Starting phenix.real_space_refine on Sat Jul 4 07:44:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ap9_15562/07_2026/8ap9_15562_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ap9_15562/07_2026/8ap9_15562.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ap9_15562/07_2026/8ap9_15562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ap9_15562/07_2026/8ap9_15562.map" model { file = "/net/cci-nas-00/data/ceres_data/8ap9_15562/07_2026/8ap9_15562_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ap9_15562/07_2026/8ap9_15562_trim.cif" } 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 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. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.08, per 1000 atoms: 0.16 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 590.5 milliseconds 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... Secondary structure from input PDB file: 44 helices and 5 sheets defined 73.5% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'G' and resid 3 through 37 Processing helix chain 'G' and resid 38 through 43 removed outlier: 3.803A pdb=" N THR G 42 " --> pdb=" O GLY G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 55 removed outlier: 3.880A pdb=" N LEU G 52 " --> pdb=" O ARG G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 66 Processing helix chain 'G' and resid 85 through 97 Processing helix chain 'G' and resid 108 through 119 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 136 through 151 removed outlier: 3.655A pdb=" N ALA G 140 " --> pdb=" O HIS G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 193 Processing helix chain 'G' and resid 199 through 209 removed outlier: 3.688A pdb=" N GLU G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 280 removed outlier: 3.532A pdb=" N ILE G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 removed outlier: 3.575A pdb=" N PHE H 30 " --> pdb=" O GLY H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 155 removed outlier: 3.874A pdb=" N ALA H 142 " --> pdb=" O ASP H 138 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY H 154 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 155 " --> pdb=" O ALA H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 182 removed outlier: 3.709A pdb=" N HIS H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 17 Processing helix chain 'I' and resid 19 through 34 Processing helix chain 'I' and resid 36 through 44 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) Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'O' and resid 49 through 83 removed outlier: 3.809A pdb=" N VAL O 53 " --> pdb=" O GLY O 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY O 64 " --> pdb=" O ILE O 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 116 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 81 removed outlier: 4.017A pdb=" N VAL P 53 " --> pdb=" O GLY P 49 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY P 64 " --> pdb=" O ILE P 60 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU P 67 " --> pdb=" O ALA P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 85 No H-bonds generated for 'chain 'P' and resid 83 through 85' Processing helix chain 'P' and resid 86 through 117 removed outlier: 3.908A pdb=" N ALA P 103 " --> pdb=" O ALA P 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY P 105 " --> pdb=" O THR P 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 61 removed outlier: 3.535A pdb=" N GLY Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 83 removed outlier: 3.687A pdb=" N VAL Q 65 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 117 removed outlier: 3.808A pdb=" N ALA Q 103 " --> pdb=" O ALA Q 99 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE Q 104 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY Q 105 " --> pdb=" O THR Q 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 60 Processing helix chain 'R' and resid 61 through 83 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 86 through 118 Processing helix chain 'S' and resid 49 through 83 removed outlier: 3.903A pdb=" N VAL S 53 " --> pdb=" O GLY S 49 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR S 55 " --> pdb=" O HIS S 51 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU S 62 " --> pdb=" O ALA S 58 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA S 63 " --> pdb=" O ALA S 59 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY S 64 " --> pdb=" O ILE S 60 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY S 68 " --> pdb=" O GLY S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 117 removed outlier: 3.559A pdb=" N LEU S 90 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE S 104 " --> pdb=" O LEU S 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 59 removed outlier: 3.923A pdb=" N VAL T 53 " --> pdb=" O GLY T 49 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY T 54 " --> pdb=" O LEU T 50 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR T 55 " --> pdb=" O HIS T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 83 removed