Starting phenix.real_space_refine on Mon Mar 18 01:43:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/03_2024/8ap9_15562_trim_updated.pdb" } resolution = 3.7 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= -0.001 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 53 5.16 5 C 6295 2.51 5 N 1591 2.21 5 O 1744 1.98 5 H 9972 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19658 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4448 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 5, 'TRANS': 273} Chain: "H" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 2483 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain: "I" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1046 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "O" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1165 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "P" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1165 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "Q" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1165 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "R" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1165 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1166 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "T" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1166 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "U" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1165 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "V" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1165 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "W" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1165 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "X" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1165 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'UTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.47, per 1000 atoms: 0.48 Number of scatterers: 19658 At special positions: 0 Unit cell: (116.2, 77.19, 171.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 3 15.00 O 1744 8.00 N 1591 7.00 C 6295 6.00 H 9972 1.00 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 - 3.50 Amino acid : False - 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: 17.14 Conformation dependent library (CDL) restraints added in 2.2 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 4 sheets defined 70.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'G' and resid 4 through 42 removed outlier: 4.392A pdb=" N GLY G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ARG G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR G 42 " --> pdb=" O GLY G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 62 through 65 No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 86 through 97 Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.278A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 192 Processing helix chain 'G' and resid 200 through 208 Processing helix chain 'G' and resid 211 through 279 Processing helix chain 'H' and resid 27 through 30 removed outlier: 3.575A pdb=" N PHE H 30 " --> pdb=" O GLY H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 27 through 30' Processing helix chain 'H' and resid 139 through 154 removed outlier: 3.757A pdb=" N GLY H 154 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 181 Processing helix chain 'I' and resid 14 through 16 No H-bonds generated for 'chain 'I' and resid 14 through 16' Processing helix chain 'I' and resid 20 through 33 Processing helix chain 'I' and resid 37 through 46 removed outlier: 4.222A pdb=" N ALA I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS I 42 " --> pdb=" O SER I 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TRP I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 82 removed outlier: 3.961A pdb=" N GLY O 54 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR O 55 " --> pdb=" O TYR O 52 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY O 64 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 65 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY O 66 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU O 67 " --> pdb=" O GLY O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 117 removed outlier: 3.627A pdb=" N LEU O 111 " --> pdb=" O PHE O 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 80 removed outlier: 4.036A pdb=" N GLY P 54 " --> pdb=" O HIS P 51 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY P 66 " --> pdb=" O ALA P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 116 removed outlier: 5.259A pdb=" N LYS P 88 " --> pdb=" O ASN P 85 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU P 102 " --> pdb=" O ALA P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 82 removed outlier: 