Starting phenix.real_space_refine on Sun Feb 18 01:18:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/02_2024/7pkp_13476.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/02_2024/7pkp_13476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/02_2024/7pkp_13476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/02_2024/7pkp_13476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/02_2024/7pkp_13476.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/02_2024/7pkp_13476.pdb" } resolution = 3.1 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= 0.000 sd= 0.005 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 120 5.16 5 C 13064 2.51 5 N 3456 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U GLU 3": "OE1" <-> "OE2" Residue "U ASP 15": "OD1" <-> "OD2" Residue "U PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 65": "OD1" <-> "OD2" Residue "U PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 73": "OE1" <-> "OE2" Residue "U PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 86": "OE1" <-> "OE2" Residue "U ARG 104": "NH1" <-> "NH2" Residue "U GLU 153": "OE1" <-> "OE2" Residue "U TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 256": "OD1" <-> "OD2" Residue "U ASP 261": "OD1" <-> "OD2" Residue "U ASP 283": "OD1" <-> "OD2" Residue "U ASP 306": "OD1" <-> "OD2" Residue "U ASP 310": "OD1" <-> "OD2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C ASP 310": "OD1" <-> "OD2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 283": "OD1" <-> "OD2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D ASP 310": "OD1" <-> "OD2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 86": "OE1" <-> "OE2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E ASP 283": "OD1" <-> "OD2" Residue "E ASP 306": "OD1" <-> "OD2" Residue "E ASP 310": "OD1" <-> "OD2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F ASP 306": "OD1" <-> "OD2" Residue "F ASP 310": "OD1" <-> "OD2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 65": "OD1" <-> "OD2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G ASP 283": "OD1" <-> "OD2" Residue "G ASP 306": "OD1" <-> "OD2" Residue "G ASP 310": "OD1" <-> "OD2" Residue "G GLU 311": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20360 Number of models: 1 Model: "" Number of chains: 8 Chain: "U" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2545 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "A" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2545 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "B" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2545 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "C" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2545 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "D" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2545 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "E" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2545 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "F" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2545 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "G" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2545 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Time building chain proxies: 11.14, per 1000 atoms: 0.55 Number of scatterers: 20360 At special positions: 0 Unit cell: (133.75, 133.75, 108.07, 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 120 16.00 O 3720 8.00 N 3456 7.00 C 13064 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: 7.62 Conformation dependent library (CDL) restraints added in 4.1 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 24 sheets defined 43.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'U' and resid 23 through 32 removed outlier: 3.855A pdb=" N THR U 32 " --> pdb=" O LYS U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 61 removed outlier: 4.865A pdb=" N LYS U 59 " --> pdb=" O GLN U 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG U 60 " --> pdb=" O PHE U 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR U 61 " --> pdb=" O LYS U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 91 removed outlier: 3.994A pdb=" N THR U 78 " --> pdb=" O THR U 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER U 90 " --> pdb=" O GLU U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 102 Processing helix chain 'U' and resid 107 through 119 Processing helix chain 'U' and resid 128 through 141 removed outlier: 3.696A pdb=" N LEU U 132 " --> pdb=" O SER U 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU U 133 " --> pdb=" O LYS U 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 152 Processing helix chain 'U' and resid 199 through 210 removed outlier: 3.684A pdb=" N GLU U 208 " --> pdb=" O GLU U 204 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 247 removed outlier: 4.016A pdb=" N ALA U 243 " --> pdb=" O ASP U 239 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR U 244 " --> pdb=" O ARG U 240 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 Processing helix chain 'U' and resid 281 through 286 Processing helix chain 'U' and resid 287 through 289 No H-bonds generated for 'chain 'U' and resid 287 through 289' Processing helix chain 'U' and resid 303 through 313 removed outlier: 3.752A pdb=" N SER U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.855A pdb=" N THR A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 removed outlier: 4.865A pdb=" N LYS A 59 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 91 removed outlier: 3.995A pdb=" N THR A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.695A pdb=" N LEU A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 199 through 210 removed outlier: 3.685A pdb=" N GLU