outlier: 3.925A pdb=" N GLY T 64 " --> pdb=" O ILE T 60 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY T 68 " --> pdb=" O GLY T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 117 Processing helix chain 'U' and resid 49 through 60 removed outlier: 3.864A pdb=" N VAL U 53 " --> pdb=" O GLY U 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR U 55 " --> pdb=" O HIS U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 83 removed outlier: 4.010A pdb=" N GLY U 64 " --> pdb=" O ILE U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 117 removed outlier: 3.747A pdb=" N ALA U 103 " --> pdb=" O ALA U 99 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE U 117 " --> pdb=" O PHE U 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 81 removed outlier: 4.314A pdb=" N VAL V 53 " --> pdb=" O GLY V 49 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA V 61 " --> pdb=" O LEU V 57 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU V 62 " --> pdb=" O ALA V 58 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA V 63 " --> pdb=" O ALA V 59 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY V 64 " --> pdb=" O ILE V 60 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY V 68 " --> pdb=" O GLY V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 85 No H-bonds generated for 'chain 'V' and resid 83 through 85' Processing helix chain 'V' and resid 86 through 115 removed outlier: 4.079A pdb=" N ASN V 92 " --> pdb=" O LYS V 88 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA V 103 " --> pdb=" O ALA V 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 83 removed outlier: 3.956A pdb=" N VAL W 53 " --> pdb=" O GLY W 49 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR W 55 " --> pdb=" O HIS W 51 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA W 61 " --> pdb=" O LEU W 57 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU W 62 " --> pdb=" O ALA W 58 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY W 64 " --> pdb=" O ILE W 60 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL W 65 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU W 77 " --> pdb=" O PHE W 73 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 117 removed outlier: 3.680A pdb=" N ILE W 104 " --> pdb=" O LEU W 100 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 83 removed outlier: 3.982A pdb=" N VAL X 53 " --> pdb=" O GLY X 49 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA X 61 " --> pdb=" O LEU X 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU X 62 " --> pdb=" O ALA X 58 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY X 64 " --> pdb=" O ILE X 60 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY X 68 " --> pdb=" O GLY X 64 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU X 77 " --> pdb=" O PHE X 73 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL X 78 " --> pdb=" O GLY X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 87 Processing helix chain 'X' and resid 88 through 117 removed outlier: 3.707A pdb=" N LEU X 111 " --> pdb=" O PHE X 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 102 through 104 removed outlier: 6.303A pdb=" N ALA G 70 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG G 156 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE G 160 " --> 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=AA2, first strand: chain 'G' and resid 126 through 129 Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 67 removed outlier: 6.854A pdb=" N LEU H 61 " --> pdb=" O ARG H 56 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ARG H 56 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG H 63 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU H 54 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG H 51 " --> pdb=" O CYS H 124 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL H 126 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR H 53 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR H 128 " --> pdb=" O THR H 53 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR H 55 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 123 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY H 114 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR H 73 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 60 through 67 removed outlier: 6.854A pdb=" N LEU H 61 " --> pdb=" O ARG H 56 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ARG H 56 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG H 63 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU H 54 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG H 51 " --> pdb=" O CYS H 124 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL H 126 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR H 53 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR H 128 " --> pdb=" O THR H 53 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR H 55 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 123 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY H 114 " --> pdb=" O LEU H 