Starting phenix.real_space_refine on Sun Sep 13 03:22:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqd_23943/09_2026/7mqd_23943.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqd_23943/09_2026/7mqd_23943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mqd_23943/09_2026/7mqd_23943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqd_23943/09_2026/7mqd_23943.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqd_23943/09_2026/7mqd_23943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqd_23943/09_2026/7mqd_23943.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mqd_23943/09_2026/7mqd_23943.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqd_23943/09_2026/7mqd_23943.cif" } resolution = 3.25 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= 0.001 sd= 0.016 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 10912 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 7632 2.51 5 N 2176 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 11960 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1449 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 11, 'ASN:plan1': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Restraints were copied for chains: C, E, G, I, K, M, O, D, F, H, J, L, N, P Time building chain proxies: 1.68, per 1000 atoms: 0.14 Number of scatterers: 11960 At special positions: 0 Unit cell: (105.4, 105.4, 85.56, 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 2088 8.00 N 2176 7.00 C 7632 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: 1.02 Conformation dependent library (CDL) restraints added in 573.9 milliseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 46.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.911A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A 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: 3.912A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.601A 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 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: 3.911A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A 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: 3.912A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.501A 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: 3.911A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A 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: 3.912A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A 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: 3.912A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.501A 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: 3.911A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.501A 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: 6.181A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.181A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.180A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.180A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.181A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.649A 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: 6.181A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.181A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU M 27 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL M 41 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP M 25 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU M 43 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.181A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1659 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: 1.86 Time building geometry restraints manager: 1.38 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: 3841 1.34 - 1.45: 1632 1.45 - 1.57: 6655 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12216 Sorted by residual: bond pdb=" N VAL A 156 " pdb=" CA VAL A 156 " ideal model delta sigma weight residual 1.456 1.463 -0.007 1.08e-02 8.57e+03 4.43e-01 bond pdb=" N VAL M 156 " pdb=" CA VAL M 156 " ideal model delta sigma weight residual 1.456 1.463 -0.007 1.08e-02 8.57e+03 4.28e-01 bond pdb=" CB VAL I 40 " pdb=" CG1 VAL I 40 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.13e-01 bond pdb=" CB VAL C 40 " pdb=" CG1 VAL C 40 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.02e-01 bond pdb=" C ARG M 161 " pdb=" O ARG M 161 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.17e-02 7.31e+03 3.94e-01 ... (remaining 12211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 15728 1.13 - 2.26: 759 2.26 - 3.40: 156 3.40 - 4.53: 37 4.53 - 5.66: 32 Bond angle restraints: 16712 Sorted by residual: angle pdb=" CA GLN A 42 " pdb=" CB GLN A 42 " pdb=" CG GLN A 42 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.01e+00 angle pdb=" CA GLN C 42 " pdb=" CB GLN C 42 " pdb=" CG GLN C 42 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.99e+00 angle pdb=" CA GLN M 42 " pdb=" CB GLN M 42 " pdb=" CG GLN M 42 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.92e+00 angle pdb=" CA GLN I 42 " pdb=" CB GLN I 42 " pdb=" CG GLN I 42 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.89e+00 angle pdb=" CA GLN O 42 " pdb=" CB GLN O 42 " pdb=" CG GLN O 42 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.88e+00 ... (remaining 16707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6738 17.83 - 35.66: 294 35.66 - 53.49: 64 53.49 - 71.32: 24 71.32 - 89.15: 16 Dihedral angle restraints: 7136 sinusoidal: 2504 harmonic: 4632 Sorted by residual: dihedral pdb=" CA PHE A 78 " pdb=" C PHE A 78 " pdb=" N HIS A 79 " pdb=" CA HIS A 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 C 78 " pdb=" C PHE C 78 " pdb=" N HIS C 79 " pdb=" CA HIS C 79 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE G 78 " pdb=" C PHE G 78 " pdb=" N HIS G 79 " pdb=" CA HIS G 79 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1724 0.065 - 0.130: 300 0.130 - 0.195: 8 0.195 - 0.260: 8 0.260 - 0.325: 8 Chirality restraints: 2048 Sorted by residual: chirality pdb=" P G P 603 " pdb=" OP1 G P 603 " pdb=" OP2 G P 603 " pdb=" O5' G P 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" P G N 603 " pdb=" OP1 G N 603 " pdb=" OP2 G N 603 " pdb=" O5' G N 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" P G J 603 " pdb=" OP1 G J 603 " pdb=" OP2 G J 603 " pdb=" O5' G J 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2045 not shown) Planarity restraints: 2048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 83 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.76e+00 pdb=" C PHE G 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE G 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 84 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 83 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C PHE E 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE E 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP E 84 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 83 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C PHE O 83 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE O 83 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP O 84 " -0.008 2.00e-02 2.50e+03 ... (remaining 2045 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 5116 2.94 - 3.43: 11286 3.43 - 3.92: 19745 3.92 - 4.41: 23107 4.41 - 4.90: 37981 Nonbonded interactions: 97235 Sorted by model distance: nonbonded pdb=" O HIS G 205 " pdb=" NZ LYS O 103 " model vdw 2.456 3.120 nonbonded pdb=" NZ LYS E 103 " pdb=" O HIS I 205 " model vdw 2.490 3.120 nonbonded pdb=" OG1 THR G 26 " pdb=" OD1 ASP G 84 " model vdw 2.499 3.040 nonbonded pdb=" OG1 THR C 26 " pdb=" OD1 ASP C 84 " model vdw 2.499 3.040 nonbonded pdb=" OG1 THR I 26 " pdb=" OD1 ASP I 84 " model vdw 2.499 3.040 ... (remaining 97230 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.670 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12216 Z= 0.148 Angle : 0.634 5.660 16712 Z= 0.372 Chirality : 0.052 0.325 2048 Planarity : 0.004 0.026 2048 Dihedral : 13.133 89.151 4112 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 1.04 (0.21), residues: 1560 helix: 0.79 (0.19), residues: 704 sheet: 0.50 (0.22), residues: 240 loop : 0.94 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG C 37 TYR 0.005 0.001 TYR M 17 PHE 0.013 0.002 PHE K 78 TRP 0.016 0.002 TRP M 197 HIS 0.002 0.001 HIS E 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (12216) covalent geometry : angle 0.63374 / 0.37 (16712) hydrogen bonds : bond 0.10484 / 6.99 ( 553) hydrogen bonds : angle 7.48907 / 5.32 ( 1659) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.413 Fit side-chains REVERT: A 137 SER cc_start: 0.8402 (t) cc_final: 0.8122 (p) REVERT: A 146 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7413 (tpp-160) REVERT: C 146 ARG cc_start: 0.7610 (tpt170) cc_final: 0.7176 (tpp-160) REVERT: E 146 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7277 (tpp-160) REVERT: G 146 ARG cc_start: 0.7808 (tpt170) cc_final: 0.7471 (tpp-160) REVERT: I 146 ARG cc_start: 0.7775 (tpt170) cc_final: 0.7423 (tpp-160) REVERT: K 137 SER cc_start: 0.8430 (t) cc_final: 0.8148 (p) REVERT: M 146 ARG cc_start: 0.7579 (tpt170) cc_final: 0.7288 (tpp-160) REVERT: O 146 ARG cc_start: 0.7612 (tpt170) cc_final: 0.7170 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1122 time to fit residues: 22.9432 Evaluate side-chains 137 