A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 4.016A pdb=" N ALA A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.752A pdb=" N SER A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.855A pdb=" N THR B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 removed outlier: 4.865A pdb=" N LYS B 59 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 61 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 91 removed outlier: 3.995A pdb=" N THR B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.696A pdb=" N LEU B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 199 through 210 removed outlier: 3.685A pdb=" N GLU B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 4.016A pdb=" N ALA B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 303 through 313 removed outlier: 3.752A pdb=" N SER B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 removed outlier: 3.855A pdb=" N THR C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 61 removed outlier: 4.865A pdb=" N LYS C 59 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 91 removed outlier: 3.995A pdb=" N THR C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.697A pdb=" N LEU C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 199 through 210 removed outlier: 3.685A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 247 removed outlier: 4.016A pdb=" N ALA C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.753A pdb=" N SER C 313 " --> pdb=" O MET C 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 32 removed outlier: 3.855A pdb=" N THR D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 61 removed outlier: 4.865A pdb=" N LYS D 59 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 61 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 91 removed outlier: 3.995A pdb=" N THR D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 79 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 107 through 119 Processing helix chain 'D' and resid 128 through 141 removed outlier: 3.696A pdb=" N LEU D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.685A pdb=" N GLU D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 4.016A pdb=" N ALA D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 279 Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 303 through 313 removed outlier: 3.752A pdb=" N SER D 313 " --> pdb=" O MET D 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 32 removed outlier: 3.855A pdb=" N THR E 32 " --> pdb=" O LYS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 61 removed outlier: 4.865A pdb=" N LYS E 59 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG E 60 " --> pdb=" O PHE E 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR E 61 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 91 removed outlier: 3.995A pdb=" N THR E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER E 90 " --> pdb=" O GLU E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 Processing helix chain 'E' and resid 107 through 119 Processing helix chain 'E' and resid 128 through 141 removed outlier: 3.696A pdb=" N LEU E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 199 through 210 removed outlier: 3.685A pdb=" N GLU E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 247 removed outlier: 4.016A pdb=" N ALA E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 303 through 313 removed outlier: 3.752A pdb=" N SER E 313 " --> pdb=" O MET E 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 32 removed outlier: 3.855A pdb=" N THR F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 61 removed outlier: 4.865A pdb=" N LYS F 59 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 61 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 91 removed outlier: 3.995A pdb=" N THR F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 79 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER F 90 " --> pdb=" O GLU F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 Processing helix chain 'F' and resid 107 through 119 Processing helix chain 'F' and resid 128 through 141 removed outlier: 3.696A pdb=" N LEU F 132 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU F 133 " --> pdb=" O LYS F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.685A pdb=" N GLU F 208 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 247 removed outlier: 4.016A pdb=" N ALA F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 279 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 303 through 313 removed outlier: 3.752A pdb=" N SER F 313 " --> pdb=" O MET F 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 32 removed outlier: 3.855A pdb=" N THR G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 61 removed outlier: 4.865A pdb=" N LYS G 59 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG G 60 " --> pdb=" O PHE G 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR G 61 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 91 removed outlier: 3.995A pdb=" N THR G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 90 " --> pdb=" O GLU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 102 Processing helix chain 'G' and resid 107 through 119 Processing helix chain 'G' and resid 128 through 141 removed outlier: 3.696A pdb=" N LEU G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU G 133 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'G' and resid 199 through 210 removed outlier: 3.685A pdb=" N GLU G 208 " --> pdb=" O GLU G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 247 removed outlier: 4.016A pdb=" N ALA G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 279 Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'G' and resid 287 through 289 No H-bonds generated for 'chain 'G' and resid 