Starting phenix.real_space_refine on Sat Sep 28 18:33:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/09_2024/7pkp_13476.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/09_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_13476/09_2024/7pkp_13476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/09_2024/7pkp_13476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/09_2024/7pkp_13476.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkp_13476/09_2024/7pkp_13476.cif" } 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. Time to flip 144 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.01, per 1000 atoms: 0.54 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.3 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: 1.97 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: 5.48 Time building geometry restraints manager: 5.49 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: 0.00 - 1.43: 26695 1.43 - 2.86: 1186 2.86 - 4.29: 135 4.29 - 5.72: 40 5.72 - 7.15: 16 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 Time spend for trying shortcut: 0.00 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: 0.740 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: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.330 Set scattering table: 0.160 Process input model: 41.090 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.610 ------------------------------------------------------------------------------- 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 : 2.397 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: 0.4143 time to fit residues: 196.3036 Evaluate side-chains 264 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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: 0.7980 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 0.0770 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 175 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN C 95 GLN C 110 HIS C 127 HIS ** 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 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1516 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= 0.135 Angle : 0.476 6.416 28072 Z= 0.255 Chirality : 0.040 0.135 3136 Planarity : 0.003 0.025 3552 Dihedral : 4.136 14.106 2680 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.70 % Allowed : 7.48 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.15), residues: 2488 helix: -0.40 (0.17), residues: 960 sheet: -1.57 (0.27), residues: 264 loop : -2.94 (0.14), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 167 HIS 0.002 0.001 HIS G 225 PHE 0.007 0.001 PHE A 19 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 289 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 273 time to evaluate : 2.372 Fit side-chains REVERT: U 240 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7441 (ttm170) REVERT: A 240 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7439 (ttm170) REVERT: B 240 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7438 (ttm170) REVERT: C 240 ARG cc_start: 0.7774 (ttm170) cc_final: 0.7436 (ttm170) REVERT: C 256 ASP cc_start: 0.7659 (t70) cc_final: 0.7435 (t70) REVERT: D 240 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7437 (ttm170) REVERT: E 240 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7439 (ttm170) REVERT: F 240 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7441 (ttm170) REVERT: G 240 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7440 (ttm170) outliers start: 16 outliers final: 16 residues processed: 281 average time/residue: 0.3589 time to fit residues: 148.5437 Evaluate side-chains 276 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 260 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 305 THR 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: 6.9990 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 223 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 62 ASN U 95 GLN U 175 GLN ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 ASN A 62 ASN A 95 GLN A 175 GLN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 62 ASN B 95 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN C 62 ASN C 95 GLN C 175 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN D 62 ASN D 95 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 62 ASN E 95 