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.118208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.099248 restraints weight = 13649.084| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.39 r_work: 0.2886 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12216 Z= 0.227 Angle : 0.546 4.642 16712 Z= 0.286 Chirality : 0.047 0.133 2048 Planarity : 0.004 0.031 2048 Dihedral : 5.520 43.407 1872 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.76 % Allowed : 1.04 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.22), residues: 1560 helix: 1.66 (0.20), residues: 704 sheet: 0.64 (0.26), residues: 240 loop : 0.93 (0.29), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 189 TYR 0.010 0.002 TYR O 17 PHE 0.016 0.002 PHE K 78 TRP 0.012 0.002 TRP E 197 HIS 0.004 0.001 HIS O 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (12216) covalent geometry : angle 0.54620 / 0.29 (16712) hydrogen bonds : bond 0.04287 / 2.91 ( 553) hydrogen bonds : angle 6.06157 / 4.33 ( 1659) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.515 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 136 average time/residue: 0.1109 time to fit residues: 21.9595 Evaluate side-chains 126 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.099880 restraints weight = 13821.335| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.42 r_work: 0.2915 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12216 Z= 0.222 Angle : 0.516 4.466 16712 Z= 0.271 Chirality : 0.047 0.127 2048 Planarity : 0.004 0.033 2048 Dihedral : 5.518 42.051 1872 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.76 % Allowed : 2.18 % Favored : 97.06 % 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: 1.42 (0.22), residues: 1560 helix: 1.35 (0.20), residues: 704 sheet: 0.93 (0.27), residues: 240 loop : 0.65 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.011 0.002 TYR C 17 PHE 0.013 0.002 PHE E 78 TRP 0.008 0.001 TRP G 197 HIS 0.003 0.001 HIS E 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (12216) covalent geometry : angle 0.51645 / 0.27 (16712) hydrogen bonds : bond 0.04030 / 2.75 ( 553) hydrogen bonds : angle 5.85905 / 4.18 ( 1659) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.364 Fit side-chains REVERT: A 146 ARG cc_start: 0.7667 (tpt170) cc_final: 0.7003 (tpp-160) REVERT: E 146 ARG cc_start: 0.7894 (tpt-90) cc_final: 0.7289 (tpp-160) REVERT: G 146 ARG cc_start: 0.7907 (tpt-90) cc_final: 0.7290 (tpp-160) REVERT: I 146 ARG cc_start: 0.7885 (tpt-90) cc_final: 0.7381 (tpp-160) REVERT: K 146 ARG cc_start: 0.7406 (tpp-160) cc_final: 0.7160 (tpp-160) REVERT: M 146 ARG cc_start: 0.7710 (tpt170) cc_final: 0.7033 (tpp-160) REVERT: O 146 ARG cc_start: 0.7895 (tpt-90) cc_final: 0.7441 (tpp-160) outliers start: 8 outliers final: 0 residues processed: 121 average time/residue: 0.1220 time to fit residues: 21.4039 Evaluate side-chains 121 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 0.0670 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100874 restraints weight = 13821.895| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.45 r_work: 0.2888 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12216 Z= 0.158 Angle : 0.453 4.389 16712 Z= 0.240 Chirality : 0.045 0.124 2048 Planarity : 0.003 0.031 2048 Dihedral : 5.293 43.223 1872 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: 1.49 (0.22), residues: 1560 helix: 1.39 (0.20), residues: 704 sheet: 1.15 (0.27), residues: 240 loop : 0.63 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 189 TYR 0.009 0.001 TYR K 17 PHE 0.012 0.001 PHE E 78 TRP 0.005 0.001 TRP A 197 HIS 0.002 0.001 HIS E 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (12216) covalent geometry : angle 0.45287 / 0.24 (16712) hydrogen bonds : bond 0.03537 / 2.41 ( 553) hydrogen bonds : angle 5.63514 / 4.03 ( 1659) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.559 Fit side-chains REVERT: G 146 ARG cc_start: 0.7881 (tpt-90) cc_final: 0.7394 (tpp-160) REVERT: I 146 ARG cc_start: 0.7848 (tpt170) cc_final: 0.7320 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1043 time to fit residues: 18.5450 Evaluate side-chains 117 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.117734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.098076 restraints weight = 13939.772| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.47 r_work: 0.2983 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 : 0.007 0.043 12216 Z= 0.299 Angle : 0.565 4.483 16712 Z= 0.292 Chirality : 0.048 0.132 2048 Planarity : 0.004 0.037 2048 Dihedral : 5.755 48.541 1872 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.19 % Allowed : 2.94 % Favored : 96.88 % 