3.598A pdb=" N CYS Q 80 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 116 removed outlier: 5.076A pdb=" N LYS Q 88 " --> pdb=" O ASN Q 85 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU Q 102 " --> pdb=" O ALA Q 99 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA Q 103 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE Q 104 " --> pdb=" O THR Q 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 82 removed outlier: 3.878A pdb=" N ALA R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA R 63 " --> pdb=" O ALA R 59 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY R 64 " --> pdb=" O ILE R 60 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 117 removed outlier: 5.550A pdb=" N LYS R 88 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE R 117 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 82 removed outlier: 4.078A pdb=" N GLY S 54 " --> pdb=" O HIS S 51 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY S 66 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU S 67 " --> pdb=" O GLY S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 116 removed outlier: 3.646A pdb=" N THR S 87 " --> pdb=" O PRO S 84 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LYS S 88 " --> pdb=" O ASN S 85 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET S 89 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 82 removed outlier: 3.675A pdb=" N VAL T 53 " --> pdb=" O LEU T 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY T 54 " --> pdb=" O HIS T 51 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA T 59 " --> pdb=" O GLY T 56 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY T 66 " --> pdb=" O ALA T 63 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU T 67 " --> pdb=" O GLY T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 116 removed outlier: 5.156A pdb=" N LYS T 88 " --> pdb=" O ASN T 85 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET T 89 " --> pdb=" O LEU T 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 82 removed outlier: 4.626A pdb=" N GLY U 54 " --> pdb=" O HIS U 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL U 65 " --> pdb=" O LEU U 62 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY U 66 " --> pdb=" O ALA U 63 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA U 81 " --> pdb=" O VAL U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 115 removed outlier: 5.102A pdb=" N LYS U 88 " --> pdb=" O ASN U 85 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU U 102 " --> pdb=" O ALA U 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 80 removed outlier: 3.957A pdb=" N HIS V 51 " --> pdb=" O GLN V 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR V 52 " --> pdb=" O GLY V 49 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY V 54 " --> pdb=" O HIS V 51 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY V 66 " --> pdb=" O ALA V 63 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU V 67 " --> pdb=" O GLY V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 114 removed outlier: 4.827A pdb=" N LYS V 88 " --> pdb=" O ASN V 85 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE V 91 " --> pdb=" O LYS V 88 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR V 101 " --> pdb=" O PHE V 98 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU V 102 " --> pdb=" O ALA V 99 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU V 106 " --> pdb=" O ALA V 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 82 removed outlier: 4.297A pdb=" N GLY W 54 " --> pdb=" O HIS W 51 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA W 58 " --> pdb=" O THR W 55 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY W 64 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY W 66 " --> pdb=" O ALA W 63 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU W 76 " --> pdb=" O PHE W 73 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA W 81 " --> pdb=" O VAL W 78 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG W 82 " --> pdb=" O ALA W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 116 removed outlier: 3.524A pdb=" N THR W 87 " --> pdb=" O PRO W 84 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS W 88 " --> pdb=" O ASN W 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU W 90 " --> pdb=" O THR W 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 82 removed outlier: 4.025A pdb=" N GLY X 54 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA X 61 " --> pdb=" O ALA X 58 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU X 67 " --> pdb=" O GLY X 64 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU X 76 " --> pdb=" O PHE X 73 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU X 77 " --> pdb=" O GLY X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 