GLN E 175 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN F 62 ASN F 95 GLN F 175 GLN ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 62 ASN G 95 GLN G 175 GLN G 255 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1623 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= 0.322 Angle : 0.534 5.947 28072 Z= 0.278 Chirality : 0.042 0.125 3136 Planarity : 0.003 0.031 3552 Dihedral : 4.349 15.411 2680 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.11 % Allowed : 10.52 % Favored : 87.37 % 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: -2.35 (0.15), residues: 2488 helix: -0.20 (0.17), residues: 1008 sheet: -1.42 (0.27), residues: 264 loop : -2.87 (0.15), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 167 HIS 0.002 0.001 HIS B 110 PHE 0.017 0.001 PHE C 77 TYR 0.008 0.001 TYR C 9 ARG 0.005 0.000 ARG E 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 335 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 287 time to evaluate : 2.550 Fit side-chains REVERT: U 40 MET cc_start: 0.7644 (tpp) cc_final: 0.7401 (tpp) REVERT: U 240 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7538 (ttm170) REVERT: A 40 MET cc_start: 0.7642 (tpp) cc_final: 0.7400 (tpp) REVERT: A 240 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7538 (ttm170) REVERT: B 40 MET cc_start: 0.7642 (tpp) cc_final: 0.7399 (tpp) REVERT: B 240 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7541 (ttm170) REVERT: C 40 MET cc_start: 0.7643 (tpp) cc_final: 0.7402 (tpp) REVERT: C 240 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7535 (ttm170) REVERT: D 40 MET cc_start: 0.7616 (tpp) cc_final: 0.7389 (tpp) REVERT: D 240 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7538 (ttm170) REVERT: E 40 MET cc_start: 0.7645 (tpp) cc_final: 0.7404 (tpp) REVERT: E 240 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7539 (ttm170) REVERT: F 40 MET cc_start: 0.7616 (tpp) cc_final: 0.7392 (tpp) REVERT: F 240 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7541 (ttm170) REVERT: G 40 MET cc_start: 0.7642 (tpp) cc_final: 0.7399 (tpp) REVERT: G 240 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7536 (ttm170) outliers start: 48 outliers final: 39 residues processed: 303 average time/residue: 0.3804 time to fit residues: 166.3730 Evaluate side-chains 294 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 255 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 173 GLU Chi-restraints excluded: chain U residue 305 THR Chi-restraints excluded: chain U residue 310 ASP Chi-restraints excluded: chain A residue 91 LEU 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 91 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 310 ASP Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 173 GLU 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: 0.7980 chunk 169 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 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 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 255 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1829 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= 0.327 Angle : 0.528 5.704 28072 Z= 0.275 Chirality : 0.042 0.124 3136 Planarity : 0.003 0.034 3552 Dihedral : 4.336 15.680 2680 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.95 % Allowed : 13.73 % Favored : 83.32 % 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: -0.20 (0.16), residues: 1056 sheet: -1.27 (0.28), residues: 264 loop : -2.80 (0.15), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP U 167 HIS 0.004 0.001 HIS B 127 PHE 0.015 0.002 PHE D 77 TYR 0.007 0.001 TYR E 226 ARG 0.006 0.001 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 333 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 266 time to evaluate : 2.372 Fit side-chains REVERT: U 40 MET cc_start: 0.7738 (tpp) cc_final: 0.7478 (tpp) REVERT: U 240 ARG cc_start: 0.7819 (ttm170) cc_final: 0.7535 (ttm170) REVERT: A 40 MET cc_start: 0.7734 (tpp) cc_final: 0.7472 (tpp) REVERT: A 240 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7533 (ttm170) REVERT: B 40 MET cc_start: 0.7732 (tpp) cc_final: 0.7475 (tpp) REVERT: B 240 ARG cc_start: 0.7819 (ttm170) cc_final: 0.7534 (ttm170) REVERT: C 40 MET cc_start: 0.7737 (tpp) cc_final: 0.7476 (tpp) REVERT: C 240 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7530 (ttm170) REVERT: D 40 MET cc_start: 0.7735 (tpp) cc_final: 0.7474 (tpp) REVERT: D 240 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7530 (ttm170) REVERT: E 40 MET cc_start: 0.7740 (tpp) cc_final: 0.7478 (tpp) REVERT: E 240 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7534 (ttm170) REVERT: F 40 MET cc_start: 0.7739 (tpp) cc_final: 0.7474 (tpp) REVERT: F 240 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7533 (ttm170) REVERT: G 40 MET cc_start: 0.7733 (tpp) cc_final: 0.7476 (tpp) REVERT: G 240 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7532 (ttm170) outliers start: 67 outliers final: 52 residues processed: 306 average time/residue: 0.3528 time to fit residues: 159.8412 Evaluate side-chains 309 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 257 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 200 VAL 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 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 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 93 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 200 VAL 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 93 VAL 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 93 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 200 VAL 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 93 VAL 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 93 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 200 VAL 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 93 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 200 VAL 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: 5.9990 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2144 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= 0.128 Angle : 0.425 5.644 28072 Z= 0.228 Chirality : 0.039 0.124 3136 Planarity : 0.003 0.028 3552 Dihedral : 3.790 13.003 2680 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.77 % Allowed : 15.32 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.64 (0.16), residues: 2488 helix: 0.44 (0.17), residues: 1056 sheet: -1.30 (0.27), residues: 280 loop : -2.58 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 167 HIS 0.003 0.001 HIS A 225 PHE 0.007 0.001 PHE C 19 TYR 0.005 0.001 TYR C 226 ARG 0.006 0.000 ARG A 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 364 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 301 time to evaluate : 2.200 Fit side-chains REVERT: U 30 MET cc_start: 0.8775 (tmm) cc_final: 0.8460 (tmm) REVERT: U 40 MET cc_start: 0.7694 (tpp) cc_final: 0.7461 (tpp) REVERT: U 197 ILE cc_start: 0.8600 (mm) cc_final: 0.8223 (mm) REVERT: U 256 ASP cc_start: 0.7675 (t70) cc_final: 0.7409 (t70) REVERT: A 30 MET cc_start: 0.8775 (tmm) cc_final: 0.8459 (tmm) REVERT: A 40 MET cc_start: 0.7689 (tpp) cc_final: 0.7457 (tpp) REVERT: A 197 ILE cc_start: 0.8599 (mm) cc_final: 0.8216 (mm) REVERT: A 256 ASP cc_start: 0.7674 (t70) cc_final: 0.7408 (t70) REVERT: B 30 MET cc_start: 0.8774 (tmm) cc_final: 0.8461 (tmm) REVERT: B 40 MET cc_start: 0.7683 (tpp) cc_final: 0.7451 (tpp) REVERT: B 197 ILE cc_start: 0.8601 (mm) cc_final: 0.8224 (mm) REVERT: B 256 ASP cc_start: 0.7675 (t70) cc_final: 0.7407 (t70) REVERT: C 30 MET cc_start: 0.8773 (tmm) cc_final: 0.8458 (tmm) REVERT: C 40 MET cc_start: 0.7686 (tpp) cc_final: 0.7458 (tpp) REVERT: C 197 ILE cc_start: 0.8604 (mm) cc_final: 0.8227 (mm) REVERT: C 256 ASP cc_start: 0.7686 (t70) cc_final: 0.7417 (t70) REVERT: D 30 MET cc_start: 0.8774 (tmm) cc_final: 0.8460 (tmm) REVERT: D 40 MET cc_start: 0.7691 (tpp) cc_final: 0.7455 (tpp) REVERT: D 197 ILE cc_start: 0.8601 (mm) cc_final: 0.8223 (mm) REVERT: D 256 ASP cc_start: 0.7675 (t70) cc_final: 0.7406 (t70) REVERT: E 30 MET cc_start: 0.8764 (tmm) cc_final: 0.8426 (tmm) REVERT: E 40 MET cc_start: 0.7693 (tpp) cc_final: 0.7459 (tpp) REVERT: E 197 ILE cc_start: 0.8601 (mm) cc_final: 0.8223 (mm) REVERT: E 256 ASP cc_start: 0.7674 (t70) cc_final: 0.7410 (t70) REVERT: F 30 MET cc_start: 0.8774 (tmm) cc_final: 0.8460 (tmm) REVERT: F 40 MET cc_start: 0.7695 (tpp) cc_final: 0.7463 (tpp) REVERT: F 197 ILE cc_start: 0.8599 (mm) cc_final: 0.8212 (mm) REVERT: F 256 ASP cc_start: 0.7666 (t70) cc_final: 0.7399 (t70) REVERT: G 30 MET cc_start: 0.8773 (tmm) cc_final: 0.8458 (tmm) REVERT: G 40 MET cc_start: 0.7686 (tpp) cc_final: 