Starting phenix.real_space_refine on Mon Mar 25 02:25:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trg_41579/03_2024/8trg_41579_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trg_41579/03_2024/8trg_41579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trg_41579/03_2024/8trg_41579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trg_41579/03_2024/8trg_41579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trg_41579/03_2024/8trg_41579_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trg_41579/03_2024/8trg_41579_trim_updated.pdb" } resolution = 2.93 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= 0.002 sd= 0.030 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: 7 Type Number sf(0) Gaussians P 50 5.49 5 Mg 8 5.21 5 S 111 5.16 5 C 14198 2.51 5 N 3989 2.21 5 O 4510 1.98 5 H 22935 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 233": "OE1" <-> "OE2" Residue "I PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J GLU 189": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45801 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "C" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "D" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "E" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "F" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "G" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "H" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "I" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2916 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain breaks: 1 Chain: "J" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 881 Classifications: {'DNA': 27} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.18, per 1000 atoms: 0.44 Number of scatterers: 45801 At special positions: 0 Unit cell: (144.9, 131.1, 208.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 111 16.00 P 50 15.00 Mg 8 11.99 O 4510 8.00 N 3989 7.00 C 14198 6.00 H 22935 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.73 Conformation dependent library (CDL) restraints added in 4.6 seconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5226 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 33 sheets defined 36.8% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.570A pdb=" N SER A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 166 through 185 removed outlier: 4.722A pdb=" N GLY A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.592A pdb=" N TYR A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 218' Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 313 through 326 removed outlier: 4.078A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 21 removed outlier: 3.680A pdb=" N ALA B 9 " --> pdb=" O ASN B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 45 through 51 Processing helix chain 'B' and resid 72 through 86 removed outlier: 4.032A pdb=" N GLU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.747A pdb=" N ARG B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 184 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 270 through 280 removed outlier: 3.546A pdb=" N ASP B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 326 removed outlier: 3.560A pdb=" N LYS B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 21 Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 72 through 86 removed outlier: 3.792A pdb=" N ARG C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 152 through 155 No H-bonds generated for 'chain 'C' and resid 152 through 155' Processing helix chain 'C' and resid 166 through 185 removed outlier: 3.640A pdb=" N ARG C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 270 through 280 removed outlier: 4.008A pdb=" N VAL C 275 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 313 through 326 removed outlier: 3.605A pdb=" N LYS C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 21 removed outlier: 3.640A pdb=" N LYS D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 45 through 51 Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.564A pdb=" N ALA D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 152 through 155 No H-bonds generated for 'chain 'D' and resid 152 through 155' Processing helix chain 'D' and resid 166 through 185 removed outlier: 5.108A pdb=" N GLY D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.508A pdb=" N VAL D 275 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 Processing helix chain 'D' and resid 313 through 326 removed outlier: 3.505A pdb=" N LYS D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 326 " --> pdb=" O LYS D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 21 removed outlier: 3.605A pdb=" N ALA E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 72 through 86 removed outlier: 4.039A pdb=" N GLU E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 166 through 185 removed outlier: 5.324A pdb=" N GLY E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 302 through 310 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'F' and resid 4 through 21 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.618A pdb=" N ARG F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 122 through 135 removed outlier: 3.564A pdb=" N CYS F 129 " --> pdb=" O ALA F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 166 through 185 removed outlier: 4.937A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 270 through 281 Processing helix chain 'F' and resid 301 through 311 removed outlier: 3.603A pdb=" N ASP F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 326 removed outlier: 3.624A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 45 through 50 Processing helix chain 'G' and resid 72 through 86 removed outlier: 3.981A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 107 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 166 through 185 removed outlier: 5.169A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS G 183 " --> pdb=" O ALA G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 