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: 1560 helix: 1.00 (0.20), residues: 704 sheet: 0.96 (0.27), residues: 240 loop : 0.34 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 189 TYR 0.016 0.002 TYR K 17 PHE 0.011 0.002 PHE E 78 TRP 0.007 0.002 TRP A 197 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.30 (12216) covalent geometry : angle 0.56460 / 0.29 (16712) hydrogen bonds : bond 0.04406 / 3.01 ( 553) hydrogen bonds : angle 5.98169 / 4.27 ( 1659) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.456 Fit side-chains REVERT: I 146 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7176 (tpp-160) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.1269 time to fit residues: 22.6422 Evaluate side-chains 128 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 146 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 19 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.119548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100226 restraints weight = 13891.626| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.45 r_work: 0.2885 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12216 Z= 0.168 Angle : 0.455 4.380 16712 Z= 0.241 Chirality : 0.045 0.124 2048 Planarity : 0.004 0.033 2048 Dihedral : 5.490 50.393 1872 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.76 % Allowed : 2.46 % Favored : 96.78 % 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: 1.21 (0.21), residues: 1560 helix: 1.21 (0.20), residues: 704 sheet: 1.08 (0.27), residues: 240 loop : 0.38 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 82 TYR 0.010 0.002 TYR M 17 PHE 0.011 0.001 PHE K 78 TRP 0.004 0.001 TRP G 197 HIS 0.002 0.001 HIS G 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (12216) covalent geometry : angle 0.45475 / 0.24 (16712) hydrogen bonds : bond 0.03575 / 2.44 ( 553) hydrogen bonds : angle 5.66183 / 4.05 ( 1659) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.399 Fit side-chains REVERT: I 146 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7291 (tpp-160) outliers start: 8 outliers final: 1 residues processed: 127 average time/residue: 0.0993 time to fit residues: 18.9904 Evaluate side-chains 120 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.098444 restraints weight = 13862.695| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.47 r_work: 0.3004 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12216 Z= 0.275 Angle : 0.538 4.467 16712 Z= 0.280 Chirality : 0.048 0.129 2048 Planarity : 0.004 0.036 2048 Dihedral : 5.740 50.295 1872 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.85 % Allowed : 3.03 % Favored : 96.12 % 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: 0.88 (0.21), residues: 1560 helix: 0.98 (0.19), residues: 704 sheet: 0.88 (0.28), residues: 240 loop : 0.16 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 82 TYR 0.015 0.002 TYR K 17 PHE 0.011 0.002 PHE K 78 TRP 0.006 0.001 TRP K 197 HIS 0.004 0.001 HIS G 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.27 (12216) covalent geometry : angle 0.53841 / 0.28 (16712) hydrogen bonds : bond 0.04234 / 2.90 ( 553) hydrogen bonds : angle 5.90103 / 4.22 ( 1659) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.457 Fit side-chains REVERT: I 146 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7101 (tpp-160) REVERT: M 146 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7309 (tpp-160) outliers start: 9 outliers final: 2 residues processed: 131 average time/residue: 0.1213 time to fit residues: 22.6478 Evaluate side-chains 128 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain I residue 146 ARG Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain M residue 146 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 9 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103672 restraints weight = 13746.508| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.34 r_work: 0.2961 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12216 Z= 0.116 Angle : 0.411 4.349 16712 Z= 0.222 Chirality : 0.043 0.121 2048 Planarity : 0.003 0.032 2048 Dihedral : 5.317 51.204 1872 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.14 % Allowed : 2.65 % Favored : 96.21 % 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: 1.33 (0.21), residues: 1560 helix: 1.37 (0.20), residues: 704 sheet: 1.10 (0.27), residues: 240 loop : 0.37 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 82 TYR 0.006 0.001 TYR M 17 PHE 0.013 0.001 PHE E 78 TRP 0.004 0.001 TRP I 139 HIS 0.001 0.000 HIS K 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (12216) covalent geometry : angle 0.41135 / 0.22 (16712) hydrogen bonds : bond 0.03196 / 2.18 ( 553) hydrogen bonds : angle 5.45535 / 3.90 ( 1659) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.441 Fit side-chains REVERT: C 146 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7367 (tpp-160) REVERT: I 146 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7435 (tpp-160) outliers start: 12 outliers final: 6 residues processed: 121 average time/residue: 0.0986 time to fit residues: 18.2176 Evaluate side-chains 114 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 146 ARG Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain O residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 99 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.118748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099641 restraints weight = 13902.360| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.42 r_work: 0.2913 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 12216 Z= 0.287 Angle : 0.547 4.559 16712 Z= 0.284 Chirality : 0.048 0.129 2048 Planarity : 0.004 0.035 2048 Dihedral : 5.712 50.396 1872 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.14 % Allowed : 2.65 % Favored : 96.21 % 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: 0.82 (0.21), residues: 1560 helix: 0.96 (0.19), residues: 704 sheet: 0.81 (0.27), residues: 240 loop : 0.11 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 189 TYR 0.016 0.002 TYR K 17 PHE 0.011 0.002 PHE A 78 TRP 0.006 0.001 TRP A 197 HIS 0.004 0.001 HIS I 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.29 (12216) covalent geometry : angle 0.54678 / 0.28 (16712) hydrogen bonds : bond 0.04273 / 2.93 ( 553) hydrogen bonds : angle 5.91408 / 4.23 ( 1659) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.492 Fit side-chains REVERT: A 146 ARG cc_start: 0.7839 (tpt-90) cc_final: 0.7228 (tpp-160) REVERT: M 146 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7166 (tpp-160) outliers start: 12 outliers final: 5 residues processed: 127 average time/residue: 0.1098 time to fit residues: 20.6509 Evaluate side-chains 122 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain M residue 146 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.101564 restraints weight = 13906.506| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.45 r_work: 0.2948 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12216 Z= 0.128 Angle : 0.421 4.389 16712 Z= 0.227 Chirality : 0.044 0.123 2048 Planarity : 0.003 0.033 2048 Dihedral : 5.381 51.503 1872 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.85 % Allowed : 2.94 % Favored : 96.21 % 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: 1.22 (0.21), residues: 1560 helix: 1.30 (0.20), residues: 704 sheet: 1.03 (0.27), residues: 240 loop : 0.29 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 82 TYR 0.007 0.001 TYR C 17 PHE 0.012 0.001 PHE M 78 TRP 0.004 0.001 TRP K 139 HIS 0.002 0.000 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (12216) covalent geometry : angle 0.42147 / 0.23 (16712) hydrogen bonds : bond 0.03282 / 2.24 ( 553) hydrogen bonds : angle 5.46655 / 3.91 ( 1659) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.466 Fit side-chains REVERT: M 42 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8537 (mp10) REVERT: M 146 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7439 (tpp-160) outliers start: 9 outliers final: 6 residues processed: 114 average time/residue: 0.0857 time to fit residues: 15.9437 Evaluate side-chains 113 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain M residue 146 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.122894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103581 restraints weight = 13723.468| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.44 r_work: 0.2987 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 12216 Z= 0.111 Angle : 0.400 4.421 16712 Z= 0.216 Chirality : 0.043 0.120 2048 Planarity : 0.003 0.032 2048 Dihedral : 5.202 51.204 1872 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.76 % Allowed : 3.03 % Favored : 96.21 % 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: 1560 helix: 1.47 (0.20), residues: 704 sheet: 1.30 (0.27), residues: 240 loop : 0.40 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 82 TYR 0.005 0.001 TYR K 17 PHE 0.013 0.001 PHE A 78 TRP 0.004 0.001 TRP E 139 HIS 0.001 0.000 HIS M 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (12216) covalent geometry : angle 0.39997 / 0.22 (16712) hydrogen bonds : bond 0.03081 / 2.10 ( 553) hydrogen bonds : angle 5.29437 / 3.78 ( 1659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2226.69 seconds wall clock time: 39 minutes 4.41 seconds (2344.41 seconds total)