0.7457 (tpp) REVERT: G 197 ILE cc_start: 0.8601 (mm) cc_final: 0.8224 (mm) REVERT: G 256 ASP cc_start: 0.7697 (t70) cc_final: 0.7426 (t70) outliers start: 63 outliers final: 51 residues processed: 333 average time/residue: 0.3794 time to fit residues: 182.5552 Evaluate side-chains 321 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 270 time to evaluate : 2.389 ------------------------------------------------------------------------------- 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 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 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 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 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 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 101 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 20792 Z= 0.350 Angle : 0.539 5.494 28072 Z= 0.277 Chirality : 0.042 0.121 3136 Planarity : 0.003 0.034 3552 Dihedral : 4.262 15.623 2680 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.70 % Allowed : 16.24 % Favored : 80.06 % 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: -1.76 (0.16), residues: 2488 helix: 0.18 (0.17), residues: 1056 sheet: -0.90 (0.28), residues: 264 loop : -2.59 (0.15), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 167 HIS 0.002 0.001 HIS G 237 PHE 0.017 0.002 PHE C 77 TYR 0.008 0.002 TYR C 9 ARG 0.007 0.001 ARG G 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 344 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 260 time to evaluate : 2.560 Fit side-chains REVERT: U 40 MET cc_start: 0.7727 (tpp) cc_final: 0.7435 (tpp) REVERT: U 240 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7531 (ttm-80) REVERT: A 40 MET cc_start: 0.7724 (tpp) cc_final: 0.7430 (tpp) REVERT: A 240 ARG cc_start: 0.7803 (ttm170) cc_final: 0.7526 (ttm-80) REVERT: B 40 MET cc_start: 0.7722 (tpp) cc_final: 0.7432 (tpp) REVERT: B 240 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7523 (ttm-80) REVERT: C 40 MET cc_start: 0.7728 (tpp) cc_final: 0.7439 (tpp) REVERT: C 240 ARG cc_start: 0.7800 (ttm170) cc_final: 0.7526 (ttm-80) REVERT: D 40 MET cc_start: 0.7724 (tpp) cc_final: 0.7433 (tpp) REVERT: D 240 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7529 (ttm-80) REVERT: E 40 MET cc_start: 0.7729 (tpp) cc_final: 0.7437 (tpp) REVERT: E 240 ARG cc_start: 0.7803 (ttm170) cc_final: 0.7528 (ttm-80) REVERT: F 40 MET cc_start: 0.7723 (tpp) cc_final: 0.7429 (tpp) REVERT: F 240 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7529 (ttm-80) REVERT: G 40 MET cc_start: 0.7724 (tpp) cc_final: 0.7436 (tpp) REVERT: G 240 ARG cc_start: 0.7792 (ttm170) cc_final: 0.7515 (ttm-80) outliers start: 84 outliers final: 72 residues processed: 308 average time/residue: 0.3547 time to fit residues: 162.4841 Evaluate side-chains 319 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 247 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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 305 THR Chi-restraints excluded: chain U residue 310 ASP 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 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 305 THR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 20 ILE 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 101 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 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 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 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 20 ILE 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 305 THR Chi-restraints excluded: chain G residue 310 ASP 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: 0.9990 chunk 136 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 110 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 255 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20792 Z= 0.123 Angle : 0.423 5.387 28072 Z= 0.226 Chirality : 0.039 0.123 3136 Planarity : 0.003 0.028 3552 Dihedral : 3.757 12.921 2680 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.52 % Allowed : 15.89 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2488 helix: 0.70 (0.17), residues: 1056 sheet: -0.78 (0.27), residues: 264 loop : -2.42 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 167 HIS 0.004 0.001 HIS D 127 PHE 0.006 0.001 PHE F 19 