Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 21:58:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/05_2023/7pkp_13476.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/05_2023/7pkp_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_13476/05_2023/7pkp_13476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/05_2023/7pkp_13476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/05_2023/7pkp_13476.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/05_2023/7pkp_13476.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-4953/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: 10.61, per 1000 atoms: 0.52 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: 7.18 Conformation dependent library (CDL) restraints added in 3.0 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: 0.99 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: 5.64 Time building geometry restraints manager: 7.85 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: 0.570 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: 4.130 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 48.500 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.980 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.435 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.4234 time to fit residues: 200.4267 Evaluate side-chains 264 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5889 ------------------------------------------------------------------------------- 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: 0.8980 chunk 225 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN E 95 GLN E 110 HIS E 127 HIS ** 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 248 ASN G 258 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1513 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= 0.152 Angle : 0.473 5.817 28072 Z= 0.253 Chirality : 0.040 0.128 3136 Planarity : 0.003 0.026 3552 Dihedral : 4.221 14.320 2680 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.84 % 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: -2.66 (0.15), residues: 2488 helix: -0.48 (0.17), residues: 960 sheet: -1.54 (0.27), residues: 264 loop : -2.95 (0.14), residues: 1264 *********************** 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 299 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 280 time to evaluate : 2.571 Fit side-chains outliers start: 19 outliers final: 19 residues processed: 288 average time/residue: 0.3783 time to fit residues: 160.5110 Evaluate side-chains 267 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 248 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1918 time to fit residues: 10.5495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 225 optimal weight: 0.0970 chunk 243 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 180 optimal weight: 0.5980 overall best weight: 2.9384 ------------------------------------------------------------------------------- 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 95 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 95 GLN E 175 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 255 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 20792 Z= 0.348 Angle : 0.549 5.458 28072 Z= 0.281 Chirality : 0.042 0.116 3136 Planarity : 0.003 0.033 3552 Dihedral : 4.381 15.422 2680 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 1.63 % 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: -2.49 (0.15), residues: 2488 helix: -0.29 (0.17), residues: 1008 sheet: -1.42 (0.27), residues: 264 loop : -3.00 (0.14), residues: 1216 *********************** 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 301 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 264 time to evaluate : 1.820 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 280 average time/residue: 0.3193 time to fit residues: 127.5999 Evaluate side-chains 269 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 248 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1380 time to fit residues: 7.9917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 175 GLN ** 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 175 GLN ** 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 175 GLN G 255 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 20792 Z= 0.348 Angle : 0.539 5.512 28072 Z= 0.278 Chirality : 0.042 0.117 3136 Planarity : 0.003 0.035 3552 Dihedral : 4.363 15.859 2680 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2488 helix: -0.06 (0.17), residues: 1008 sheet: -1.26 (0.28), residues: 264 loop : -2.86 (0.14), residues: 1216 *********************** 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 316 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 264 time to evaluate : 2.492 Fit side-chains outliers start: 52 outliers final: 31 residues processed: 288 average time/residue: 0.3755 time to fit residues: 159.0926 Evaluate side-chains 271 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1805 time to fit residues: 13.9620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 165 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 255 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2063 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: