Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 05:22:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tat_10427/07_2023/6tat_10427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tat_10427/07_2023/6tat_10427.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tat_10427/07_2023/6tat_10427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tat_10427/07_2023/6tat_10427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tat_10427/07_2023/6tat_10427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tat_10427/07_2023/6tat_10427.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4310 2.51 5 N 1190 2.21 5 O 1270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C ASP 49": "OD1" <-> "OD2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D ASP 49": "OD1" <-> "OD2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E ASP 49": "OD1" <-> "OD2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E ASP 104": "OD1" <-> "OD2" Residue "E TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 6790 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "B" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "C" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "D" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "E" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Time building chain proxies: 3.79, per 1000 atoms: 0.56 Number of scatterers: 6790 At special positions: 0 Unit cell: (116.592, 112.428, 62.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1270 8.00 N 1190 7.00 C 4310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 68.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 44 through 63 removed outlier: 3.642A pdb=" N VAL A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.877A pdb=" N LEU A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 79 through 86 removed outlier: 4.079A pdb=" N VAL A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.734A pdb=" N ASP A 91 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 92' Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.762A pdb=" N PHE A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.786A pdb=" N ILE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.750A pdb=" N PHE A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.529A pdb=" N ILE A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.652A pdb=" N GLU A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.153A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 removed outlier: 3.642A pdb=" N VAL B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.877A pdb=" N LEU B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 79 through 86 removed outlier: 4.079A pdb=" N VAL B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.733A pdb=" N ASP B 91 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 92 " --> pdb=" O ARG B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 92' Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.761A pdb=" N PHE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.786A pdb=" N ILE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.750A pdb=" N PHE B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 159 removed outlier: 3.529A pdb=" N ILE B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.652A pdb=" N GLU B 168 " --> pdb=" O PRO B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 removed outlier: 4.154A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 63 removed outlier: 3.642A pdb=" N VAL C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.876A pdb=" N LEU C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 79 through 86 removed outlier: 4.079A pdb=" N VAL C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.733A pdb=" N ASP C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 92 " --> pdb=" O ARG C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 92' Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.761A pdb=" N PHE C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 removed outlier: 3.787A pdb=" N ILE C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.750A pdb=" N PHE C 133 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 159 removed outlier: 3.530A pdb=" N ILE C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.652A pdb=" N GLU C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 removed outlier: 4.154A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 63 removed outlier: 3.642A pdb=" N VAL D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 70 removed outlier: 3.877A pdb=" N LEU D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 79 through 86 removed outlier: 4.079A pdb=" N VAL D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.733A pdb=" N ASP D 91 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 92 " --> pdb=" O ARG D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing helix chain 'D' and resid 94 through 107 removed outlier: 3.761A pdb=" N PHE D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 120 removed outlier: 3.787A pdb=" N ILE D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.749A pdb=" N PHE D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.530A pdb=" N ILE D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.652A pdb=" N GLU D 168 " --> pdb=" O PRO D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 removed outlier: 4.153A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 63 removed outlier: 3.643A pdb=" N VAL E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.876A pdb=" N LEU E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 79 through 86 removed outlier: 4.079A pdb=" N VAL E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.733A pdb=" N ASP E 91 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA E 92 " --> pdb=" O ARG E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 92' Processing helix chain 'E' and resid 94 through 107 removed outlier: 3.761A pdb=" N PHE E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.786A pdb=" N ILE E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 