287 through 289' Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.752A pdb=" N SER G 313 " --> pdb=" O MET G 309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 8 through 12 Processing sheet with id=AA2, first strand: chain 'U' and resid 44 through 46 Processing sheet with id=AA3, first strand: chain 'U' and resid 157 through 160 removed outlier: 6.189A pdb=" N ILE U 157 " --> pdb=" O LYS U 168 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS U 168 " --> pdb=" O ILE U 157 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE U 159 " --> pdb=" O MET U 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 8 through 12 Processing sheet with id=AA5, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.189A pdb=" N ILE A 157 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS A 168 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 159 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12 Processing sheet with id=AA8, first strand: chain 'B' and resid 44 through 46 Processing sheet with id=AA9, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.189A pdb=" N ILE B 157 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS B 168 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 159 " --> pdb=" O MET B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 8 through 12 Processing sheet with id=AB2, first strand: chain 'C' and resid 44 through 46 Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.189A pdb=" N ILE C 157 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS C 168 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 159 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 8 through 12 Processing sheet with id=AB5, first strand: chain 'D' and resid 44 through 46 Processing sheet with id=AB6, first strand: chain 'D' and resid 157 through 160 removed outlier: 6.189A pdb=" N ILE D 157 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS D 168 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D 159 " --> pdb=" O MET D 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 8 through 12 Processing sheet with id=AB8, first strand: chain 'E' and resid 44 through 46 Processing sheet with id=AB9, first strand: chain 'E' and resid 157 through 160 removed outlier: 6.189A pdb=" N ILE E 157 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS E 168 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE E 159 " --> pdb=" O MET E 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 8 through 12 Processing sheet with id=AC2, first strand: chain 'F' and resid 44 through 46 Processing sheet with id=AC3, first strand: chain 'F' and resid 157 through 160 removed outlier: 6.189A pdb=" N ILE F 157 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS F 168 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE F 159 " --> pdb=" O MET F 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 8 through 12 Processing sheet with id=AC5, first strand: chain 'G' and resid 44 through 46 Processing sheet with id=AC6, first strand: chain 'G' and resid 157 through 160 removed outlier: 6.188A pdb=" N ILE G 157 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS G 168 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE G 159 " --> pdb=" O MET G 166 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2112 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: 5.93 Time building geometry restraints manager: 8.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6496 1.34 - 1.45: 2980 1.45 - 1.57: 11108 1.57 - 1.69: 0 1.69 - 1.80: 208 Bond restraints: 20792 Sorted by residual: bond pdb=" C SER U 67 " pdb=" N ARG U 68 " ideal model delta sigma weight residual 1.334 1.375 -0.041 1.24e-02 6.50e+03 1.10e+01 bond pdb=" C SER F 67 " pdb=" N ARG F 68 " ideal model delta sigma weight residual 1.334 1.374 -0.041 1.24e-02 6.50e+03 1.08e+01 bond pdb=" C SER A 67 " pdb=" N ARG A 68 " ideal model delta sigma weight residual 1.334 1.374 -0.041 1.24e-02 6.50e+03 1.08e+01 bond pdb=" C SER B 67 " pdb=" N ARG B 68 " ideal model delta sigma weight residual 1.334 1.374 -0.041 1.24e-02 6.50e+03 1.08e+01 bond pdb=" C SER G 67 " pdb=" N ARG G 68 " ideal model delta sigma weight residual 1.334 1.374 -0.041 1.24e-02 6.50e+03 1.08e+01 ... (remaining 20787 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.27: 448 106.27 - 113.18: 11522 113.18 - 120.10: 7222 120.10 - 127.01: 8664 127.01 - 133.92: 216 Bond angle restraints: 28072 Sorted by residual: angle pdb=" N LYS D 38 " pdb=" CA LYS D 38 " pdb=" C LYS D 38 " ideal model delta sigma weight residual 114.56 107.41 7.15 1.27e+00 6.20e-01 3.17e+01 angle pdb=" N LYS U 38 " pdb=" CA LYS U 38 " pdb=" C LYS U 38 " ideal model delta sigma weight residual 114.56 107.41 7.15 1.27e+00 6.20e-01 3.17e+01 angle pdb=" N LYS E 38 " pdb=" CA LYS E 38 " pdb=" C LYS E 38 " ideal model delta sigma weight residual 114.56 107.41 7.15 1.27e+00 6.20e-01 3.17e+01 angle pdb=" N LYS F 38 " pdb=" CA LYS F 38 " pdb=" C LYS F 38 " ideal model delta sigma weight residual 114.56 107.41 7.15 1.27e+00 6.20e-01 3.17e+01 angle pdb=" N LYS B 38 " pdb=" CA LYS B 38 " pdb=" C LYS B 38 " ideal model delta sigma weight residual 114.56 107.41 7.15 1.27e+00 6.20e-01 3.17e+01 ... (remaining 28067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 11111 16.07 - 32.14: 1184 32.14 - 48.21: 289 48.21 - 64.28: 31 64.28 - 80.34: 25 Dihedral angle restraints: 12640 sinusoidal: 5200 harmonic: 7440 Sorted by residual: dihedral pdb=" CA GLU G 13 " pdb=" C GLU G 13 " pdb=" N ASN G 14 " pdb=" CA ASN G 14 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLU E 13 " pdb=" C GLU E 13 " pdb=" N ASN E 14 " pdb=" CA ASN E 14 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLU F 13 " pdb=" C GLU F 13 " pdb=" N ASN F 14 " pdb=" CA ASN F 14 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 12637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1356 0.025 - 0.050: 1049 0.050 - 0.074: 491 0.074 - 0.099: 128 0.099 - 0.124: 112 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA ILE G 228 " pdb=" N ILE G 228 " pdb=" C ILE G 228 " pdb=" CB ILE G 228 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE A 228 " pdb=" N ILE A 228 " pdb=" C ILE A 228 " pdb=" CB ILE A 228 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE F 228 " pdb=" N ILE F 228 " pdb=" C ILE F 228 " pdb=" CB ILE F 228 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 3133 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG U 68 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ARG U 68 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG U 68 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY U 69 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 68 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ARG F 68 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG F 68 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY F 69 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 68 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ARG A 68 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG A 68 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY A 69 " 0.014 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4654 2.77 - 3.30: 17831 3.30 - 3.84: 30948 3.84 - 4.37: 38945 4.37 - 4.90: 67639 Nonbonded interactions: 160017 Sorted by model distance: nonbonded pdb=" CD2 PHE F 257 " pdb=" CD1 LEU F 259 " model vdw 2.238 3.760 nonbonded pdb=" CD2 PHE A 257 " pdb=" CD1 LEU A 259 " model vdw 2.238 3.760 nonbonded pdb=" CD2 PHE D 257 " pdb=" CD1 LEU D 259 " model vdw 2.238 3.760 nonbonded pdb=" CD2 PHE B 257 " pdb=" CD1 LEU B 259 " model vdw 2.238 3.760 nonbonded pdb=" CD2 PHE U 257 " pdb=" CD1 LEU U 259 " model vdw 2.238 3.760 ... (remaining 160012 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' selection = chain 'G' selection = chain 'U' } 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 individual isotropic 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.630 Check model and map are aligned: 0.330 Set scattering table: 0.170 Process input model: 54.930 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.008 0.041 20792 Z= 0.490 Angle : 0.688 7.145 28072 Z= 0.411 Chirality : 0.043 0.124 3136 Planarity : 0.004 0.039 3552 Dihedral : 14.184 80.344 7792 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.14), residues: 2488 helix: -1.85 (0.15), residues: 912 sheet: -1.94 (0.27), residues: 264 loop : -3.63 (0.13), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 167 HIS 0.003 0.001 HIS G 225 PHE 0.017 0.002 PHE C 77 TYR 0.009 0.002 TYR D 44 ARG 0.002 0.000 ARG U 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.622 Fit side-chains REVERT: U 40 MET cc_start: 0.7977 (mmt) cc_final: 0.7759 (tpp) REVERT: U 183 ASN cc_start: 0.7993 (m-40) cc_final: 0.7770 (p0) REVERT: U 197 ILE cc_start: 0.8700 (mm) cc_final: 0.8308 (mm) REVERT: U 240 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7686 (ttm-80) REVERT: A 40 MET cc_start: 0.7975 (mmt) cc_final: 0.7754 (tpp) REVERT: A 183 ASN cc_start: 0.7993 (m-40) cc_final: 0.7769 (p0) REVERT: A 197 ILE cc_start: 0.8697 (mm) cc_final: 0.8306 (mm) REVERT: A 240 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7687 (ttm-80) REVERT: B 40 MET cc_start: 0.7973 (mmt) cc_final: 0.7753 (tpp) REVERT: B 183 ASN cc_start: 0.7996 (m-40) cc_final: 0.7771 (p0) REVERT: B 197 ILE cc_start: 0.8694 (mm) cc_final: 0.8304 (mm) REVERT: B 240 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7686 (ttm-80) REVERT: C 40 MET cc_start: 0.7974 (mmt) cc_final: 0.7753 (tpp) REVERT: C 183 ASN cc_start: 0.7992 (m-40) cc_final: 0.7769 (p0) REVERT: C 197 ILE cc_start: 0.8702 (mm) cc_final: 0.8311 (mm) REVERT: C 240 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7682 (ttm-80) REVERT: D 40 MET cc_start: 0.7975 (mmt) cc_final: 0.7755 (tpp) REVERT: D 183 ASN cc_start: 0.7995 (m-40) cc_final: 0.7771 (p0) REVERT: D 197 ILE cc_start: 0.8712 (mm) cc_final: 0.8321 (mm) REVERT: D 240 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7686 (ttm-80) REVERT: E 40 MET cc_start: 0.7975 (mmt) cc_final: 0.7757 (tpp) REVERT: E 183 ASN cc_start: 0.7991 (m-40) cc_final: 0.7766 (p0) REVERT: E 197 ILE cc_start: 0.8697 (mm) cc_final: 0.8307 (mm) REVERT: E 240 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7687 (ttm-80) REVERT: F 40 MET cc_start: 0.7977 (mmt) cc_final: 0.7758 (tpp) REVERT: F 183 ASN cc_start: 0.7991 (m-40) cc_final: 0.7767 (p0) REVERT: F 197 ILE cc_start: 0.8697 (mm) cc_final: 0.8306 (mm) REVERT: F 240 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7688 (ttm-80) REVERT: G 40 MET cc_start: 0.7974 (mmt) cc_final: 0.7753 (tpp) REVERT: G 183 ASN cc_start: 0.7994 (m-40) cc_final: 0.7770 (p0) REVERT: G 197 ILE cc_start: 0.8695 (mm) cc_final: 0.8306 (mm) REVERT: G 240 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7688 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.4235 time to fit residues: 199.8490 Evaluate side-chains 264 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 95 GLN U 110 HIS U 127 HIS ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 258 ASN A 95 GLN A 110 HIS A 127 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN B 95 GLN B 110 HIS B 127 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN C 95 GLN C 110 HIS C 127 HIS C 175 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN D 95 GLN D 110 HIS D 127 HIS D 175 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN E 95 GLN E 110 HIS E 127 HIS E 175 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN F 95 GLN F 110 HIS F 127 HIS ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN G 95 GLN G 110 HIS G 127 HIS G 175 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20792 Z= 0.148 Angle : 0.473 5.742 28072 Z= 0.252 Chirality : 0.040 0.127 3136 Planarity : 0.003 0.025 3552 Dihedral : 4.199 14.385 2680 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.06 % Allowed : 6.69 % Favored : 92.25 % 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: -2.72 (0.15), residues: 2488 helix: -0.47 (0.17), residues: 960 sheet: -1.56 (0.27), residues: 264 loop : -3.04 (0.14), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 167 HIS 0.002 0.001 HIS B 225 PHE 0.007 0.001 PHE D 77 TYR 0.005 0.001 TYR G 226 ARG 0.003 0.000 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 280 time to evaluate : 2.662 Fit side-chains REVERT: U 240 ARG cc_start: 0.7803 (ttm170) cc_final: 0.7486 (ttm170) REVERT: U 256 ASP cc_start: 0.7669 (t70) cc_final: 0.7443 (t70) REVERT: A 240 ARG cc_start: 0.7805 (ttm170) cc_final: 0.7486 (ttm170) REVERT: A 256 ASP cc_start: 0.7665 (t70) cc_final: 0.7441 (t70) REVERT: B 240 ARG cc_start: 0.7806 (ttm170) cc_final: 0.7486 (ttm170) REVERT: B 256 ASP cc_start: 0.7670 (t70) cc_final: 0.7444 (t70) REVERT: C 240 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7483 (ttm170) REVERT: C 256 ASP cc_start: 0.7670 (t70) cc_final: 0.7443 (t70) REVERT: D 240 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7484 (ttm170) REVERT: D 256 ASP cc_start: 0.7668 (t70) cc_final: 0.7441 (t70) REVERT: E 240 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7484 (ttm170) REVERT: E 256 ASP cc_start: 0.7667 (t70) cc_final: 0.7443 (t70) REVERT: F 240 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7486 (ttm170) REVERT: F 256 ASP cc_start: 0.7667 (t70) cc_final: 0.7444 (t70) REVERT: G 240 ARG cc_start: 0.7803 (ttm170) cc_final: 0.7482 (ttm170) REVERT: G 256 ASP cc_start: 0.7665 (t70) cc_final: 0.7440 (t70) outliers start: 24 outliers final: 24 residues processed: 288 average time/residue: 0.3725 time to fit residues: 157.2774 Evaluate side-chains 281 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain U residue 310 ASP Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 310 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 95 GLN U 175 GLN ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 ASN A 95 GLN A 175 GLN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 95 GLN B 175 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN C 95 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN D 95 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 95 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN F 95 GLN F 175 GLN ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 95 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 20792 Z= 0.575 Angle : 0.658 6.681 28072 Z= 0.337 Chirality : 0.047 0.126 3136 Planarity : 0.004 0.038 3552 Dihedral : 4.838 19.623 2680 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.17 % Allowed : 13.82 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.15), residues: 2488 helix: -0.83 (0.16), residues: 1056 sheet: -1.58 (0.27), residues: 264 loop : -3.32 (0.14), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP U 167 HIS 0.003 0.001 HIS C 237 PHE 0.025 0.002 PHE C 77 TYR 0.009 0.002 TYR F 226 ARG 0.005 0.001 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 266 time to evaluate : 2.532 Fit side-chains REVERT: U 40 MET cc_start: 0.7730 (tpp) cc_final: 0.7502 (tpp) REVERT: U 240 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7573 (ttm170) REVERT: A 40 MET cc_start: 0.7728 (tpp) cc_final: 0.7501 (tpp) REVERT: A 240 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7572 (ttm170) REVERT: B 40 MET cc_start: 0.7726 (tpp) cc_final: 0.7498 (tpp) REVERT: B 240 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7573 (ttm170) REVERT: C 40 MET cc_start: 0.7730 (tpp) cc_final: 0.7502 (tpp) REVERT: C 240 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7562 (ttm170) REVERT: D 40 MET cc_start: 0.7729 (tpp) cc_final: 0.7502 (tpp) REVERT: D 240 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7570 (ttm170) REVERT: E 40 MET cc_start: 0.7730 (tpp) cc_final: 0.7504 (tpp) REVERT: E 240 ARG cc_start: 0.7858 (ttm170) cc_final: 0.7574 (ttm170) REVERT: F 40 MET cc_start: 0.7730 (tpp) cc_final: 0.7503 (tpp) REVERT: F 240 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7571 (ttm170) REVERT: G 40 MET cc_start: 0.7730 (tpp) cc_final: 0.7501 (tpp) REVERT: G 240 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7571 (ttm170) outliers start: 72 outliers final: 48 residues processed: 305 average time/residue: 0.3887 time to fit residues: 170.0911 Evaluate side-chains 301 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain U residue 310 ASP Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 310 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 95 GLN U 127 HIS ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 ASN A 95 GLN A 127 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 95 GLN B 127 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN C 95 GLN C 127 HIS ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN D 95 GLN D 127 HIS ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 95 GLN E 127 HIS ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN F 95 GLN F 127 HIS ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 95 GLN G 127 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 20792 Z= 0.182 Angle : 0.460 5.299 28072 Z= 0.244 Chirality : 0.039 0.124 3136 Planarity : 0.003 0.026 3552 Dihedral : 4.140 14.781 2680 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.46 % Allowed : 16.59 