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 44 through 47 removed outlier: 6.645A pdb=" N VAL P 43 " --> pdb=" O SER Q 46 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL R 43 " --> pdb=" O SER S 46 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL T 43 " --> pdb=" O SER U 46 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE X 45 " --> pdb=" O ALA O 44 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER O 46 " --> pdb=" O ILE X 45 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL X 47 " --> pdb=" O SER O 46 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2277 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 2.07 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=" O3B UTP H 201 " pdb=" PG UTP H 201 " ideal model delta sigma weight residual 1.726 1.596 0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" O3A UTP H 201 " pdb=" PB UTP H 201 " ideal model delta sigma weight residual 1.664 1.592 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" O5' UTP H 201 " pdb=" PA UTP H 201 " ideal model delta sigma weight residual 1.652 1.604 0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" O3A UTP H 201 " pdb=" PA UTP H 201 " ideal model delta sigma weight residual 1.632 1.591 0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" C5' UTP H 201 " pdb=" O5' UTP H 201 " ideal model delta sigma weight residual 1.408 1.443 -0.035 2.00e-02 2.50e+03 2.98e+00 ... (remaining 19818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 35651 1.64 - 3.29: 167 3.29 - 4.93: 21 4.93 - 6.57: 5 6.57 - 8.22: 2 Bond angle restraints: 35846 Sorted by residual: angle pdb=" O2B UTP H 201 " pdb=" PB UTP H 201 " pdb=" O3A UTP H 201 " ideal model delta sigma weight residual 103.69 111.91 -8.22 3.00e+00 1.11e-01 7.50e+00 angle pdb=" O1A UTP H 201 " pdb=" PA UTP H 201 " pdb=" O2A UTP H 201 " ideal model delta sigma weight residual 121.55 114.98 6.57 3.00e+00 1.11e-01 4.80e+00 angle pdb=" O1A UTP H 201 " pdb=" PA UTP H 201 " pdb=" O5' UTP H 201 " ideal model delta sigma weight residual 104.84 111.26 -6.42 3.00e+00 1.11e-01 4.58e+00 angle pdb=" O2G UTP H 201 " pdb=" PG UTP H 201 " pdb=" O3B UTP H 201 " ideal model delta sigma weight residual 104.85 111.12 -6.27 3.00e+00 1.11e-01 4.37e+00 angle pdb=" C SER X 41 " pdb=" N THR X 42 " pdb=" CA THR X 42 " ideal model delta sigma weight residual 121.50 118.98 2.52 1.43e+00 4.89e-01 3.12e+00 ... (remaining 35841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 8433 14.55 - 29.10: 553 29.10 - 43.65: 92 43.65 - 58.19: 190 58.19 - 72.74: 25 Dihedral angle restraints: 9293 sinusoidal: 4996 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 9290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1020 0.028 - 0.056: 377 0.056 - 0.084: 129 0.084 - 0.112: 73 0.112 - 0.140: 11 Chirality restraints: 1610 Sorted by residual: chirality pdb=" C1' UTP H 201 " pdb=" C2' UTP H 201 " pdb=" N1 UTP H 201 " pdb=" O4' UTP H 201 " both_signs ideal model delta sigma weight residual False 2.31 2.45 -0.14 2.00e-01 2.50e+01 4.89e-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 chirality pdb=" CA ILE H 89 " pdb=" N ILE H 89 " pdb=" C ILE H 89 " pdb=" CB ILE H 89 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1607 not shown) Planarity restraints: 2915 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 2912 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 962 2.20 - 2.80: 42533 2.80 - 3.40: 54625 3.40 - 4.00: 72014 4.00 - 4.60: 116415 Nonbonded interactions: 286549 Sorted by model distance: nonbonded pdb=" OD1 ASP G 186 " pdb="HE22 GLN G 196 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASN G 208 " pdb="HH21 ARG R 82 " model vdw 1.643 2.450 nonbonded pdb=" O LEU G 52 " pdb="HH11 ARG G 199 " model vdw 1.655 2.450 nonbonded pdb=" H ARG H 56 " pdb=" O GLU H 59 " model vdw 1.660 2.450 nonbonded pdb="HH12 ARG V 82 " pdb=" O2G UTP H 201 " model vdw 1.673 2.450 ... (remaining 286544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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: 16.390 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: 0.130 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.005 0.130 9851 Z= 0.202 Angle : 0.454 8.217 13354 Z= 0.246 Chirality : 0.038 0.140 1610 Planarity : 0.004 0.042 1667 Dihedral : 9.950 72.742 3452 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (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 ARG 0.003 0.000 ARG I 40 TYR 0.009 0.001 TYR G 200 PHE 0.014 0.001 PHE H 60 TRP 0.003 0.001 TRP G 183 HIS 0.005 0.001 HIS G 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 9851) covalent geometry : angle 0.45392 / 0.25 (13354) hydrogen bonds : bond 0.17384 / 11.36 ( 756) hydrogen bonds : angle 7.79100 / 5.70 ( 2277) *********************** 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 to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.319 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: 0.7230 (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: 0.2450 time to fit residues: 43.3966 Evaluate side-chains 85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN X 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109062 restraints weight = 34643.