Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 06:59:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/04_2023/8ap9_15562_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/04_2023/8ap9_15562.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/04_2023/8ap9_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_15562/04_2023/8ap9_15562_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/04_2023/8ap9_15562_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/04_2023/8ap9_15562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/04_2023/8ap9_15562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/04_2023/8ap9_15562_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap9_15562/04_2023/8ap9_15562_trim_updated.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 8.64, per 1000 atoms: 0.44 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: 18.56 Conformation dependent library (CDL) restraints added in 1.6 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: 1.17 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: 7.55 Time building geometry restraints manager: 18.78 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: 7279 14.55 - 29.10: 496 29.10 - 43.65: 40 43.65 - 58.19: 19 58.19 - 72.74: 5 Dihedral angle restraints: 7839 sinusoidal: 3542 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 7836 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: 12.680 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: 0.270 Extract box with map and model: 36.990 Check model and map are aligned: 0.270 Set scattering table: 0.190 Process input model: 66.140 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.060 ------------------------------------------------------------------------------- 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 : 9.612 72.742 3417 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 % 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 *********************** 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 : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 133 average time/residue: 0.6473 time to fit residues: 112.9971 Evaluate side-chains 82 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2567 time to fit residues: 3.2015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.0020 overall best weight: 0.7588 ------------------------------------------------------------------------------- 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: 0.8124 moved from start: 0.1982 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= 0.201 Angle : 0.478 4.834 13354 Z= 0.281 Chirality : 0.038 0.142 1610 Planarity : 0.006 0.037 1666 Dihedral : 4.094 59.405 1371 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.40 % 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: -0.40 (0.17), residues: 856 sheet: 0.08 (0.65), residues: 75 loop : -0.62 (0.35), residues: 328 *********************** 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 108 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 106 average time/residue: 0.4707 time to fit residues: 71.5097 Evaluate side-chains 97 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1986 time to fit residues: 3.0790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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: 0.8180 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 9851 Z= 0.214 Angle : 0.456 4.685 13354 Z= 0.266 Chirality : 0.038 0.153 1610 Planarity : 0.005 0.036 1666 Dihedral : 4.150 54.343 1371 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.23), residues: 1259 helix: -0.76 (0.17), residues: 858 sheet: -0.10 (0.64), residues: 75 loop : -0.64 (0.34), residues: 326 *********************** 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 117 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.669 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 113 average time/residue: 0.4603 time to fit residues: 75.6534 Evaluate side-chains 101 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2436 time to fit residues: 4.0620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** V 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9851 Z= 0.174 Angle : 0.424 4.594 13354 Z= 0.246 Chirality : 0.037 0.139 1610 Planarity : 0.005 0.036 1666 Dihedral : 4.084 55.965 1371 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.50 % 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: -1.34 (0.23), residues: 1259 helix: -0.86 (0.17), residues: 859 sheet: -0.11 (0.64), residues: 75 loop : -0.60 (0.34), residues: 325 *********************** 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 107 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 105 average time/residue: 0.4686 time to fit residues: 70.8041 Evaluate side-chains 101 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2242 time to fit residues: 3.2034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** R 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3479 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= 0.202 Angle : 0.432 4.809 13354 Z= 0.250 Chirality : 0.037 0.140 1610 Planarity : 0.005 0.037 1666 Dihedral : 4.200 63.637 1371 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.71 % 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: -1.42 (0.23), residues: 1259 helix: -0.92 (0.17), residues: 858 sheet: -0.17 (0.63), residues: 75 loop : -0.62 (0.34), residues: 326 *********************** 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 115 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 2.226 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 114 average time/residue: 0.5480 time to fit residues: 89.0199 Evaluate side-chains 108 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4406 time to fit residues: 5.7187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** P 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 9851 Z= 0.211 Angle : 0.437 4.767 13354 Z= 0.252 Chirality : 0.037 0.139 1610 Planarity : 0.005 0.036 1666 Dihedral : 4.373 73.131 1371 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.23), residues: 1259 helix: -0.95 (0.17), residues: 858 sheet: -0.16 (0.63), residues: 75 loop : -0.66 (0.34), residues: 326 *********************** 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 104 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 104 average time/residue: 0.4548 time to fit residues: 69.3700 Evaluate side-chains 100 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.667 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2708 time to fit residues: 2.9257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** P 85 ASN T 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 9851 Z= 0.192 Angle : 0.424 4.729 13354 Z= 0.245 Chirality : 0.037 0.139 1610 Planarity : 0.005 0.036 1666 Dihedral : 4.399 78.534 1371 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.10 % 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: -0.95 (0.17), residues: 858 sheet: -0.14 (0.64), residues: 75 loop : -0.64 (0.34), residues: 326 *********************** 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 102 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.4791 time to fit residues: 71.0078 Evaluate side-chains 96 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 9851 Z= 0.167 Angle : 0.413 4.641 13354 Z= 0.239 Chirality : 0.037 0.138 1610 Planarity : 0.005 0.036 1666 Dihedral : 4.344 81.626 1371 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1259 helix: -0.92 (0.17), residues: 858 sheet: -0.11 (0.64), residues: 75 loop : -0.61 (0.34), residues: 326 *********************** 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 100 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 100 average time/residue: 0.4744 time to fit residues: 68.9685 Evaluate side-chains 98 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5377 time to fit residues: 4.1385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.0370 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 9851 Z= 0.131 Angle : 0.396 4.530 13354 Z= 0.229 Chirality : 0.036 0.137 1610 Planarity : 0.005 0.035 1666 Dihedral : 4.134 81.161 1371 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.00 % 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: -1.31 (0.23), residues: 1259 helix: -0.86 (0.17), residues: 859 sheet: -0.03 (0.64), residues: 75 loop : -0.54 (0.34), residues: 325 *********************** 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 104 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.5093 time to fit residues: 75.2314 Evaluate side-chains 96 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 9851 Z= 0.167 Angle : 0.410 4.629 13354 Z= 0.237 Chirality : 0.036 0.139 1610 Planarity : 0.005 0.036 1666 Dihedral : 4.222 83.172 1371 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.10 % 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: -1.30 (0.23), residues: 1259 helix: -0.86 (0.17), residues: 858 sheet: -0.00 (0.64), residues: 75 loop : -0.54 (0.34), residues: 326 ********************** 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 101 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.4538 time to fit residues: 67.2679 Evaluate side-chains 100 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3891 time to fit residues: 2.4803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099395 restraints weight = 37361.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.102191 restraints weight = 15360.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103770 restraints weight = 8060.769| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9851 Z= 0.219 Angle : 0.433 4.771 13354 Z= 0.250 Chirality : 0.037 0.139 1610 Planarity : 0.005 0.037 1666 Dihedral : 4.495 86.585 1371 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.10 % 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: -1.38 (0.23), residues: 1259 helix: -0.91 (0.17), residues: 858 sheet: -0.07 (0.63), residues: 75 loop : -0.58 (0.34), residues: 326 =============================================================================== Job complete usr+sys time: 4074.04 seconds wall clock time: 73 minutes 24.90 seconds (4404.90 seconds total)