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.16), residues: 2488 helix: 0.06 (0.17), residues: 1008 sheet: -1.15 (0.28), residues: 264 loop : -2.88 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 167 HIS 0.005 0.001 HIS C 127 PHE 0.008 0.001 PHE E 77 TYR 0.006 0.001 TYR E 226 ARG 0.006 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 301 time to evaluate : 2.425 Fit side-chains REVERT: U 176 LEU cc_start: 0.8887 (tp) cc_final: 0.8687 (tp) REVERT: U 240 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7500 (ttm170) REVERT: U 256 ASP cc_start: 0.7704 (t70) cc_final: 0.7426 (t70) REVERT: A 176 LEU cc_start: 0.8888 (tp) cc_final: 0.8682 (tp) REVERT: A 240 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7501 (ttm170) REVERT: A 256 ASP cc_start: 0.7700 (t70) cc_final: 0.7424 (t70) REVERT: B 176 LEU cc_start: 0.8887 (tp) cc_final: 0.8686 (tp) REVERT: B 240 ARG cc_start: 0.7783 (ttm170) cc_final: 0.7500 (ttm170) REVERT: B 256 ASP cc_start: 0.7704 (t70) cc_final: 0.7426 (t70) REVERT: C 240 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7526 (ttm170) REVERT: C 256 ASP cc_start: 0.7702 (t70) cc_final: 0.7423 (t70) REVERT: D 176 LEU cc_start: 0.8885 (tp) cc_final: 0.8683 (tp) REVERT: D 240 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7499 (ttm170) REVERT: D 256 ASP cc_start: 0.7704 (t70) cc_final: 0.7427 (t70) REVERT: E 176 LEU cc_start: 0.8884 (tp) cc_final: 0.8683 (tp) REVERT: E 240 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7498 (ttm170) REVERT: E 256 ASP cc_start: 0.7705 (t70) cc_final: 0.7429 (t70) REVERT: F 240 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7501 (ttm170) REVERT: F 256 ASP cc_start: 0.7700 (t70) cc_final: 0.7423 (t70) REVERT: G 240 ARG cc_start: 0.7784 (ttm170) cc_final: 0.7499 (ttm170) REVERT: G 256 ASP cc_start: 0.7698 (t70) cc_final: 0.7423 (t70) outliers start: 56 outliers final: 46 residues processed: 333 average time/residue: 0.3785 time to fit residues: 182.8345 Evaluate side-chains 323 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 277 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 173 GLU Chi-restraints excluded: chain U residue 310 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 310 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 204 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 95 GLN U 127 HIS ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 ASN A 95 GLN A 127 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 95 GLN B 127 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN C 95 GLN C 127 HIS ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN D 127 HIS ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 95 GLN E 127 HIS ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN F 95 GLN F 127 HIS ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 95 GLN G 127 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20792 Z= 0.148 Angle : 0.428 5.339 28072 Z= 0.227 Chirality : 0.039 0.126 3136 Planarity : 0.003 0.027 3552 Dihedral : 3.818 13.585 2680 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.82 % Allowed : 18.22 % Favored : 78.96 % 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: -1.49 (0.16), residues: 2488 helix: 0.62 (0.17), residues: 1008 sheet: -0.92 (0.27), residues: 264 loop : -2.51 (0.15), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 167 HIS 0.004 0.001 HIS D 225 PHE 0.008 0.001 PHE F 77 TYR 0.006 0.001 TYR D 226 ARG 0.007 0.000 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 299 time to evaluate : 2.431 Fit side-chains REVERT: U 197 ILE cc_start: 0.8612 (mm) cc_final: 0.8238 (mm) REVERT: U 240 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7444 (ttm170) REVERT: A 197 ILE cc_start: 0.8612 (mm) cc_final: 0.8237 (mm) REVERT: A 240 ARG cc_start: 0.7709 (ttm170) cc_final: 0.7439 (ttm170) REVERT: B 197 ILE cc_start: 0.8610 (mm) cc_final: 0.8228 (mm) REVERT: B 240 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7442 (ttm170) REVERT: C 197 ILE cc_start: 0.8623 (mm) cc_final: 0.8245 (mm) REVERT: C 240 ARG cc_start: 0.7747 (ttm170) cc_final: 0.7480 (ttm170) REVERT: D 197 ILE cc_start: 0.8611 (mm) cc_final: 0.8237 (mm) REVERT: D 240 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7440 (ttm170) REVERT: E 197 ILE cc_start: 0.8611 (mm) cc_final: 0.8236 (mm) REVERT: E 240 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7443 (ttm170) REVERT: F 197 ILE cc_start: 0.8610 (mm) cc_final: 0.8236 (mm) REVERT: F 240 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7441 (ttm170) REVERT: G 197 ILE cc_start: 0.8610 (mm) cc_final: 0.8228 (mm) outliers start: 64 outliers final: 56 residues processed: 339 average time/residue: 0.3841 time to fit residues: 188.9156 Evaluate side-chains 346 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 290 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 173 GLU Chi-restraints excluded: chain U residue 310 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 310 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 95 GLN ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 ASN A 95 GLN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 95 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN C 95 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 95 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN F 95 GLN ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 95 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20792 Z= 0.123 Angle : 0.421 6.443 28072 Z= 0.220 Chirality : 0.038 0.125 3136 Planarity : 0.003 0.028 3552 Dihedral : 3.545 12.135 2680 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.46 % Allowed : 19.15 % Favored : 78.39 % 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: -1.03 (0.16), residues: 