86 No H-bonds generated for 'chain 'X' and resid 84 through 86' Processing helix chain 'X' and resid 89 through 116 removed outlier: 3.707A pdb=" N LEU X 111 " --> pdb=" O PHE X 107 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 102 through 104 removed outlier: 6.282A pdb=" N LEU G 71 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL G 72 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR G 157 " --> pdb=" O VAL G 72 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE G 74 " --> pdb=" O TYR G 157 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL G 159 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL G 169 " --> pdb=" O VAL G 165 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.641A pdb=" N SER H 123 " --> pdb=" O ASN H 119 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 78 through 82 removed outlier: 4.099A pdb=" N THR H 73 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 54 through 56 744 hydrogen bonds defined for protein. 855 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: 7.27 Time building geometry restraints manager: 17.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9955 1.03 - 1.23: 18 1.23 - 1.42: 4026 1.42 - 1.61: 5735 1.61 - 1.81: 89 Bond restraints: 19823 Sorted by residual: bond pdb=" C2' UTP H 201 " pdb=" C3' UTP H 201 " ideal model delta sigma weight residual 1.301 1.531 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' UTP H 201 " pdb=" N1 UTP H 201 " ideal model delta sigma weight residual 1.305 1.471 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C1' UTP H 201 " pdb=" O4' UTP H 201 " ideal model delta sigma weight residual 1.553 1.413 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C4' UTP H 201 " pdb=" O4' UTP H 201 " ideal model delta sigma weight residual 1.320 1.446 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C3' UTP H 201 " pdb=" C4' UTP H 201 " ideal model delta sigma weight residual 1.654 1.531 0.123 2.00e-02 2.50e+03 3.79e+01 ... (remaining 19818 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.39: 164 106.39 - 113.28: 23649 113.28 - 120.18: 6334 120.18 - 127.07: 5644 127.07 - 133.96: 55 Bond angle restraints: 35846 Sorted by residual: angle pdb=" PA UTP H 201 " pdb=" O3A UTP H 201 " pdb=" PB UTP H 201 " ideal model delta sigma weight residual 123.59 133.23 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" PB UTP H 201 " pdb=" O3B UTP H 201 " pdb=" PG UTP H 201 " ideal model delta sigma weight residual 123.27 132.49 -9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" O3A UTP H 201 " pdb=" PB UTP H 201 " pdb=" O3B UTP H 201 " ideal model delta sigma weight residual 109.68 101.89 7.79 3.00e+00 1.11e-01 6.74e+00 angle pdb=" C2 UTP H 201 " pdb=" N3 UTP H 201 " pdb=" C4 UTP H 201 " ideal model delta sigma weight residual 120.04 126.92 -6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" O1B UTP H 201 " pdb=" PB UTP H 201 " pdb=" O2B UTP H 201 " ideal model delta sigma weight residual 109.50 116.11 -6.61 3.00e+00 1.11e-01 4.85e+00 ... (remaining 35841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 8413 14.55 - 29.10: 551 29.10 - 43.65: 90 43.65 - 58.19: 185 58.19 - 72.74: 26 Dihedral angle restraints: 9265 sinusoidal: 4968 harmonic: 4297 Sorted by residual: dihedral pdb=" CG ARG I 40 " pdb=" CD ARG I 40 " pdb=" NE ARG I 40 " pdb=" CZ ARG I 40 " ideal model delta sinusoidal sigma weight residual 90.00 132.47 -42.47 2 1.50e+01 4.44e-03 9.73e+00 dihedral pdb=" N PHE X 107 " pdb=" CA PHE X 107 " pdb=" CB PHE X 107 " pdb=" CG PHE X 107 " ideal model delta sinusoidal sigma weight residual -60.00 -118.50 58.50 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LYS H 34 " pdb=" CA LYS H 34 " pdb=" CB LYS H 34 " pdb=" CG LYS H 34 " ideal model delta sinusoidal sigma weight residual -60.00 -109.80 49.80 3 1.50e+01 4.44e-03 8.82e+00 ... (remaining 9262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1365 0.052 - 0.104: 214 0.104 - 0.155: 29 0.155 - 0.207: 1 0.207 - 0.259: 1 Chirality restraints: 1610 Sorted by residual: chirality pdb=" C2' UTP H 201 " pdb=" C1' UTP H 201 " pdb=" C3' UTP H 201 " pdb=" O2' UTP H 201 " both_signs ideal model delta sigma weight residual False -2.41 -2.67 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C3' UTP H 201 " pdb=" C2' UTP H 201 " pdb=" C4' UTP H 201 " pdb=" O3' UTP H 201 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE H 118 " pdb=" N ILE H 118 " pdb=" C ILE H 118 " pdb=" CB ILE H 118 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1607 not shown) Planarity restraints: 2914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER S 41 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C SER S 41 " -0.056 2.00e-02 2.50e+03 pdb=" O SER S 41 " 0.021 2.00e-02 2.50e+03 pdb=" N THR S 42 