Starting phenix.real_space_refine on Wed Feb 14 00:01:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/02_2024/6tau_10428.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/02_2024/6tau_10428.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/6tau_10428/02_2024/6tau_10428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/02_2024/6tau_10428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/02_2024/6tau_10428.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/02_2024/6tau_10428.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 24 5.16 5 C 5172 2.51 5 N 1428 2.21 5 O 1524 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 GLU 60": "OE1" <-> "OE2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" 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 ARG 89": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" 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 GLU 50": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" 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 ARG 89": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" 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" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F ARG 138": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 167": "NH1" <-> "NH2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F ARG 186": "NH1" <-> "NH2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8148 Number of models: 1 Model: "" Number of chains: 6 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} Chain: "F" 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: 4.67, per 1000 atoms: 0.57 Number of scatterers: 8148 At special positions: 0 Unit cell: (131.86, 63.848, 129.084, 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 24 16.00 O 1524 8.00 N 1428 7.00 C 5172 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 44 through 63 removed outlier: 3.700A pdb=" N VAL A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.718A pdb=" N LEU A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.611A pdb=" N ALA A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.785A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.844A pdb=" N ILE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.518A pdb=" N PHE A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.839A pdb=" N GLU A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.615A pdb=" N GLU A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 192 removed outlier: 4.163A pdb=" N LEU A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 removed outlier: 3.570A pdb=" N VAL B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.875A pdb=" N LEU B 75 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.515A pdb=" N TRP B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 88 " --> pdb=" O TRP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.965A pdb=" N PHE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.641A pdb=" N ILE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.592A pdb=" N PHE B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.808A pdb=" N GLU B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.223A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 63 removed outlier: 3.783A pdb=" N VAL C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 4.195A pdb=" N LYS C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'C' and resid 73 through 76 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.988A pdb=" N VAL C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 88 " --> pdb=" O TRP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.888A pdb=" N HIS C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.782A pdb=" N ILE C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.790A pdb=" N PHE C 133 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 removed outlier: 4.078A pdb=" N GLU C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.696A pdb=" N ARG C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 168' Processing helix chain 'C' and resid 177 through 192 removed outlier: 4.003A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 63 removed outlier: 3.700A pdb=" N VAL D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.718A pdb=" N LEU D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 80 through 86 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.611A pdb=" N ALA D 92 " --> pdb=" O ARG D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 107 removed outlier: 3.785A pdb=" N LEU