218 removed outlier: 3.571A pdb=" N TYR G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 214 through 218' Processing helix chain 'G' and resid 270 through 280 removed outlier: 3.744A pdb=" N VAL G 279 " --> pdb=" O VAL G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 313 through 326 Processing helix chain 'H' and resid 4 through 21 removed outlier: 4.080A pdb=" N ALA H 11 " --> pdb=" O GLN H 7 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA H 12 " --> pdb=" O LYS H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 45 through 50 Processing helix chain 'H' and resid 72 through 86 removed outlier: 3.752A pdb=" N THR H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 122 through 135 removed outlier: 4.296A pdb=" N GLU H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 152 through 156 Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 181 through 185 Processing helix chain 'H' and resid 214 through 218 Processing helix chain 'H' and resid 270 through 281 removed outlier: 3.692A pdb=" N ASP H 276 " --> pdb=" O GLY H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 313 through 326 Processing helix chain 'I' and resid 9 through 22 removed outlier: 3.735A pdb=" N SER I 20 " --> pdb=" O ARG I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 35 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.671A pdb=" N HIS I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 104 No H-bonds generated for 'chain 'I' and resid 102 through 104' Processing helix chain 'J' and resid 91 through 93 No H-bonds generated for 'chain 'J' and resid 91 through 93' Processing helix chain 'J' and resid 102 through 104 No H-bonds generated for 'chain 'J' and resid 102 through 104' Processing helix chain 'J' and resid 118 through 120 No H-bonds generated for 'chain 'J' and resid 118 through 120' Processing sheet with id= A, first strand: chain 'A' and resid 221 through 224 removed outlier: 3.969A pdb=" N VAL A 221 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 189 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE A 64 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE A 191 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 93 removed outlier: 6.593A pdb=" N LEU A 115 " --> pdb=" O PHE A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.632A pdb=" N ARG A 243 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG A 227 " --> pdb=" O ARG A 243 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.010A pdb=" N TYR A 293 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LYS A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 257 through 263 removed outlier: 6.667A pdb=" N ARG B 222 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 221 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 189 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE B 64 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE B 191 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLY B 66 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 195 through 197 Processing sheet with id= G, first strand: chain 'B' and resid 285 through 287 removed outlier: 3.659A pdb=" N GLY B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 257 through 263 removed outlier: 6.298A pdb=" N ARG C 222 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 221 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 189 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE C 64 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE C 191 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N GLY C 66 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 91 through 93 removed outlier: 6.107A pdb=" N LEU C 115 " --> pdb=" O PHE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 285 through 287 removed outlier: 3.806A pdb=" N GLY C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 257 through 263 removed outlier: 6.283A pdb=" N ARG D 222 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 221 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 189 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 64 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE D 191 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLY D 66 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN D 193 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU D 115 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 285 through 287 Processing sheet with id= M, first strand: chain 'D' and resid 230 through 232 removed outlier: 3.502A pdb=" N GLY D 239 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 257 through 263 removed outlier: 3.516A pdb=" N PHE E 260 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG E 222 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 221 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU E 189 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 64 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE E 191 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU E 115 " --> pdb=" O PHE E 92 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 195 through 197 Processing sheet with id= P, first strand: chain 'E' and resid 285 through 287 removed outlier: 3.564A pdb=" N GLY E 299 " --> pdb=" O TYR E 291 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR E 293 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS E 297 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 229 through 232 removed outlier: 4.038A pdb=" N GLY E 229 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 231 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 257 through 263 removed outlier: 3.604A pdb=" N PHE F 260 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU F 189 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE F 64 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE F 191 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N GLY F 66 " --> pdb=" O PHE F 191 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 91 through 93 removed outlier: 6.360A