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER W 41 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C SER W 41 " -0.053 2.00e-02 2.50e+03 pdb=" O SER W 41 " 0.020 2.00e-02 2.50e+03 pdb=" N THR W 42 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER V 41 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.14e+00 pdb=" C SER V 41 " 0.046 2.00e-02 2.50e+03 pdb=" O SER V 41 " -0.017 2.00e-02 2.50e+03 pdb=" N THR V 42 " -0.016 2.00e-02 2.50e+03 ... (remaining 2911 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1223 2.20 - 2.80: 42439 2.80 - 3.40: 54433 3.40 - 4.00: 71668 4.00 - 4.60: 116838 Nonbonded interactions: 286601 Sorted by model distance: nonbonded pdb=" OD1 ASP G 186 " pdb="HE22 GLN G 196 " model vdw 1.603 1.850 nonbonded pdb=" O LEU Q 106 " pdb=" H MET Q 110 " model vdw 1.607 1.850 nonbonded pdb=" O GLU G 51 " pdb=" H SER G 55 " model vdw 1.617 1.850 nonbonded pdb=" O GLY X 70 " pdb=" H GLY X 74 " model vdw 1.634 1.850 nonbonded pdb=" OD1 ASN G 208 " pdb="HH21 ARG R 82 " model vdw 1.643 1.850 ... (remaining 286596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = (chain 'S' and (resid 41 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 52 through 118)) selection = (chain 'T' and (resid 41 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 52 through 118)) selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 36.990 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 67.490 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.006 0.230 9851 Z= 0.423 Angle : 0.478 9.639 13354 Z= 0.251 Chirality : 0.038 0.259 1610 Planarity : 0.004 0.042 1666 Dihedral : 9.769 72.742 3424 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.40 % Allowed : 3.63 % Favored : 95.97 % 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: -0.08 (0.24), residues: 1259 helix: 0.27 (0.18), residues: 857 sheet: 0.10 (0.65), residues: 75 loop : -0.62 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 183 HIS 0.005 0.001 HIS G 221 PHE 0.014 0.001 PHE H 60 TYR 0.009 0.001 TYR G 200 ARG 0.003 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7897 (tptt) REVERT: I 48 LYS cc_start: 0.7767 (mttt) cc_final: 0.7231 (tmtt) REVERT: P 83 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7861 (tp40) REVERT: V 88 LYS cc_start: 0.8490 (tptt) cc_final: 0.7895 (tttt) REVERT: X 107 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7773 (m-80) outliers start: 4 outliers final: 3 residues processed: 133 average time/residue: 0.6410 time to fit residues: 112.4820 Evaluate side-chains 86 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN Q 51 HIS V 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9851 Z= 0.234 Angle : 0.499 5.224 13354 Z= 0.293 Chirality : 0.038 0.142 1610 Planarity : 0.006 0.040 1666 Dihedral : 5.222 60.404 1386 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.81 % Allowed : 7.26 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.23), residues: 1259 helix: -0.39 (0.17), residues: 856 sheet: 0.01 (0.64), residues: 75 loop : -0.67 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 13 HIS 0.007 0.002 HIS H 181 PHE 0.015 0.001 PHE O 73 TYR 0.011 0.001 TYR G 49 ARG 0.003 0.000 ARG G 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7820 (tptt) REVERT: H 135 ASP cc_start: 0.7802 (t70) cc_final: 0.7586 (t70) REVERT: V 88 LYS cc_start: 0.8719 (tptt) cc_final: 0.8136 (tttt) REVERT: X 107 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8006 (m-80) outliers start: 8 outliers final: 5 residues processed: 114 average time/residue: 0.4785 time to fit residues: 77.3946 Evaluate side-chains 104 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 96 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9851 Z= 0.194 Angle : 0.434 4.508 13354 Z= 0.254 Chirality : 0.037 0.152 1610 Planarity : 0.005 0.041 1666 Dihedral : 4.880 58.383 1382 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.31 % Allowed : 8.37 % Favored : 90.32 % 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: -1.27 (0.23), residues: 1259 helix: -0.77 (0.17), residues: 857 sheet: -0.11 (0.64), residues: 75 loop : -0.68 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 183 HIS 0.005 0.001 HIS P 51 PHE 0.012 0.001 PHE H 60 TYR 0.007 0.001 TYR W 52 ARG 0.002 0.000 ARG Q 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7769 (tptt) REVERT: H 135 ASP cc_start: 0.7893 (t70) cc_final: 0.7674 (t70) REVERT: T 82 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7569 (ttt90) REVERT: V 88 LYS cc_start: 0.8763 (tptt) cc_final: 0.8138 (tttt) REVERT: V 115 MET cc_start: 0.8366 (mtm) cc_final: 0.7961 (mtp) REVERT: X 107 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7888 (m-80) outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.4241 time to fit residues: 68.7350 Evaluate side-chains 105 