D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 120 removed outlier: 3.845A pdb=" N ILE D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.518A pdb=" N PHE D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.777A pdb=" N PHE D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.614A pdb=" N GLU D 168 " --> pdb=" O PRO D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 4.162A pdb=" N LEU D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 63 removed outlier: 3.570A pdb=" N VAL E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 76 removed outlier: 3.876A pdb=" N LEU E 75 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 88 removed outlier: 3.515A pdb=" N TRP E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY E 87 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL E 88 " --> pdb=" O TRP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 Processing helix chain 'E' and resid 94 through 107 removed outlier: 3.965A pdb=" N PHE E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.641A pdb=" N ILE E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 142 removed outlier: 3.592A pdb=" N PHE E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 162 removed outlier: 3.625A pdb=" N GLU E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 192 removed outlier: 4.222A pdb=" N LEU E 182 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL E 188 " --> pdb=" O ARG E 184 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 63 removed outlier: 3.783A pdb=" N VAL F 48 " --> pdb=" O ASP F 44 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 4.195A pdb=" N LYS F 71 " --> pdb=" O LYS F 67 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 73 through 76 Processing helix chain 'F' and resid 79 through 88 removed outlier: 3.988A pdb=" N VAL F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 87 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL F 88 " --> pdb=" O TRP F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 removed outlier: 3.889A pdb=" N HIS F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.783A pdb=" N ILE F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 142 removed outlier: 3.791A pdb=" N PHE F 133 " --> pdb=" O VAL F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.941A pdb=" N GLU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET F 162 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 168 removed outlier: 3.696A pdb=" N ARG F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU F 168 " --> pdb=" O PRO F 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 163 through 168' Processing helix chain 'F' and resid 177 through 192 removed outlier: 4.004A pdb=" N LEU F 181 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU F 182 " --> pdb=" O PHE F 178 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL F 188 " --> pdb=" O ARG F 184 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 924 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: 1.79 Time building geometry restraints manager: 3.11 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: 2673 1.34 - 1.46: 1681 1.46 - 1.58: 3938 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 8328 Sorted by residual: bond pdb=" N MET A 162 " pdb=" CA MET A 162 " ideal model delta sigma weight residual 1.454 1.514 -0.059 1.15e-02 7.56e+03 2.66e+01 bond pdb=" C GLU C 154 " pdb=" O GLU C 154 " ideal model delta sigma weight residual 1.237 1.295 -0.058 1.17e-02 7.31e+03 2.48e+01 bond pdb=" C ILE C 158 " pdb=" O ILE C 158 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.17e-02 7.31e+03 2.03e+01 bond pdb=" N MET F 162 " pdb=" CA MET F 162 " ideal model delta sigma weight residual 1.453 1.511 -0.058 1.31e-02 5.83e+03 1.94e+01 bond pdb=" N MET C 162 " pdb=" CA MET C 162 " ideal model delta sigma weight residual 1.456 1.506 -0.050 1.25e-02 6.40e+03 1.61e+01 ... (remaining 8323 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.27: 248 107.27 - 113.97: 4484 113.97 - 120.67: 3785 120.67 - 127.36: 2609 127.36 - 134.06: 88 Bond angle restraints: 11214 Sorted by residual: angle pdb=" C MET C 162 " pdb=" N GLN C 163 " pdb=" CA GLN C 163 " ideal model delta sigma weight residual 120.60 132.59 -11.99 1.53e+00 4.27e-01 6.14e+01 angle pdb=" C MET E 162 " pdb=" N GLN E 163 " pdb=" CA GLN E 163 " ideal model delta sigma weight residual 120.39 130.35 -9.96 1.39e+00 5.18e-01 5.14e+01 angle pdb=" N PHE D 157 " pdb=" CA PHE D 157 " pdb=" C PHE D 157 " ideal model delta sigma