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112347 restraints weight = 12558.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114063 restraints weight = 5959.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114992 restraints weight = 3557.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115436 restraints weight = 2555.593| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9851 Z= 0.174 Angle : 0.469 4.737 13354 Z= 0.265 Chirality : 0.039 0.141 1610 Planarity : 0.003 0.043 1667 Dihedral : 6.234 62.120 1414 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.81 % Allowed : 7.06 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.24), residues: 1259 helix: 1.92 (0.18), residues: 857 sheet: 0.02 (0.65), residues: 75 loop : -0.38 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 45 TYR 0.010 0.001 TYR G 49 PHE 0.019 0.001 PHE T 73 TRP 0.004 0.001 TRP I 13 HIS 0.007 0.002 HIS W 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 9851) covalent geometry : angle 0.46905 / 0.27 (13354) hydrogen bonds : bond 0.06076 / 4.02 ( 756) hydrogen bonds : angle 4.51799 / 3.23 ( 2277) *********************** 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 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8143 (tptt) REVERT: I 48 LYS cc_start: 0.8006 (mttt) cc_final: 0.7751 (tmtt) REVERT: S 82 ARG cc_start: 0.8112 (ptp-170) cc_final: 0.7691 (mtp180) REVERT: V 88 LYS cc_start: 0.8384 (tptt) cc_final: 0.7871 (mptt) REVERT: X 107 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7984 (m-80) outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 0.1876 time to fit residues: 28.5194 Evaluate side-chains 101 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain W residue 89 MET Chi-restraints excluded: chain X residue 83 GLN 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 98 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN R 51 HIS X 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102236 restraints weight = 36205.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105401 restraints weight = 13619.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107090 restraints weight = 6701.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108034 restraints weight = 4108.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108477 restraints weight = 2999.424| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9851 Z= 0.169 Angle : 0.455 4.557 13354 Z= 0.255 Chirality : 0.039 0.147 1610 Planarity : 0.003 0.042 1667 Dihedral : 5.795 60.725 1410 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.31 % Allowed : 7.86 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.24), residues: 1259 helix: 2.25 (0.18), residues: 849 sheet: -0.20 (0.64), residues: 75 loop : -0.33 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 82 TYR 0.010 0.001 TYR G 49 PHE 0.017 0.001 PHE R 73 TRP 0.004 0.001 TRP I 13 HIS 0.006 0.002 HIS W 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 9851) covalent geometry : angle 0.45540 / 0.26 (13354) hydrogen bonds : bond 0.05922 / 3.92 ( 756) hydrogen bonds : angle 4.17984 / 2.96 ( 2277) *********************** 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 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8091 (tptt) REVERT: S 82 ARG cc_start: 0.8275 (ptp-170) cc_final: 0.7857 (mtp180) REVERT: S 115 MET cc_start: 0.7580 (mtp) cc_final: 0.7369 (mtp) REVERT: V 88 LYS cc_start: 0.8466 (tptt) cc_final: 0.7944 (mptt) REVERT: X 107 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8049 (m-80) outliers start: 13 outliers final: 8 residues processed: 118 average time/residue: 0.1848 time to fit residues: 31.9157 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 W residue 89 MET 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 115 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101406 restraints weight = 36710.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104468 restraints weight = 13952.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106225 restraints weight = 6979.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107050 restraints weight = 4275.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107660 restraints weight = 3243.697| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3367 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= 0.157 Angle : 0.434 3.939 13354 Z= 0.242 Chirality : 0.038 0.141 1610 Planarity : 0.003 0.041 1667 Dihedral : 5.732 58.803 1410 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.92 % Allowed : 7.96 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.24), residues: 1259 helix: 2.40 (0.18), residues: 849 sheet: -0.43 (0.63), residues: 75 loop : -0.40 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 82 TYR 0.010 0.001 TYR G 49 PHE 0.014 0.001 PHE O 73 TRP 0.004 0.001 TRP I 13 HIS 0.005 0.002 HIS W 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 9851) covalent geometry : angle 0.43414 / 0.24 (13354) hydrogen bonds : bond 0.05616 / 3.73 ( 756) hydrogen bonds : angle 3.99215 / 2.82 ( 2277) *********************** 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 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8056 (tptt) REVERT: S 82 ARG cc_start: 0.8258 (ptp-170) cc_final: 0.7890 (mtp180) REVERT: V 88 LYS cc_start: 0.8536 (tptt) cc_final: 0.8105 (tttt) REVERT: X 107 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7985 (m-80) outliers start: 19 outliers final: 14 residues processed: 117 average time/residue: 0.1730 time to fit residues: 30.3816 Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 155 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 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 109 LEU Chi-restraints excluded: chain T residue 110 MET Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain W residue 89 MET Chi-restraints excluded: chain X residue 60 ILE 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 97 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.101340 restraints weight = 36747.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104406 restraints weight = 14089.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106116 restraints weight = 7044.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107023 restraints weight = 4339.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107585 restraints weight = 3194.542| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3667 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= 0.150 Angle : 0.423 3.940 13354 Z= 0.236 Chirality : 0.038 0.140 1610 Planarity : 0.003 0.041 1667 Dihedral : 5.867 59.679 1410 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.02 % Allowed : 8.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.24), residues: 1259 helix: 2.47 (0.18), residues: 848 sheet: -0.54 (0.63), residues: 75 loop : -0.46 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 82 TYR 0.009 0.001 TYR G 49 PHE 0.014 0.001 PHE R 73 TRP 0.003 0.001 TRP I 13 HIS 0.005 0.002 HIS H 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 9851) covalent geometry : angle 0.42287 / 0.24 (13354) hydrogen bonds : bond 0.05465 / 3.63 ( 756) hydrogen bonds : angle 3.90538 / 2.75 ( 2277) *********************** 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 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 107 LYS cc_start: 0.8275 (ttmt) cc_final: 0.8032 (tptt) REVERT: S 82 ARG cc_start: 0.8264 (ptp-170) cc_final: 0.7920 (mtp180) REVERT: T 109 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8569 (mt) REVERT: V 88 LYS cc_start: 0.8542 (tptt) cc_final: 0.8019 (mptt) REVERT: X 107 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8005 (m-80) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.1911 time to fit residues: 34.8897 Evaluate side-chains 123 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 155 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 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 109 LEU Chi-restraints excluded: chain T residue 110 MET Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain W residue 89 MET Chi-restraints excluded: chain X residue 60 ILE 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 75 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.098509 restraints weight = 37439.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101513 restraints weight = 14497.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103214 restraints weight = 7312.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104107 restraints weight = 4512.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104629 restraints weight = 3347.647| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9851 Z= 0.196 Angle : 0.462 3.939 13354 Z= 0.261 Chirality : 0.039 0.142 1610 Planarity : 0.003 0.043 1667 Dihedral : 5.897 64.929 1410 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.02 % Allowed : 9.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.24), residues: 1259 helix: 2.29 (0.18), residues: 854 sheet: -0.59 (0.63), residues: 73 loop : -0.67 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 258 TYR 0.011 0.001 TYR G 49 PHE 0.015 0.001 PHE S 73 TRP 0.003 0.001 TRP I 13 HIS 0.006 0.002 HIS V 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 ( 9851) covalent geometry : angle 0.46206 / 0.26 (13354) hydrogen bonds : bond 0.05960 / 3.96 ( 756) hydrogen bonds : angle 4.00735 / 2.82 ( 2277) *********************** 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 139 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 82 ARG cc_start: 0.8292 (ptp-170) cc_final: 0.7929 (mtp180) REVERT: V 88 LYS cc_start: 0.8626 (tptt) cc_final: 0.8174 (tttt) REVERT: X 107 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8060 (m-80) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.1991 time to fit residues: 37.6755 Evaluate side-chains 126 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 155 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 I residue 51 TYR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 115 MET Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain T residue 110 MET Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain W residue 89 MET Chi-restraints excluded: chain X residue 60 ILE 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 7 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101042 restraints weight = 36958.