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 118 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 HIS T 85 ASN V 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9851 Z= 0.226 Angle : 0.451 4.713 13354 Z= 0.261 Chirality : 0.038 0.141 1610 Planarity : 0.005 0.042 1666 Dihedral : 5.123 67.347 1382 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.41 % Allowed : 8.57 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.23), residues: 1259 helix: -0.95 (0.17), residues: 857 sheet: -0.22 (0.63), residues: 75 loop : -0.79 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 183 HIS 0.006 0.001 HIS H 181 PHE 0.014 0.001 PHE H 60 TYR 0.009 0.001 TYR G 49 ARG 0.002 0.000 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7743 (tptt) REVERT: T 82 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7618 (ttt90) REVERT: V 88 LYS cc_start: 0.8795 (tptt) cc_final: 0.8184 (tttt) REVERT: X 107 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7966 (m-80) outliers start: 14 outliers final: 10 residues processed: 118 average time/residue: 0.4993 time to fit residues: 82.5928 Evaluate side-chains 114 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9851 Z= 0.226 Angle : 0.441 4.693 13354 Z= 0.255 Chirality : 0.038 0.139 1610 Planarity : 0.005 0.042 1666 Dihedral : 5.289 79.885 1382 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.61 % Allowed : 9.17 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.60 (0.23), residues: 1259 helix: -0.99 (0.17), residues: 858 sheet: -0.54 (0.61), residues: 79 loop : -0.80 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 13 HIS 0.005 0.001 HIS G 221 PHE 0.013 0.001 PHE H 60 TYR 0.008 0.001 TYR G 49 ARG 0.004 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7885 (mmtt) REVERT: T 82 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7623 (ttt90) REVERT: V 88 LYS cc_start: 0.8802 (tptt) cc_final: 0.8189 (tttt) REVERT: W 89 MET cc_start: 0.8015 (ttp) cc_final: 0.7800 (ttp) REVERT: X 107 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7938 (m-80) outliers start: 16 outliers final: 14 residues processed: 116 average time/residue: 0.5226 time to fit residues: 86.9629 Evaluate side-chains 116 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 118 SER Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 9851 Z= 0.231 Angle : 0.443 4.747 13354 Z= 0.256 Chirality : 0.038 0.140 1610 Planarity : 0.005 0.044 1666 Dihedral : 5.391 86.040 1382 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.92 % Allowed : 8.97 % Favored : 89.11 % 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: -1.64 (0.23), residues: 1259 helix: -1.02 (0.17), residues: 858 sheet: -0.50 (0.61), residues: 79 loop : -0.82 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 13 HIS 0.005 0.001 HIS G 221 PHE 0.014 0.001 PHE R 73 TYR 0.009 0.001 TYR G 49 ARG 0.003 0.000 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: G 267 ARG cc_start: 0.7992 (ttt90) cc_final: 0.7563 (ttm170) REVERT: H 107 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7870 (mmtt) REVERT: T 82 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7633 (ttt90) REVERT: T 102 GLU cc_start: 0.7749 (tp30) cc_final: 0.7485 (tp30) REVERT: V 88 LYS cc_start: 0.8789 (tptt) cc_final: 0.8183 (tttt) REVERT: X 88 LYS cc_start: 0.8093 (mttt) cc_final: 0.7736 (tttm) REVERT: X 107 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8024 (m-80) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.4901 time to fit residues: 84.7676 Evaluate side-chains 121 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 118 SER Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9851 Z= 0.131 Angle : 0.398 4.451 13354 Z= 0.232 Chirality : 0.036 0.138 1610 Planarity : 0.005 0.042 1666 Dihedral : 5.086 87.448 1382 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.31 % Allowed : 9.27 % Favored : 89.42 % 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: -1.48 (0.23), residues: 1259 helix: -0.95 (0.17), residues: 858 sheet: -0.38 (0.62), residues: 79 loop : -0.65 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 13 HIS 0.004 0.001 HIS P 51 PHE 0.011 0.001 PHE R 73 TYR 0.006 0.001 TYR W 52 ARG 0.003 0.000 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7857 (mmtt) REVERT: T 82 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7636 (ttt90) REVERT: T 102 GLU cc_start: 0.7716 (tp30) cc_final: 0.7451 (tp30) REVERT: V 88 LYS cc_start: 0.8780 (tptt) cc_final: 0.8171 (tttt) REVERT: X 107 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7965 (m-80) outliers start: 13 outliers final: 12 residues processed: 119 average time/residue: 0.4162 time to fit residues: 72.5715 Evaluate side-chains 113 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9851 Z= 0.207 Angle : 0.426 4.561 13354 Z= 0.246 