weight residual 111.07 117.01 -5.94 1.07e+00 8.73e-01 3.08e+01 angle pdb=" N MET C 162 " pdb=" CA MET C 162 " pdb=" C MET C 162 " ideal model delta sigma weight residual 110.35 117.56 -7.21 1.36e+00 5.41e-01 2.81e+01 angle pdb=" C MET A 162 " pdb=" N GLN A 163 " pdb=" CA GLN A 163 " ideal model delta sigma weight residual 120.86 128.51 -7.65 1.60e+00 3.91e-01 2.28e+01 ... (remaining 11209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4491 17.72 - 35.44: 449 35.44 - 53.16: 70 53.16 - 70.88: 26 70.88 - 88.60: 16 Dihedral angle restraints: 5052 sinusoidal: 2166 harmonic: 2886 Sorted by residual: dihedral pdb=" CA LYS F 78 " pdb=" C LYS F 78 " pdb=" N SER F 79 " pdb=" CA SER F 79 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+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 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA SER C 107 " pdb=" C SER C 107 " pdb=" N PRO C 108 " pdb=" CA PRO C 108 " ideal model delta harmonic sigma weight residual 180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 937 0.055 - 0.110: 159 0.110 - 0.164: 68 0.164 - 0.219: 17 0.219 - 0.274: 7 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CB THR D 109 " pdb=" CA THR D 109 " pdb=" OG1 THR D 109 " pdb=" CG2 THR D 109 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.88e+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 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 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 2.28 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1185 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 155 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C LEU F 155 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU F 155 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP F 156 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 155 " -0.018 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU D 155 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU D 155 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP D 156 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 163 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO E 164 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.045 5.00e-02 4.00e+02 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 4 2.01 - 2.73: 528 2.73 - 3.45: 10972 3.45 - 4.18: 15381 4.18 - 4.90: 27118 Nonbonded interactions: 54003 Sorted by model distance: nonbonded pdb=" OD1 ASP A 156 " pdb=" NH2 ARG A 172 " model vdw 1.283 2.520 nonbonded pdb=" O ASP A 150 " pdb=" OE2 GLU A 154 " model vdw 1.337 3.040 nonbonded pdb=" O ASP A 150 " pdb=" CD GLU A 154 " model vdw 1.634 3.270 nonbonded pdb=" O ASP A 150 " pdb=" OE1 GLU A 154 " model vdw 1.719 3.040 nonbonded pdb=" O PHE B 157 " pdb=" CD2 LEU B 161 " model vdw 2.090 3.460 ... (remaining 53998 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' selection = chain 'F' } 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: 0.250 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: 1.130 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 23.140 Find NCS groups from input model: 0.530 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8328 Z= 0.379 Angle : 0.992 11.992 11214 Z= 0.647 Chirality : 0.056 0.274 1188 Planarity : 0.009 0.082 1446 Dihedral : 15.437 88.596 3180 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.23 % Allowed : 5.74 % Favored : 94.03 % 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 (0.19), residues: 972 helix: -2.49 (0.17), residues: 512 sheet: None (None), residues: 0 loop : -3.19 (0.20), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 95 HIS 0.005 0.001 HIS E 173 PHE 0.016 0.002 PHE E 77 TYR 0.018 0.002 TYR F 126 ARG 0.002 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7822 (tp30) cc_final: 0.7499 (tp30) REVERT: B 50 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6793 (tm-30) REVERT: B 117 MET cc_start: 0.7398 (tpt) cc_final: 0.6139 (mtt) REVERT: B 123 LYS cc_start: 0.8106 (mttt) cc_final: 0.7882 (mtpp) REVERT: C 43 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7970 (mtp85) REVERT: C 90 ARG cc_start: 0.8341 (ptt90) cc_final: 0.8107 (ptt-90) REVERT: E 50 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7231 (tp30) REVERT: E 117 MET cc_start: 0.7716 (tpt) cc_final: 0.6373 (mtt) REVERT: F 168 GLU cc_start: 0.7779 (pp20) cc_final: 0.7480 (pp20) outliers start: 2 outliers final: 1 residues processed: 206 average time/residue: 0.2998 time to fit residues: 75.8098 Evaluate side-chains 