142 removed outlier: 3.749A pdb=" N PHE E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.530A pdb=" N ILE E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 168 removed outlier: 3.652A pdb=" N GLU E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 192 removed outlier: 4.153A pdb=" N LEU E 181 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU E 182 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 188 " --> pdb=" O ARG E 184 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2230 1.34 - 1.46: 987 1.46 - 1.57: 3693 1.57 - 1.68: 0 1.68 - 1.80: 30 Bond restraints: 6940 Sorted by residual: bond pdb=" N GLU D 56 " pdb=" CA GLU D 56 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.54e+00 bond pdb=" N GLU E 56 " pdb=" CA GLU E 56 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.49e+00 bond pdb=" N THR A 57 " pdb=" CA THR A 57 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.46e+00 bond pdb=" N GLU C 56 " pdb=" CA GLU C 56 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.40e+00 bond pdb=" N THR E 57 " pdb=" CA THR E 57 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.40e+00 ... (remaining 6935 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.39: 196 107.39 - 114.02: 3774 114.02 - 120.66: 3190 120.66 - 127.30: 2110 127.30 - 133.93: 75 Bond angle restraints: 9345 Sorted by residual: angle pdb=" CA THR E 109 " pdb=" CB THR E 109 " pdb=" CG2 THR E 109 " ideal model delta sigma weight residual 110.50 117.50 -7.00 1.70e+00 3.46e-01 1.70e+01 angle pdb=" CA THR A 109 " pdb=" CB THR A 109 " pdb=" CG2 THR A 109 " ideal model delta sigma weight residual 110.50 117.49 -6.99 1.70e+00 3.46e-01 1.69e+01 angle pdb=" CA THR B 109 " pdb=" CB THR B 109 " pdb=" CG2 THR B 109 " ideal model delta sigma weight residual 110.50 117.48 -6.98 1.70e+00 3.46e-01 1.69e+01 angle pdb=" CA THR D 109 " pdb=" CB THR D 109 " pdb=" CG2 THR D 109 " ideal model delta sigma weight residual 110.50 117.46 -6.96 1.70e+00 3.46e-01 1.68e+01 angle pdb=" CA THR C 109 " pdb=" CB THR C 109 " pdb=" CG2 THR C 109 " ideal model delta sigma weight residual 110.50 117.44 -6.94 1.70e+00 3.46e-01 1.67e+01 ... (remaining 9340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3705 17.96 - 35.92: 405 35.92 - 53.88: 80 53.88 - 71.84: 10 71.84 - 89.80: 10 Dihedral angle restraints: 4210 sinusoidal: 1805 harmonic: 2405 Sorted by residual: dihedral pdb=" C THR A 109 " pdb=" N THR A 109 " pdb=" CA THR A 109 " pdb=" CB THR A 109 " ideal model delta harmonic sigma weight residual -122.00 -130.55 8.55 0 2.50e+00 1.60e-01 1.17e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N SER C 79 " pdb=" CA SER C 79 " ideal model delta harmonic sigma weight residual -180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LYS D 78 " pdb=" C LYS D 78 " pdb=" N SER D 79 " pdb=" CA SER D 79 " ideal model delta harmonic sigma weight residual 180.00 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 740 0.048 - 0.095: 184 0.095 - 0.143: 46 0.143 - 0.190: 10 0.190 - 0.238: 10 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA THR A 109 " pdb=" N THR A 109 " pdb=" C THR A 109 " pdb=" CB THR A 109 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR A 109 " pdb=" CA THR A 109 " pdb=" OG1 THR A 109 " pdb=" CG2 THR A 109 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA THR D 109 " pdb=" N THR D 109 " pdb=" C THR D 109 " pdb=" CB THR D 109 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 987 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 163 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO E 164 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 163 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.12e+00 pdb=" N PRO A 164 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 163 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO C 164 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.039 5.00e-02 4.00e+02 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 0.56 - 1.43: 45 1.43 - 2.30: 70 2.30 - 3.16: 4996 3.16 - 4.03: 14818 4.03 - 4.90: 25484 Warning: very small nonbonded interaction distances. Nonbonded interactions: 45413 Sorted by model distance: nonbonded pdb=" CA PRO B 111 " pdb=" NH2 ARG C 190 " model vdw 0.562 3.550 nonbonded pdb=" CA PRO D 111 " pdb=" NH2 ARG E 190 " model vdw 0.562 3.550 nonbonded pdb=" CA PRO A 111 " pdb=" NH2 ARG B 190 " model vdw 0.563 3.550 nonbonded pdb=" CA PRO C 111 " pdb=" NH2 ARG D 190 " model vdw 0.563 3.550 nonbonded pdb=" NH2 ARG A 190 " pdb=" CA PRO E 111 " model vdw 0.563 3.550 ... (remaining 45408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.180 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: 0.010 Extract box with map and model: 1.320 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 20.320 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 0.039 6940 Z= 0.301 Angle : 0.913 7.000 9345 Z= 0.557 Chirality : 0.051 0.238 990 Planarity : 0.008 0.071 1205 Dihedral : 15.557 89.801 2650 Min Nonbonded Distance : 0.562 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.20), residues: 810 helix: -2.87 (0.16), residues: 425 sheet: None (None), residues: 0 loop : -2.67 (0.24), residues: 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 0.771 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 195 average time/residue: 0.3267 time to fit residues: 75.1038 Evaluate side-chains 140 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0589 time to fit residues: 1.6009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.0050 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 overall best weight: 1.