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104103 restraints weight = 14169.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105796 restraints weight = 7079.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106678 restraints weight = 4343.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107221 restraints weight = 3227.941| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4019 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= 0.135 Angle : 0.413 4.267 13354 Z= 0.230 Chirality : 0.038 0.146 1610 Planarity : 0.003 0.041 1667 Dihedral : 5.563 59.993 1410 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.12 % Allowed : 9.27 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.24), residues: 1259 helix: 2.52 (0.18), residues: 848 sheet: -0.57 (0.64), residues: 73 loop : -0.55 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 63 TYR 0.007 0.001 TYR G 49 PHE 0.013 0.001 PHE R 73 TRP 0.004 0.001 TRP I 13 HIS 0.005 0.001 HIS O 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 9851) covalent geometry : angle 0.41274 / 0.23 (13354) hydrogen bonds : bond 0.05387 / 3.58 ( 756) hydrogen bonds : angle 3.84164 / 2.70 ( 2277) *********************** 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 131 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 82 ARG cc_start: 0.8254 (ptp-170) cc_final: 0.7921 (mtp180) REVERT: V 88 LYS cc_start: 0.8547 (tptt) cc_final: 0.8107 (tttt) REVERT: X 107 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8024 (m-80) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.1825 time to fit residues: 34.0961 Evaluate side-chains 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 123 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 T residue 110 MET Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain W residue 89 MET Chi-restraints excluded: chain X residue 60 ILE 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 18 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100245 restraints weight = 36994.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.103314 restraints weight = 14277.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105006 restraints weight = 7150.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105902 restraints weight = 4395.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106437 restraints weight = 3233.894| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9851 Z= 0.155 Angle : 0.426 3.939 13354 Z= 0.238 Chirality : 0.038 0.140 1610 Planarity : 0.003 0.041 1667 Dihedral : 5.498 61.658 1410 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.02 % Allowed : 9.58 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.24), residues: 1259 helix: 2.53 (0.18), residues: 848 sheet: -0.62 (0.63), residues: 73 loop : -0.54 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 63 TYR 0.010 0.001 TYR G 49 PHE 0.014 0.001 PHE R 73 TRP 0.003 0.001 TRP I 13 HIS 0.005 0.001 HIS G 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 9851) covalent geometry : angle 0.42558 / 0.24 (13354) hydrogen bonds : bond 0.05497 / 3.66 ( 756) hydrogen bonds : angle 3.85109 / 2.71 ( 2277) *********************** 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 128 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: S 82 ARG cc_start: 0.8256 (ptp-170) cc_final: 0.7923 (mtp180) REVERT: V 88 LYS cc_start: 0.8580 (tptt) cc_final: 0.8137 (tttt) REVERT: X 107 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8064 (m-80) outliers start: 20 outliers final: 17 residues processed: 122 average time/residue: 0.2059 time to fit residues: 36.9856 Evaluate side-chains 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 155 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 123 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 P residue 104 ILE Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain T residue 110 MET Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain W residue 89 MET Chi-restraints excluded: chain X residue 60 ILE 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 97 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100830 restraints weight = 36850.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103862 restraints weight = 14260.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105570 restraints weight = 7179.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106510 restraints weight = 4410.