158 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN B 114 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN E 114 GLN E 163 GLN F 45 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8328 Z= 0.212 Angle : 0.574 9.309 11214 Z= 0.308 Chirality : 0.041 0.187 1188 Planarity : 0.005 0.058 1446 Dihedral : 4.637 23.227 1100 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.24 % Allowed : 11.94 % Favored : 86.82 % 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: -2.20 (0.23), residues: 972 helix: -0.65 (0.20), residues: 520 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 95 HIS 0.005 0.001 HIS E 173 PHE 0.016 0.002 PHE A 120 TYR 0.013 0.002 TYR B 166 ARG 0.005 0.000 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 0.923 Fit side-chains REVERT: B 50 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7111 (tm-30) REVERT: C 67 LYS cc_start: 0.8413 (tptt) cc_final: 0.8180 (tptt) REVERT: C 90 ARG cc_start: 0.8370 (ptt90) cc_final: 0.8103 (ptt-90) REVERT: D 162 MET cc_start: 0.6482 (mpp) cc_final: 0.6078 (mmm) outliers start: 11 outliers final: 7 residues processed: 169 average time/residue: 0.2689 time to fit residues: 57.3177 Evaluate side-chains 160 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN C 45 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8328 Z= 0.166 Angle : 0.511 7.549 11214 Z= 0.272 Chirality : 0.040 0.199 1188 Planarity : 0.004 0.052 1446 Dihedral : 4.108 24.979 1098 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.80 % Allowed : 13.63 % Favored : 84.57 % 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: -1.29 (0.25), residues: 972 helix: 0.19 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.23 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.004 0.001 HIS B 173 PHE 0.009 0.001 PHE A 120 TYR 0.010 0.001 TYR B 166 ARG 0.005 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 0.950 Fit side-chains REVERT: A 117 MET cc_start: 0.8056 (tpp) cc_final: 0.7139 (ttp) REVERT: B 117 MET cc_start: 0.7570 (tpp) cc_final: 0.7312 (tpp) REVERT: C 43 ARG cc_start: 0.8597 (mtp85) cc_final: 0.8336 (mtp85) REVERT: C 67 LYS cc_start: 0.8426 (tptt) cc_final: 0.8209 (tptt) REVERT: D 162 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.6022 (mmm) REVERT: E 117 MET cc_start: 0.7546 (tpp) cc_final: 0.7289 (tpp) REVERT: F 128 GLU cc_start: 0.7894 (tp30) cc_final: 0.7128 (mt-10) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.2908 time to fit residues: 58.6356 Evaluate side-chains 158 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8328 Z= 0.204 Angle : 0.516 6.636 11214 Z= 0.276 Chirality : 0.041 0.201 1188 Planarity : 0.004 0.049 1446 Dihedral : 4.068 25.210 1098 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.58 % Allowed : 16.22 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 972 helix: 0.62 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.06 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.006 0.001 HIS B 173 PHE 0.013 0.001 PHE E 120 TYR 0.012 0.001 TYR C 113 ARG 0.005 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 0.931 Fit side-chains REVERT: A 117 MET cc_start: 0.8087 (tpp) cc_final: 0.7245 (ttp) REVERT: B 117 MET cc_start: 0.7573 (tpp) cc_final: 0.7237 (tpp) REVERT: C 67 LYS cc_start: 0.8502 (tptt) cc_final: 0.8296 (tptt) REVERT: D 52 ILE cc_start: 0.7898 (tt) cc_final: 0.7643 (tt) REVERT: D 162 MET cc_start: 0.6414 (mpp) cc_final: 0.6046 (mmm) REVERT: E 117 MET cc_start: 0.7644 (tpp) cc_final: 0.7277 (tpp) REVERT: E 174 GLU cc_start: 0.8123 (mp0) cc_final: 0.7436 (mp0) outliers start: 14 outliers final: 11 residues processed: 170 average time/residue: 0.2775 time to fit residues: 59.4546 Evaluate side-chains 159 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8328 Z= 0.190 Angle : 0.512 7.883 11214 Z= 0.271 Chirality : 0.040 0.184 1188 Planarity : 0.004 0.048 1446 Dihedral : 3.954 24.287 1098 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.14 % Allowed : 17.57 % Favored : 80.29 % 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: -0.45 (0.26), residues: 972 helix: 0.88 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.87 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 95 HIS 0.004 0.000 HIS B 173 PHE 0.011 0.001 PHE B 120 TYR 0.010 0.001 TYR D 113 ARG 0.007 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8028 (tpp) cc_final: 0.7258 (ttp) REVERT: B 117 MET cc_start: 0.7492 (tpp) cc_final: 0.7102 (tpp) REVERT: B 141 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7155 (tt) REVERT: B 162 MET cc_start: 0.7898 (mmm) cc_final: 0.7126 (mmm) REVERT: C 60 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8144 (tm-30) REVERT: D 117 MET cc_start: 0.7986 (tpp) cc_final: 0.6915 (ttp) REVERT: E 117 MET cc_start: 0.7604 (tpp) cc_final: 0.7199 (tpp) outliers start: 19 outliers final: 10 residues processed: 167 average time/residue: 0.2734 time to fit residues: 57.4094 Evaluate side-chains 156 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8328 Z= 0.156 Angle : 0.514 9.905 11214 Z= 0.268 Chirality : 0.039 0.170 1188 Planarity : 0.004 0.048 1446 Dihedral : 3.818 27.333 1098 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.14 % Allowed : 18.47 % Favored : 79.39 % 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: -0.13 (0.26), residues: 972 helix: 1.14 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 95 HIS 0.004 0.000 HIS B 173 PHE 0.008 0.001 PHE A 157 TYR 0.010 0.001 TYR A 113 ARG 0.006 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.004 Fit side-chains REVERT: A 117 MET cc_start: 0.7948 (tpp) cc_final: 0.7224 (ttp) REVERT: B 117 MET cc_start: 0.7531 (tpp) cc_final: 0.7134 (tpp) REVERT: B 162 MET cc_start: 0.7964 (mmm) cc_final: 0.7529 (mmt) REVERT: C 118 GLU cc_start: 0.8412 (tp30) cc_final: 0.7968 (tp30) REVERT: D 117 MET cc_start: 0.7983 (tpp) cc_final: 0.7000 (ttp) REVERT: E 117 MET cc_start: 0.7471 (tpp) cc_final: 0.7067 (tpp) outliers start: 19 outliers final: 14 residues processed: 156 average time/residue: 0.2512 time to fit residues: 50.3365 Evaluate side-chains 161 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 0.0570 chunk 78 optimal weight: 0.0570 chunk 51 optimal weight: 0.0980 chunk 92 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8328 Z= 0.144 Angle : 0.521 11.330 11214 Z= 0.262 Chirality : 0.038 0.175 1188 Planarity : 0.004 0.047 1446 Dihedral : 3.537 27.262 1098 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.91 % Allowed : 19.59 % Favored : 78.49 % 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: 0.14 (0.27), residues: 972 helix: 1.27 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.49 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 85 HIS 0.004 0.000 HIS B 173 PHE 0.009 0.001 PHE A 157 TYR 0.010 0.001 TYR D 113 ARG 0.006 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.110 Fit side-chains REVERT: A 117 MET cc_start: 0.7859 (tpp) cc_final: 0.7157 (ttp) REVERT: B 117 MET cc_start: 0.7486 (tpp) cc_final: 0.7073 (tpp) REVERT: B 162 MET cc_start: 0.7954 (mmm) cc_final: 0.7542 (mmt) REVERT: C 67 LYS cc_start: 0.8575 (tptt) cc_final: 0.8206 (tptt) REVERT: C 117 MET cc_start: 0.6251 (tpp) cc_final: 0.5972 (mmt) REVERT: D 68 ASP cc_start: 0.7949 (m-30) cc_final: 0.7668 (m-30) REVERT: D 117 MET cc_start: 0.7898 (tpp) cc_final: 0.6953 (ttp) REVERT: D 162 MET cc_start: 0.6618 (mmt) cc_final: 0.6303 (mmp) REVERT: E 117 MET cc_start: 0.7525 (tpp) cc_final: 0.7150 (tpp) outliers start: 17 outliers final: 11 residues processed: 175 average time/residue: 0.2699 time to fit residues: 59.6577 Evaluate side-chains 161 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8328 Z= 0.190 Angle : 0.548 8.656 11214 Z= 0.278 Chirality : 0.040 0.233 1188 Planarity : 0.004 0.049 1446 Dihedral : 3.698 27.869 1098 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.03 % Allowed : 20.38 % Favored : 77.59 % 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: 0.43 (0.27), residues: 972 helix: 1.45 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 95 HIS 0.004 0.001 HIS B 173 PHE 0.033 0.001 PHE E 39 TYR 0.010 0.001 TYR C 113 ARG 0.007 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.939 Fit side-chains REVERT: A 52 ILE cc_start: 0.7837 (tt) cc_final: 0.7606 (tt) REVERT: A 117 MET cc_start: 0.7991 (tpp) cc_final: 0.7223 (ttp) REVERT: B 50 GLU cc_start: 0.7371 (tp30) cc_final: 0.7071 (tm-30) REVERT: B 117 MET cc_start: 0.7526 (tpp) cc_final: 0.7095 (tpp) REVERT: B 162 MET cc_start: 0.7887 (mmm) cc_final: 0.7423 (mmm) REVERT: B 174 GLU cc_start: 0.8143 (mp0) cc_final: 0.7921 (mp0) REVERT: C 67 LYS cc_start: 0.8620 (tptt) cc_final: 0.8402 (tptt) REVERT: C 141 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7248 (tt) REVERT: D 91 ASP cc_start: 0.7061 (t70) cc_final: 0.6618 (t70) REVERT: D 117 MET cc_start: 0.8008 (tpp) cc_final: 0.6961 (ttp) REVERT: E 117 MET cc_start: 0.7518 (tpp) cc_final: 0.7092 (tpp) outliers start: 18 outliers final: 14 residues processed: 161 average time/residue: 