TYR 0.005 0.001 TYR G 226 ARG 0.005 0.001 ARG A 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 361 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 281 time to evaluate : 2.371 Fit side-chains REVERT: U 40 MET cc_start: 0.7733 (tpp) cc_final: 0.7461 (tpp) REVERT: U 197 ILE cc_start: 0.8581 (mm) cc_final: 0.8195 (mm) REVERT: U 240 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7434 (ttm-80) REVERT: U 256 ASP cc_start: 0.7708 (t70) cc_final: 0.7460 (t70) REVERT: A 40 MET cc_start: 0.7702 (tpp) cc_final: 0.7429 (tpp) REVERT: A 197 ILE cc_start: 0.8554 (mm) cc_final: 0.8178 (mm) REVERT: A 240 ARG cc_start: 0.7666 (ttm170) cc_final: 0.7429 (ttm-80) REVERT: A 256 ASP cc_start: 0.7706 (t70) cc_final: 0.7460 (t70) REVERT: B 40 MET cc_start: 0.7722 (tpp) cc_final: 0.7452 (tpp) REVERT: B 197 ILE cc_start: 0.8554 (mm) cc_final: 0.8177 (mm) REVERT: B 240 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7431 (ttm-80) REVERT: B 256 ASP cc_start: 0.7706 (t70) cc_final: 0.7457 (t70) REVERT: C 40 MET cc_start: 0.7703 (tpp) cc_final: 0.7431 (tpp) REVERT: C 197 ILE cc_start: 0.8558 (mm) cc_final: 0.8180 (mm) REVERT: C 240 ARG cc_start: 0.7667 (ttm170) cc_final: 0.7431 (ttm-80) REVERT: C 256 ASP cc_start: 0.7706 (t70) cc_final: 0.7457 (t70) REVERT: D 40 MET cc_start: 0.7720 (tpp) cc_final: 0.7461 (tpp) REVERT: D 197 ILE cc_start: 0.8581 (mm) cc_final: 0.8193 (mm) REVERT: D 240 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7432 (ttm-80) REVERT: D 256 ASP cc_start: 0.7704 (t70) cc_final: 0.7459 (t70) REVERT: E 40 MET cc_start: 0.7734 (tpp) cc_final: 0.7459 (tpp) REVERT: E 197 ILE cc_start: 0.8554 (mm) cc_final: 0.8176 (mm) REVERT: E 240 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7432 (ttm-80) REVERT: E 256 ASP cc_start: 0.7708 (t70) cc_final: 0.7462 (t70) REVERT: F 40 MET cc_start: 0.7729 (tpp) cc_final: 0.7449 (tpp) REVERT: F 197 ILE cc_start: 0.8581 (mm) cc_final: 0.8187 (mm) REVERT: F 240 ARG cc_start: 0.7670 (ttm170) cc_final: 0.7433 (ttm-80) REVERT: F 256 ASP cc_start: 0.7703 (t70) cc_final: 0.7457 (t70) REVERT: G 40 MET cc_start: 0.7701 (tpp) cc_final: 0.7432 (tpp) REVERT: G 197 ILE cc_start: 0.8580 (mm) cc_final: 0.8192 (mm) REVERT: G 240 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7422 (ttm-80) REVERT: G 256 ASP cc_start: 0.7727 (t70) cc_final: 0.7476 (t70) outliers start: 80 outliers final: 68 residues processed: 333 average time/residue: 0.3569 time to fit residues: 176.3562 Evaluate side-chains 334 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 266 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 91 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 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 D residue 305 THR 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 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 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 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 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: 6.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 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 255 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 20792 Z= 0.370 Angle : 0.545 5.619 28072 Z= 0.280 Chirality : 0.043 0.120 3136 Planarity : 0.003 0.033 3552 Dihedral : 4.274 15.613 2680 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.74 % Allowed : 15.54 % Favored : 80.72 % 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: -1.57 (0.16), residues: 2488 helix: 0.29 (0.17), residues: 1056 sheet: -0.76 (0.29), residues: 264 loop : -2.45 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 167 HIS 0.003 0.001 HIS U 127 PHE 0.018 0.002 PHE G 77 TYR 0.008 0.002 TYR G 226 ARG 0.004 0.001 ARG B 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 366 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 281 time to evaluate : 2.499 Fit side-chains REVERT: U 40 MET cc_start: 0.7744 (tpp) cc_final: 0.7458 (tpp) REVERT: A 40 MET cc_start: 0.7738 (tpp) cc_final: 0.7451 (tpp) REVERT: B 40 MET cc_start: 0.7736 (tpp) cc_final: 0.7451 (tpp) REVERT: C 40 MET cc_start: 0.7740 (tpp) cc_final: 0.7457 (tpp) REVERT: C 256 ASP cc_start: 0.7748 (t70) cc_final: 0.7499 (t70) REVERT: D 40 MET cc_start: 0.7742 (tpp) cc_final: 0.7459 (tpp) REVERT: E 40 MET cc_start: 0.7763 (tpp) cc_final: 