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6940 Z= 0.219 Angle : 0.544 4.872 9345 Z= 0.293 Chirality : 0.040 0.130 990 Planarity : 0.007 0.063 1205 Dihedral : 4.120 13.458 915 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.26), residues: 810 helix: -0.96 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -2.29 (0.27), residues: 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.924 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 144 average time/residue: 0.2821 time to fit residues: 49.2644 Evaluate side-chains 131 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0621 time to fit residues: 1.3780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6940 Z= 0.159 Angle : 0.482 4.841 9345 Z= 0.255 Chirality : 0.038 0.132 990 Planarity : 0.005 0.054 1205 Dihedral : 3.593 13.322 915 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.29), residues: 810 helix: 0.14 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -2.01 (0.30), residues: 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 0.835 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 139 average time/residue: 0.2708 time to fit residues: 46.0685 Evaluate side-chains 126 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0645 time to fit residues: 1.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 6940 Z= 0.206 Angle : 0.504 5.032 9345 Z= 0.264 Chirality : 0.040 0.128 990 Planarity : 0.005 0.051 1205 Dihedral : 3.609 17.060 915 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.30), residues: 810 helix: 0.68 (0.26), residues: 445 sheet: None (None), residues: 0 loop : -1.80 (0.31), residues: 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 0.839 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 0.2826 time to fit residues: 46.3265 Evaluate side-chains 134 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0662 time to fit residues: 1.9096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 6940 Z= 0.156 Angle : 0.473 5.049 9345 Z= 0.248 Chirality : 0.039 0.142 990 Planarity : 0.005 0.045 1205 Dihedral : 3.455 16.940 915 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.31), residues: 810 helix: 1.00 (0.26), residues: 445 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.975 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 137 average time/residue: 0.2814 time to fit residues: 47.0373 Evaluate side-chains 125 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0637 time to fit residues: 1.2761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6940 Z= 0.173 Angle : 0.484 5.225 9345 Z= 0.253 Chirality : 0.039 0.123 990 Planarity : 0.005 0.050 1205 Dihedral : 3.430 17.364 915 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.31), residues: 810 helix: 1.19 (0.26), residues: 445 sheet: None (None), residues: 0 loop : -1.47 (0.33), residues: 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.839 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 138 average time/residue: 0.2857 time to fit residues: 48.4920 Evaluate side-chains 140 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0734 time to fit residues: 1.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.0870 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6940 Z= 0.207 Angle : 0.509 5.100 9345 Z= 0.266 Chirality : 0.041 0.172 990 Planarity : 0.005 0.056 1205 Dihedral : 3.512 16.866 915 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.31), residues: 810 helix: 1.20 (0.26), residues: 450 sheet: None (None), residues: 0 loop : -1.42 (0.34), residues: 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.771 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.2761 time to fit residues: 46.7414 Evaluate side-chains 138 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0691 time to fit residues: 1.5681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 6940 Z= 0.226 Angle : 0.527 5.488 9345 Z= 0.275 Chirality : 0.041 0.151 990 Planarity : 0.005 0.058 1205 Dihedral : 3.603 16.600 915 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.32), residues: 810 helix: 1.20 (0.26), residues: 450 sheet: None (None), residues: 0 loop : -1.36 (0.35), residues: 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.848 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 133 average time/residue: 0.2818 time to fit residues: 45.9598 Evaluate side-chains 132 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0639 time to fit residues: 1.5178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 67 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 6940 Z= 0.156 Angle : 0.500 5.871 9345 Z= 0.264 Chirality : 0.039 0.170 990 Planarity : 0.005 0.060 1205 Dihedral : 3.434 14.781 915 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.32), residues: 810 helix: 1.32 (0.26), residues: 450 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.984 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2779 time to fit residues: 47.2361 Evaluate side-chains 135 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6940 Z= 0.214 Angle : 0.538 9.130 9345 Z= 0.278 Chirality : 0.041 0.179 990 Planarity : 0.005 0.065 1205 Dihedral : 3.505 15.028 915 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.32), residues: 810 helix: 1.30 (0.26), residues: 450 sheet: None (None), residues: 0 loop : -1.28 (0.35), residues: 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.791 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 138 average time/residue: 0.2821 time to fit residues: 47.4752 Evaluate side-chains 136 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0598 time to fit residues: 1.2746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105990 restraints weight = 10693.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109067 restraints weight = 5917.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111185 restraints weight = 3778.086| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6940 Z= 0.184 Angle : 0.524 8.928 9345 Z= 0.271 Chirality : 0.041 0.181 990 Planarity : 0.005 0.064 1205 Dihedral : 3.582 26.026 915 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.32), residues: 810 helix: 1.31 (0.26), residues: 450 sheet: None (None), residues: 0 loop : -1.25 (0.35), residues: 360 =============================================================================== Job complete usr+sys time: 1600.65 seconds wall clock time: 29 minutes 44.11 seconds (1784.11 seconds total)