E 120 GLU cc_start: 0.7832 (mp0) cc_final: 0.7564 (mp0) REVERT: G 27 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7888 (mm-30) REVERT: G 67 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7816 (ttp-170) REVERT: G 120 GLU cc_start: 0.7834 (mp0) cc_final: 0.7566 (mp0) REVERT: I 27 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7867 (mm-30) REVERT: I 67 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7816 (ttp-170) REVERT: I 120 GLU cc_start: 0.7838 (mp0) cc_final: 0.7579 (mp0) REVERT: K 27 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7897 (mm-30) REVERT: K 67 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7820 (ttp-170) REVERT: K 120 GLU cc_start: 0.7906 (mp0) cc_final: 0.7556 (mp0) REVERT: M 27 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7571 (mm-30) REVERT: M 120 GLU cc_start: 0.7841 (mp0) cc_final: 0.7586 (mp0) REVERT: O 27 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7915 (mm-30) REVERT: O 67 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7820 (ttp-170) REVERT: O 120 GLU cc_start: 0.7872 (mp0) cc_final: 0.7523 (mp0) outliers start: 22 outliers final: 8 residues processed: 157 average time/residue: 0.2819 time to fit residues: 61.9793 Evaluate side-chains 154 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 K residue 173 GLU Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 112 optimal weight: 0.0270 chunk 44 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN G 42 GLN I 42 GLN K 42 GLN M 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2020 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= 0.333 Angle : 0.470 4.432 17760 Z= 0.251 Chirality : 0.045 0.131 2136 Planarity : 0.004 0.029 2216 Dihedral : 10.439 63.717 2040 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.56 % Allowed : 6.74 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1624 helix: 1.60 (0.20), residues: 696 sheet: 0.59 (0.29), residues: 240 loop : -0.85 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 139 HIS 0.003 0.001 HIS M 7 PHE 0.013 0.002 PHE E 78 TYR 0.010 0.002 TYR A 17 ARG 0.002 0.000 ARG M 169 *********************** 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 155 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.486 Fit side-chains REVERT: A 27 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 120 GLU cc_start: 0.7833 (mp0) cc_final: 0.7476 (mp0) REVERT: C 27 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7922 (mm-30) REVERT: C 120 GLU cc_start: 0.7830 (mp0) cc_final: 0.7477 (mp0) REVERT: E 27 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7920 (mm-30) REVERT: E 120 GLU cc_start: 0.8051 (mp0) cc_final: 0.7611 (mp0) REVERT: G 27 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7870 (mm-30) REVERT: G 120 GLU cc_start: 0.8047 (mp0) cc_final: 0.7607 (mp0) REVERT: I 27 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7862 (mm-30) REVERT: I 120 GLU cc_start: 0.7907 (mp0) cc_final: 0.7488 (mp0) REVERT: K 27 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7871 (mm-30) REVERT: K 120 GLU cc_start: 0.7841 (mp0) cc_final: 0.7485 (mp0) REVERT: M 27 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7759 (mm-30) REVERT: M 120 GLU cc_start: 0.7915 (mp0) cc_final: 0.7524 (mp0) REVERT: O 27 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7926 (mm-30) REVERT: O 120 GLU cc_start: 0.7830 (mp0) cc_final: 0.7480 (mp0) outliers start: 19 outliers final: 13 residues processed: 144 average time/residue: 0.2865 time to fit residues: 57.4686 Evaluate side-chains 149 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain E residue 42 GLN 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 K residue 173 GLU Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain O residue 42 GLN Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN G 42 GLN I 42 GLN K 42 GLN M 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2203 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= 0.112 Angle : 0.364 4.403 17760 Z= 0.204 Chirality : 0.041 0.119 2136 Planarity : 0.003 0.027 2216 Dihedral : 10.180 63.747 2040 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.23 % Allowed : 7.07 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1624 helix: 1.86 (0.20), residues: 696 sheet: 0.95 (0.29), residues: 240 loop : -0.85 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 139 HIS 0.001 0.000 HIS E 90 PHE 0.011 0.001 PHE K 78 TYR 0.005 0.001 TYR A 17 ARG 0.002 0.000 ARG M 189 ********************** 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 167 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.319 Fit side-chains REVERT: A 27 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 67 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7808 (ttp-170) REVERT: A 120 GLU cc_start: 0.7971 (mp0) cc_final: 0.7543 (mp0) REVERT: C 27 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7880 (mm-30) REVERT: C 67 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7810 (ttp-170) REVERT: C 120 GLU cc_start: 0.7969 (mp0) cc_final: 0.7550 (mp0) REVERT: E 27 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7877 (mm-30) REVERT: E 67 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7809 (ttp-170) REVERT: E 120 GLU cc_start: 0.7773 (mp0) cc_final: 0.7549 (mp0) REVERT: G 27 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7859 (mm-30) REVERT: G 61 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8478 (t) REVERT: G 67 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7792 (ttp-170) REVERT: G 120 GLU cc_start: 0.7775 (mp0) cc_final: 0.7553 (mp0) REVERT: I 27 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7837 (mm-30) REVERT: I 67 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7803 (ttp-170) REVERT: I 120 GLU cc_start: 0.7756 (mp0) cc_final: 0.7483 (mp0) REVERT: K 27 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7853 (mm-30) REVERT: K 67 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7806 (ttp-170) REVERT: K 120 GLU cc_start: 0.7885 (mp0) cc_final: 0.7527 (mp0) REVERT: M 27 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7584 (mm-30) REVERT: M 120 GLU cc_start: 0.7836 (mp0) cc_final: 0.7529 (mp0) REVERT: O 27 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7883 (mm-30) REVERT: O 67 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7809 (ttp-170) REVERT: O 120 GLU cc_start: 0.7965 (mp0) cc_final: 0.7547 (mp0) outliers start: 15 outliers final: 8 residues processed: 157 average time/residue: 0.2654 time to fit residues: 58.5470 Evaluate side-chains 159 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 K residue 173 GLU Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN G 42 GLN I 42 GLN K 42 GLN M 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.087764 restraints weight = 15159.758| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 0.99 r_work: 0.2791 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 13000 Z= 0.317 Angle : 0.473 4.432 17760 Z= 0.251 Chirality : 0.045 0.131 2136 Planarity : 0.004 0.029 2216 Dihedral : 10.401 63.714 2040 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.15 % Allowed : 6.99 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1624 helix: 1.63 (0.20), residues: 696 sheet: 0.64 (0.30), residues: 240 loop : -0.90 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 197 HIS 0.003 0.001 HIS K 90 PHE 0.013 0.002 PHE C 78 TYR 0.010 0.002 TYR G 17 ARG 0.002 0.000 ARG K 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.39 seconds wall clock time: 39 minutes 39.98 seconds (2379.98 seconds total)