Chirality : 0.037 0.139 1610 Planarity : 0.005 0.043 1666 Dihedral : 5.183 88.804 1382 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.51 % Allowed : 9.27 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.54 (0.23), residues: 1259 helix: -0.96 (0.17), residues: 858 sheet: -0.47 (0.62), residues: 79 loop : -0.74 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 13 HIS 0.005 0.001 HIS G 221 PHE 0.013 0.001 PHE R 73 TYR 0.009 0.001 TYR G 49 ARG 0.002 0.000 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7859 (mmtt) REVERT: T 82 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7629 (ttt90) REVERT: T 102 GLU cc_start: 0.7747 (tp30) cc_final: 0.7474 (tp30) REVERT: V 88 LYS cc_start: 0.8779 (tptt) cc_final: 0.8175 (tttt) REVERT: X 88 LYS cc_start: 0.8088 (mttt) cc_final: 0.7705 (tttm) REVERT: X 107 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8025 (m-80) outliers start: 15 outliers final: 14 residues processed: 116 average time/residue: 0.4873 time to fit residues: 80.6344 Evaluate side-chains 115 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9851 Z= 0.183 Angle : 0.416 4.512 13354 Z= 0.240 Chirality : 0.037 0.138 1610 Planarity : 0.005 0.043 1666 Dihedral : 5.155 89.901 1382 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.51 % Allowed : 9.48 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.23), residues: 1259 helix: -0.96 (0.17), residues: 858 sheet: -0.34 (0.62), residues: 77 loop : -0.73 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 13 HIS 0.004 0.001 HIS G 221 PHE 0.012 0.001 PHE R 73 TYR 0.007 0.001 TYR G 49 ARG 0.004 0.000 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7845 (mmtt) REVERT: T 82 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7631 (ttt90) REVERT: T 102 GLU cc_start: 0.7775 (tp30) cc_final: 0.7505 (tp30) REVERT: V 88 LYS cc_start: 0.8777 (tptt) cc_final: 0.8173 (tttt) REVERT: V 115 MET cc_start: 0.8282 (mtm) cc_final: 0.8009 (mtm) REVERT: X 88 LYS cc_start: 0.8099 (mttt) cc_final: 0.7705 (tttm) REVERT: X 107 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8008 (m-80) outliers start: 15 outliers final: 12 residues processed: 115 average time/residue: 0.4596 time to fit residues: 75.9786 Evaluate side-chains 113 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9851 Z= 0.239 Angle : 0.442 4.693 13354 Z= 0.255 Chirality : 0.038 0.139 1610 Planarity : 0.005 0.043 1666 Dihedral : 5.316 88.844 1382 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.51 % Allowed : 9.58 % Favored : 88.91 % 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: -1.61 (0.23), residues: 1259 helix: -1.00 (0.17), residues: 858 sheet: -0.41 (0.62), residues: 77 loop : -0.83 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 13 HIS 0.005 0.001 HIS G 221 PHE 0.015 0.001 PHE H 60 TYR 0.009 0.001 TYR G 49 ARG 0.003 0.000 ARG H 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7863 (mmtt) REVERT: Q 88 LYS cc_start: 0.8042 (tttt) cc_final: 0.7751 (ttpt) REVERT: T 82 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7650 (ttt90) REVERT: T 102 GLU cc_start: 0.7817 (tp30) cc_final: 0.7512 (tp30) REVERT: V 88 LYS cc_start: 0.8780 (tptt) cc_final: 0.8163 (tttt) REVERT: V 115 MET cc_start: 0.8398 (mtm) cc_final: 0.8094 (mtm) REVERT: X 88 LYS cc_start: 0.8108 (mttt) cc_final: 0.7705 (tttm) REVERT: X 107 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8029 (m-80) outliers start: 15 outliers final: 13 residues processed: 115 average time/residue: 0.5137 time to fit residues: 82.5736 Evaluate side-chains 112 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 51 TYR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 107 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 97 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 0.0980 chunk 68 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099625 restraints weight = 37281.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.102431 restraints weight = 15096.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104037 restraints weight = 7832.867| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9851 Z= 0.133 Angle : 0.397 4.410 13354 Z= 0.230 Chirality : 0.036 0.137 1610 Planarity : 0.005 0.041 1666 Dihedral : 4.974 87.833 1382 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.21 % Allowed : 10.08 % Favored : 88.71 % 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: -1.45 (0.23), residues: 1259 helix: -0.92 (0.17), residues: 859 sheet: -0.24 (0.64), residues: 77 loop : -0.70 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 13 HIS 0.004 0.001 HIS H 181 PHE 0.010 0.001 PHE R 73 TYR 0.006 0.001 TYR W 52 ARG 0.004 0.000 ARG H 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4139.47 seconds wall clock time: 76 minutes 6.14 seconds (4566.14 seconds total)