2488 helix: 1.11 (0.17), residues: 1008 sheet: -0.76 (0.27), residues: 264 loop : -2.35 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 167 HIS 0.003 0.001 HIS F 225 PHE 0.006 0.001 PHE B 19 TYR 0.005 0.001 TYR B 226 ARG 0.006 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 284 time to evaluate : 2.555 Fit side-chains REVERT: U 30 MET cc_start: 0.8802 (tmm) cc_final: 0.8493 (tmm) REVERT: U 197 ILE cc_start: 0.8576 (mm) cc_final: 0.8220 (mm) REVERT: U 240 ARG cc_start: 0.7637 (ttm170) cc_final: 0.7393 (ttm-80) REVERT: A 30 MET cc_start: 0.8802 (tmm) cc_final: 0.8493 (tmm) REVERT: A 197 ILE cc_start: 0.8574 (mm) cc_final: 0.8218 (mm) REVERT: A 240 ARG cc_start: 0.7632 (ttm170) cc_final: 0.7390 (ttm-80) REVERT: B 30 MET cc_start: 0.8802 (tmm) cc_final: 0.8492 (tmm) REVERT: B 197 ILE cc_start: 0.8573 (mm) cc_final: 0.8217 (mm) REVERT: B 240 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7390 (ttm-80) REVERT: C 30 MET cc_start: 0.8804 (tmm) cc_final: 0.8494 (tmm) REVERT: C 240 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7417 (ttm-80) REVERT: D 30 MET cc_start: 0.8801 (tmm) cc_final: 0.8492 (tmm) REVERT: D 197 ILE cc_start: 0.8575 (mm) cc_final: 0.8219 (mm) REVERT: D 240 ARG cc_start: 0.7636 (ttm170) cc_final: 0.7393 (ttm-80) REVERT: E 30 MET cc_start: 0.8801 (tmm) cc_final: 0.8492 (tmm) REVERT: E 197 ILE cc_start: 0.8575 (mm) cc_final: 0.8219 (mm) REVERT: E 240 ARG cc_start: 0.7637 (ttm170) cc_final: 0.7393 (ttm-80) REVERT: F 30 MET cc_start: 0.8801 (tmm) cc_final: 0.8489 (tmm) REVERT: F 197 ILE cc_start: 0.8575 (mm) cc_final: 0.8219 (mm) REVERT: F 240 ARG cc_start: 0.7636 (ttm170) cc_final: 0.7393 (ttm-80) REVERT: G 30 MET cc_start: 0.8802 (tmm) cc_final: 0.8495 (tmm) REVERT: G 197 ILE cc_start: 0.8574 (mm) cc_final: 0.8212 (mm) REVERT: G 240 ARG cc_start: 0.7658 (ttm170) cc_final: 0.7419 (ttm-80) outliers start: 56 outliers final: 48 residues processed: 324 average time/residue: 0.3526 time to fit residues: 169.6237 Evaluate side-chains 326 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 278 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 173 GLU Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 95 GLN ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 ASN A 95 GLN A 248 ASN A 255 ASN B 95 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN C 95 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 95 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN F 95 GLN ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 95 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 20792 Z= 0.324 Angle : 0.519 6.358 28072 Z= 0.265 Chirality : 0.041 0.120 3136 Planarity : 0.003 0.033 3552 Dihedral : 4.086 14.774 2680 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.96 % Allowed : 19.37 % Favored : 76.67 % 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 (0.16), residues: 2488 helix: 0.76 (0.17), residues: 1008 sheet: -0.71 (0.28), residues: 264 loop : -2.41 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 167 HIS 0.002 0.001 HIS U 225 PHE 0.017 0.002 PHE C 77 TYR 0.008 0.002 TYR D 226 ARG 0.007 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 274 time to evaluate : 2.630 Fit side-chains REVERT: U 240 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7444 (ttm-80) REVERT: A 240 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7440 (ttm-80) REVERT: B 240 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7441 (ttm-80) REVERT: C 240 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7442 (ttm-80) REVERT: D 240 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7443 (ttm-80) REVERT: E 240 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7444 (ttm-80) REVERT: F 240 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7444 (ttm-80) REVERT: G 240 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7441 (ttm-80) outliers start: 90 outliers final: 73 residues processed: 336 average time/residue: 0.3586 time to fit residues: 180.0822 Evaluate side-chains 345 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 272 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 173 GLU Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 310 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 162 optimal weight: 0.0570 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 ASN A 255 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN D 95 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20792 Z= 0.122 Angle : 0.422 5.006 28072 Z= 0.220 Chirality : 0.038 0.124 3136 Planarity : 0.003 0.027 3552 Dihedral : 3.608 12.194 2680 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.92 % Allowed : 19.06 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2488 helix: 1.30 (0.17), residues: 1008 sheet: -0.99 (0.27), residues: 280 loop : -2.20 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 167 HIS 0.003 0.001 HIS E 225 PHE 0.006 0.001 PHE C 77 TYR 0.006 0.001 TYR G 226 ARG 0.007 0.000 ARG U 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 297 time to evaluate : 2.923 Fit side-chains REVERT: U 197 ILE cc_start: 0.8561 (mm) cc_final: 0.8197 (mm) REVERT: U 240 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7360 (ttm-80) REVERT: A 197 ILE cc_start: 0.8563 (mm) cc_final: 0.8199 (mm) REVERT: A 240 ARG cc_start: 0.7606 (ttm170) cc_final: 0.7358 (ttm-80) REVERT: B 197 ILE cc_start: 0.8555 (mm) cc_final: 0.8192 (mm) REVERT: B 240 ARG cc_start: 0.7606 (ttm170) cc_final: 0.7358 (ttm-80) REVERT: C 240 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7360 (ttm-80) REVERT: D 197 ILE cc_start: 0.8559 (mm) cc_final: 0.8196 (mm) REVERT: D 240 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7359 (ttm-80) REVERT: E 197 ILE cc_start: 0.8559 (mm) cc_final: 