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107070 restraints weight = 3206.984| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4155 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= 0.143 Angle : 0.417 3.843 13354 Z= 0.232 Chirality : 0.038 0.139 1610 Planarity : 0.003 0.065 1667 Dihedral : 5.398 60.917 1410 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.12 % Allowed : 9.68 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.24), residues: 1259 helix: 2.63 (0.18), residues: 858 sheet: -0.59 (0.63), residues: 73 loop : -0.57 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 63 TYR 0.008 0.001 TYR G 49 PHE 0.013 0.001 PHE R 73 TRP 0.004 0.001 TRP I 13 HIS 0.005 0.001 HIS O 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9851) covalent geometry : angle 0.41705 / 0.23 (13354) hydrogen bonds : bond 0.05358 / 3.57 ( 756) hydrogen bonds : angle 3.80461 / 2.68 ( 2277) *********************** 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 128 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 82 ARG cc_start: 0.8228 (ptp-170) cc_final: 0.7919 (mtp180) REVERT: V 88 LYS cc_start: 0.8563 (tptt) cc_final: 0.8121 (tttt) REVERT: X 107 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8047 (m-80) outliers start: 21 outliers final: 18 residues processed: 121 average time/residue: 0.1988 time to fit residues: 35.8231 Evaluate side-chains 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 123 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 P residue 104 ILE Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain T residue 110 MET Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain W residue 89 MET Chi-restraints excluded: chain X residue 60 ILE 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 23 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099286 restraints weight = 37361.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.102316 restraints weight = 14582.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104050 restraints weight = 7350.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.104985 restraints weight = 4495.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105536 restraints weight = 3282.924| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9851 Z= 0.169 Angle : 0.439 4.331 13354 Z= 0.246 Chirality : 0.039 0.140 1610 Planarity : 0.003 0.057 1667 Dihedral : 5.469 64.043 1410 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.92 % Allowed : 10.08 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.24), residues: 1259 helix: 2.56 (0.17), residues: 858 sheet: -0.64 (0.62), residues: 73 loop : -0.59 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 63 TYR 0.010 0.001 TYR G 49 PHE 0.014 0.001 PHE R 73 TRP 0.003 0.001 TRP I 13 HIS 0.005 0.002 HIS G 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 9851) covalent geometry : angle 0.43912 / 0.25 (13354) hydrogen bonds : bond 0.05604 / 3.73 ( 756) hydrogen bonds : angle 3.86661 / 2.72 ( 2277) ********************** 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 125 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 93 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8564 (t0) REVERT: S 82 ARG cc_start: 0.8229 (ptp-170) cc_final: 0.7890 (mtp180) REVERT: V 88 LYS cc_start: 0.8596 (tptt) cc_final: 0.8149 (tttt) REVERT: X 107 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8099 (m-80) outliers start: 19 outliers final: 17 residues processed: 121 average time/residue: 0.1913 time to fit residues: 34.2441 Evaluate side-chains 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 123 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 P residue 104 ILE Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain T residue 110 MET Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain W residue 89 MET Chi-restraints excluded: chain X residue 60 ILE 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 45 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.101931 restraints weight = 36956.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105009 restraints weight = 14203.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106707 restraints weight = 7066.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107608 restraints weight = 4328.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108016 restraints weight = 3168.472| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4241 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= 0.125 Angle : 0.404 3.843 13354 Z= 0.224 Chirality : 0.037 0.138 1610 Planarity : 0.003 0.064 1667 Dihedral : 5.138 59.034 1410 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.02 % Allowed : 10.08 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.24), residues: 1259 helix: 2.73 (0.17), residues: 858 sheet: -0.54 (0.64), residues: 73 loop : -0.47 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 63 TYR 0.007 0.001 TYR H 79 PHE 0.012 0.001 PHE P 73 TRP 0.005 0.001 TRP I 13 HIS 0.004 0.001 HIS O 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9851) covalent geometry : angle 0.40352 / 0.22 (13354) hydrogen bonds : bond 0.05115 / 3.41 ( 756) hydrogen bonds : angle 3.73360 / 2.63 ( 2277) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.58 seconds wall clock time: 48 minutes 21.90 seconds (2901.90 seconds total)