0.7484 (tpp) REVERT: F 40 MET cc_start: 0.7745 (tpp) cc_final: 0.7451 (tpp) REVERT: G 40 MET cc_start: 0.7743 (tpp) cc_final: 0.7460 (tpp) outliers start: 85 outliers final: 77 residues processed: 333 average time/residue: 0.3644 time to fit residues: 178.3973 Evaluate side-chains 341 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 264 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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 U residue 305 THR Chi-restraints excluded: chain U residue 310 ASP Chi-restraints excluded: chain A residue 20 ILE 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 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 310 ASP Chi-restraints excluded: chain B residue 20 ILE 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 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 310 ASP Chi-restraints excluded: chain C residue 20 ILE 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 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 20 ILE 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 98 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 D residue 305 THR Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain E residue 20 ILE 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 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 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 F residue 305 THR Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 20 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 222 optimal weight: 0.2980 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 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 127 HIS U 248 ASN U 255 ASN A 127 HIS A 248 ASN A 255 ASN B 127 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN 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 127 HIS ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 ASN F 127 HIS F 248 ASN F 255 ASN G 127 HIS G 255 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2371 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= 0.131 Angle : 0.426 5.357 28072 Z= 0.226 Chirality : 0.039 0.123 3136 Planarity : 0.003 0.028 3552 Dihedral : 3.746 12.966 2680 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.74 % Allowed : 15.45 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2488 helix: 0.79 (0.17), residues: 1056 sheet: -1.08 (0.28), residues: 280 loop : -2.28 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 167 HIS 0.004 0.001 HIS D 127 PHE 0.007 0.001 PHE G 216 TYR 0.006 0.001 TYR G 226 ARG 0.003 0.000 ARG D 227 *********************** 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 358 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 273 time to evaluate : 2.564 Fit side-chains REVERT: U 40 MET cc_start: 0.7707 (tpp) cc_final: 0.7399 (tpp) REVERT: A 40 MET cc_start: 0.7701 (tpp) cc_final: 0.7393 (tpp) REVERT: B 40 MET cc_start: 0.7700 (tpp) cc_final: 0.7395 (tpp) REVERT: C 40 MET cc_start: 0.7701 (tpp) cc_final: 0.7394 (tpp) REVERT: D 40 MET cc_start: 0.7698 (tpp) cc_final: 0.7399 (tpp) REVERT: E 40 MET cc_start: 0.7693 (tpp) cc_final: 0.7387 (tpp) REVERT: F 40 MET cc_start: 0.7718 (tpp) cc_final: 0.7447 (tpp) REVERT: G 40 MET cc_start: 0.7703 (tpp) cc_final: 0.7397 (tpp) outliers start: 85 outliers final: 74 residues processed: 338 average time/residue: 0.3487 time to fit residues: 174.4056 Evaluate side-chains 338 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 264 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 101 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 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 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 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 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 310 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.4980 chunk 143 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 255 ASN A 95 GLN A 127 HIS B 95 GLN B 127 HIS B 248 ASN B 255 ASN C 95 GLN C 127 HIS C 248 ASN D 95 GLN D 127 HIS D 248 ASN E 95 GLN E 127 HIS E 248 ASN F 95 GLN F 127 HIS F 255 ASN G 95 GLN G 127 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2457 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= 0.130 Angle : 0.421 5.446 28072 Z= 0.223 Chirality : 0.039 0.124 3136 Planarity : 0.003 0.028 3552 Dihedral : 3.624 12.386 2680 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.60 % Allowed : 16.99 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2488 helix: 1.08 (0.17), residues: 1056 sheet: -0.96 (0.28), residues: 280 loop : -2.14 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 167 HIS 0.003 0.001 HIS A 225 PHE 0.007 0.001 PHE G 77 TYR 0.005 0.001 TYR G 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 335 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 276 time to evaluate : 2.447 Fit side-chains REVERT: U 40 MET cc_start: 0.7676 (tpp) cc_final: 0.7389 (tpp) REVERT: U 197 ILE cc_start: 0.8617 (mm) cc_final: 0.8281 (mm) REVERT: U 240 ARG cc_start: 0.7579 (ttm170) cc_final: 0.7318 (ttm-80) REVERT: A 40 MET cc_start: 0.7673 (tpp) cc_final: 0.7386 (tpp) REVERT: A 197 ILE cc_start: 0.8617 (mm) cc_final: 0.8280 (mm) REVERT: A 240 ARG cc_start: 0.7575 (ttm170) cc_final: 0.7315 (ttm-80) REVERT: B 40 MET cc_start: 0.7669 (tpp) cc_final: 0.7386 (tpp) REVERT: B 197 ILE cc_start: 0.8617 (mm) cc_final: 0.8280 (mm) REVERT: B 240 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7316 (ttm-80) REVERT: C 40 MET cc_start: 0.7671 (tpp) cc_final: 0.7388 (tpp) REVERT: C 197 ILE cc_start: 0.8623 (mm) cc_final: 0.8360 (mm) REVERT: C 240 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7316 (ttm-80) REVERT: D 40 MET cc_start: 0.7673 (tpp) cc_final: 0.7388 (tpp) REVERT: D 197 ILE cc_start: 0.8617 (mm) cc_final: 0.8281 (mm) REVERT: D 240 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7317 (ttm-80) REVERT: E 40 MET cc_start: 0.7739 (tpp) cc_final: 0.7457 (tpp) REVERT: E 197 ILE cc_start: 0.8618 (mm) cc_final: 0.8280 (mm) REVERT: E 240 ARG cc_start: 0.7577 (ttm170) cc_final: 0.7318 (ttm-80) REVERT: F 40 MET cc_start: 0.7768 (tpp) cc_final: 0.7473 (tpp) REVERT: F 197 ILE cc_start: 0.8619 (mm) cc_final: 0.8282 (mm) REVERT: F 240 ARG cc_start: 0.7577 (ttm170) cc_final: 0.7318 (ttm-80) REVERT: G 40 MET cc_start: 0.7673 (tpp) cc_final: 0.7390 (tpp) REVERT: G 197 ILE cc_start: 0.8619 (mm) cc_final: 0.8283 (mm) REVERT: G 240 ARG cc_start: 0.7567 (ttm170) cc_final: 0.7304 (ttm-80) outliers start: 59 outliers final: 56 residues processed: 319 average time/residue: 0.3664 time to fit residues: 171.6330 Evaluate side-chains 312 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 256 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 THR 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 310 ASP Chi-restraints excluded: chain A residue 74 THR 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 310 ASP Chi-restraints excluded: chain B residue 74 THR 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 310 ASP Chi-restraints excluded: chain C residue 74 THR 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 93 VAL Chi-restraints excluded: chain D residue 98 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 D residue 310 ASP Chi-restraints excluded: chain E residue 74 THR 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 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 F residue 310 ASP Chi-restraints excluded: chain G residue 74 THR 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 310 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 0.0970 chunk 173 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 A 95 GLN A 127 HIS B 95 GLN B 127 HIS C 95 GLN C 127 HIS D 95 GLN D 127 HIS E 95 GLN E 127 HIS F 95 GLN F 127 HIS G 95 GLN G 127 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127395 restraints weight = 22938.856| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.11 r_work: 0.3017 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20792 Z= 0.156 Angle : 0.425 5.263 28072 Z= 0.225 Chirality : 0.039 0.122 3136 Planarity : 0.003 0.028 3552 Dihedral : 3.662 12.392 2680 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.30 % Allowed : 15.80 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.78 (0.17), residues: 2488 helix: 1.17 (0.17), residues: 1056 sheet: -0.97 (0.27), residues: 280 loop : -2.11 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 167 HIS 0.004 0.001 HIS U 225 PHE 0.008 0.001 PHE F 77 TYR 0.006 0.001 TYR G 226 ARG 0.004 0.000 ARG G 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4177.51 seconds wall clock time: 75 minutes 28.46 seconds (4528.46 seconds total)