0.8196 (mm) REVERT: E 240 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7361 (ttm-80) REVERT: F 197 ILE cc_start: 0.8557 (mm) cc_final: 0.8190 (mm) REVERT: F 240 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7359 (ttm-80) REVERT: G 197 ILE cc_start: 0.8559 (mm) cc_final: 0.8197 (mm) REVERT: G 240 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7359 (ttm-80) outliers start: 89 outliers final: 65 residues processed: 359 average time/residue: 0.4091 time to fit residues: 212.9272 Evaluate side-chains 347 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 282 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 173 GLU Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 310 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 310 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 248 ASN U 255 ASN A 255 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN C 248 ASN C 255 ASN D 95 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 248 ASN F 248 ASN F 255 ASN G 248 ASN G 255 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20792 Z= 0.164 Angle : 0.446 8.184 28072 Z= 0.228 Chirality : 0.039 0.123 3136 Planarity : 0.003 0.028 3552 Dihedral : 3.652 12.638 2680 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.30 % Allowed : 19.19 % Favored : 77.51 % 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: -0.69 (0.17), residues: 2488 helix: 1.40 (0.17), residues: 1008 sheet: -0.54 (0.28), residues: 264 loop : -2.17 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 167 HIS 0.003 0.001 HIS C 225 PHE 0.009 0.001 PHE C 77 TYR 0.007 0.001 TYR A 226 ARG 0.008 0.000 ARG U 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 272 time to evaluate : 2.480 Fit side-chains REVERT: U 197 ILE cc_start: 0.8574 (mm) cc_final: 0.8200 (mm) REVERT: U 240 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7365 (ttm-80) REVERT: A 197 ILE cc_start: 0.8576 (mm) cc_final: 0.8202 (mm) REVERT: A 240 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7363 (ttm-80) REVERT: B 197 ILE cc_start: 0.8569 (mm) cc_final: 0.8195 (mm) REVERT: B 240 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7371 (ttm-80) REVERT: C 240 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7363 (ttm-80) REVERT: D 197 ILE cc_start: 0.8572 (mm) cc_final: 0.8199 (mm) REVERT: D 240 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7371 (ttm-80) REVERT: E 197 ILE cc_start: 0.8573 (mm) cc_final: 0.8198 (mm) REVERT: E 240 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7371 (ttm-80) REVERT: F 197 ILE cc_start: 0.8572 (mm) cc_final: 0.8192 (mm) REVERT: F 240 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7373 (ttm-80) REVERT: G 197 ILE cc_start: 0.8573 (mm) cc_final: 0.8200 (mm) REVERT: G 240 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7363 (ttm-80) outliers start: 75 outliers final: 68 residues processed: 334 average time/residue: 0.3440 time to fit residues: 170.4055 Evaluate side-chains 340 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 272 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 173 GLU Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN B 255 ASN D 95 GLN D 248 ASN D 255 ASN G 255 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20792 Z= 0.187 Angle : 0.456 7.910 28072 Z= 0.232 Chirality : 0.039 0.121 3136 Planarity : 0.003 0.029 3552 Dihedral : 3.692 12.815 2680 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.17 % Allowed : 19.28 % Favored : 77.55 % 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: -0.72 (0.17), residues: 2488 helix: 1.32 (0.17), residues: 1024 sheet: -0.59 (0.27), residues: 264 loop : -2.17 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 167 HIS 0.003 0.001 HIS U 225 PHE 0.010 0.001 PHE C 77 TYR 0.007 0.001 TYR C 226 ARG 0.004 0.000 ARG A 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 271 time to evaluate : 2.529 Fit side-chains REVERT: U 240 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7372 (ttm-80) REVERT: A 240 ARG cc_start: 0.7606 (ttm170) cc_final: 0.7371 (ttm-80) REVERT: B 240 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7371 (ttm-80) REVERT: C 240 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7375 (ttm-80) REVERT: D 240 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7373 (ttm-80) REVERT: E 240 ARG cc_start: 0.7605 (ttm170) cc_final: 0.7373 (ttm-80) REVERT: F 240 ARG cc_start: 0.7606 (ttm170) cc_final: 0.7371 (ttm-80) REVERT: G 240 ARG cc_start: 0.7606 (ttm170) cc_final: 0.7370 (ttm-80) outliers start: 72 outliers final: 69 residues processed: 329 average time/residue: 0.3723 time to fit residues: 182.6307 Evaluate side-chains 340 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 271 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 173 GLU Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.169537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125604 restraints weight = 22692.439| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.13 r_work: 0.3010 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20792 Z= 0.196 Angle : 0.461 7.706 28072 Z= 0.236 Chirality : 0.039 0.121 3136 Planarity : 0.003 0.029 3552 Dihedral : 3.754 13.184 2680 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.12 % Allowed : 19.19 % Favored : 77.68 % 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: -0.70 (0.17), residues: 2488 helix: 1.35 (0.17), residues: 1024 sheet: -0.56 (0.27), residues: 264 loop : -2.17 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 167 HIS 0.003 0.001 HIS C 225 PHE 0.010 0.001 PHE C 77 TYR 0.007 0.001 TYR D 226 ARG 0.007 0.000 ARG B 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4362.94 seconds wall clock time: 80 minutes 25.04 seconds (4825.04 seconds total)