0.3065 time to fit residues: 62.3175 Evaluate side-chains 163 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8328 Z= 0.181 Angle : 0.557 11.007 11214 Z= 0.280 Chirality : 0.040 0.230 1188 Planarity : 0.004 0.049 1446 Dihedral : 3.718 28.176 1098 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.14 % Allowed : 20.50 % Favored : 77.36 % 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: 0.52 (0.27), residues: 972 helix: 1.54 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.005 0.000 HIS B 173 PHE 0.025 0.001 PHE E 39 TYR 0.009 0.001 TYR F 166 ARG 0.008 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 0.925 Fit side-chains REVERT: A 52 ILE cc_start: 0.7785 (tt) cc_final: 0.7539 (tt) REVERT: A 117 MET cc_start: 0.7975 (tpp) cc_final: 0.7230 (ttp) REVERT: B 50 GLU cc_start: 0.7364 (tp30) cc_final: 0.7059 (tm-30) REVERT: B 89 ARG cc_start: 0.8005 (ttt180) cc_final: 0.7623 (ttm-80) REVERT: B 117 MET cc_start: 0.7535 (tpp) cc_final: 0.7084 (tpp) REVERT: C 141 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7270 (tt) REVERT: D 68 ASP cc_start: 0.7871 (m-30) cc_final: 0.7614 (m-30) REVERT: D 91 ASP cc_start: 0.7063 (t70) cc_final: 0.6617 (t70) REVERT: D 117 MET cc_start: 0.7996 (tpp) cc_final: 0.6952 (ttp) REVERT: E 117 MET cc_start: 0.7538 (tpp) cc_final: 0.7117 (tpp) REVERT: E 162 MET cc_start: 0.7670 (mmm) cc_final: 0.7463 (mmm) REVERT: F 90 ARG cc_start: 0.8215 (ptt90) cc_final: 0.7832 (ptt90) REVERT: F 127 ASP cc_start: 0.8635 (p0) cc_final: 0.8373 (p0) REVERT: F 128 GLU cc_start: 0.7739 (tp30) cc_final: 0.7153 (tt0) outliers start: 19 outliers final: 13 residues processed: 161 average time/residue: 0.2734 time to fit residues: 55.3660 Evaluate side-chains 162 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8328 Z= 0.161 Angle : 0.543 10.183 11214 Z= 0.272 Chirality : 0.039 0.226 1188 Planarity : 0.004 0.049 1446 Dihedral : 3.608 27.810 1098 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.58 % Allowed : 21.17 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.27), residues: 972 helix: 1.63 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.10 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 85 HIS 0.003 0.000 HIS B 173 PHE 0.021 0.001 PHE E 39 TYR 0.010 0.001 TYR A 113 ARG 0.009 0.000 ARG D 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.940 Fit side-chains REVERT: A 117 MET cc_start: 0.7915 (tpp) cc_final: 0.7199 (ttp) REVERT: B 50 GLU cc_start: 0.7296 (tp30) cc_final: 0.6986 (tm-30) REVERT: B 89 ARG cc_start: 0.7985 (ttt180) cc_final: 0.7589 (ttm-80) REVERT: B 117 MET cc_start: 0.7550 (tpp) cc_final: 0.7117 (tpp) REVERT: C 118 GLU cc_start: 0.8396 (tp30) cc_final: 0.7945 (tp30) REVERT: C 128 GLU cc_start: 0.7575 (tp30) cc_final: 0.7221 (tt0) REVERT: C 141 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7196 (tt) REVERT: D 68 ASP cc_start: 0.7927 (m-30) cc_final: 0.7612 (m-30) REVERT: D 91 ASP cc_start: 0.7093 (t70) cc_final: 0.6639 (t70) REVERT: D 117 MET cc_start: 0.7932 (tpp) cc_final: 0.6938 (ttp) REVERT: E 43 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7737 (tpt170) REVERT: E 117 MET cc_start: 0.7516 (tpp) cc_final: 0.7126 (tpp) REVERT: E 121 GLU cc_start: 0.8456 (tp30) cc_final: 0.8252 (tp30) REVERT: F 127 ASP cc_start: 0.8625 (p0) cc_final: 0.8364 (p0) REVERT: F 128 GLU cc_start: 0.7724 (tp30) cc_final: 0.7128 (tt0) outliers start: 14 outliers final: 11 residues processed: 157 average time/residue: 0.2815 time to fit residues: 55.9977 Evaluate side-chains 161 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113738 restraints weight = 13090.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117036 restraints weight = 7441.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119340 restraints weight = 4844.797| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8328 Z= 0.254 Angle : 0.602 11.514 11214 Z= 0.308 Chirality : 0.042 0.228 1188 Planarity : 0.004 0.051 1446 Dihedral : 4.038 28.334 1098 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.03 % Allowed : 20.83 % Favored : 77.14 % 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: 0.54 (0.27), residues: 972 helix: 1.52 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.12 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.005 0.001 HIS B 173 PHE 0.020 0.002 PHE E 39 TYR 0.013 0.001 TYR C 113 ARG 0.009 0.000 ARG D 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.74 seconds wall clock time: 33 minutes 25.31 seconds (2005.31 seconds total)