pdb=" N LEU F 115 " --> pdb=" O PHE F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 195 through 197 Processing sheet with id= U, first strand: chain 'F' and resid 285 through 287 removed outlier: 4.007A pdb=" N GLY F 299 " --> pdb=" O TYR F 291 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N TYR F 293 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYS F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 229 through 233 removed outlier: 3.960A pdb=" N GLY F 229 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY F 239 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 257 through 263 removed outlier: 6.454A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL G 221 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU G 189 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE G 64 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE G 191 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU G 115 " --> pdb=" O PHE G 92 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 285 through 287 removed outlier: 3.504A pdb=" N GLY G 299 " --> pdb=" O TYR G 291 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR G 293 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS G 297 " --> pdb=" O TYR G 293 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 229 through 233 removed outlier: 3.606A pdb=" N GLY G 239 " --> pdb=" O VAL G 231 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU G 233 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 257 through 263 removed outlier: 3.795A pdb=" N PHE H 260 " --> pdb=" O THR H 242 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG H 222 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE H 61 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N LEU H 223 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU H 63 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE H 225 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR H 65 " --> pdb=" O ILE H 225 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N ARG H 227 " --> pdb=" O TYR H 65 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU H 189 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE H 64 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE H 191 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N GLY H 66 " --> pdb=" O PHE H 191 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 195 through 197 Processing sheet with id= AB, first strand: chain 'H' and resid 230 through 233 removed outlier: 6.527A pdb=" N GLU H 233 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 291 through 293 removed outlier: 6.521A pdb=" N TYR H 293 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS H 297 " --> pdb=" O TYR H 293 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 96 through 98 removed outlier: 3.971A pdb=" N GLY I 96 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ARG I 114 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG I 81 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER I 116 " --> pdb=" O ARG I 81 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA I 83 " --> pdb=" O SER I 116 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE I 111 " --> pdb=" O VAL I 133 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY I 194 " --> pdb=" O ALA I 132 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS I 134 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ALA I 192 " --> pdb=" O HIS I 134 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL I 146 " --> pdb=" O GLU I 189 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU I 191 " --> pdb=" O VAL I 144 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL I 144 " --> pdb=" O LEU I 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG I 157 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.602A pdb=" N GLY I 65 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL I 59 " --> pdb=" O SER I 63 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER I 63 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 130 through 132 removed outlier: 3.849A pdb=" N GLY J 194 " --> pdb=" O ALA J 132 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 165 through 168 removed outlier: 3.858A pdb=" N GLY J 190 " --> pdb=" O VAL J 146 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG J 148 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE J 188 " --> pdb=" O ARG J 148 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2448 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: 17.67 Time building geometry restraints manager: 36.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 7612 1.06 - 1.27: 19252 1.27 - 1.47: 8564 1.47 - 1.67: 10510 1.67 - 1.88: 200 Bond restraints: 46138 Sorted by residual: bond pdb=" C3' AGS A 401 " pdb=" C4' AGS A 401 " ideal model delta sigma weight residual 1.526 1.324 0.202 1.10e-02 8.26e+03 3.37e+02 bond pdb=" C3' AGS F 401 " pdb=" C4' AGS F 401 " ideal model delta sigma weight residual 1.526 1.330 0.196 1.10e-02 8.26e+03 3.17e+02 bond pdb=" C3' AGS C 401 " pdb=" C4' AGS C 401 " ideal model delta sigma weight residual 1.526 1.331 0.195 1.10e-02 8.26e+03 3.16e+02 bond pdb=" C3' AGS E 401 " pdb=" C4' AGS E 401 " ideal model delta sigma weight residual 1.526 1.331 0.195 1.10e-02 8.26e+03 3.13e+02 bond pdb=" C3' AGS G 401 " pdb=" C4' AGS G 401 " ideal model delta sigma weight residual 1.526 1.335 0.191 1.10e-02 8.26e+03 3.02e+02 ... (remaining 46133 not shown) Histogram of bond angle deviations from ideal: 95.92 - 103.73: 340 103.73 - 111.53: 53308 111.53 - 119.34: 13027 119.34 - 127.14: 16889 127.14 - 134.94: 239 Bond angle restraints: 83803 Sorted by residual: angle pdb=" C5 AGS E 401 " pdb=" C4 AGS E 401 " pdb=" N3 AGS E 401 " ideal model delta sigma weight residual 126.80 118.35 8.45 7.41e-01 1.82e+00 1.30e+02 angle pdb=" C5 AGS D 401 " pdb=" C4 AGS D 401 " pdb=" N3 AGS D 401 " ideal model delta sigma weight residual 126.80 118.36 8.44 7.41e-01 1.82e+00 1.30e+02 angle pdb=" C5 AGS G 401 " pdb=" N7 AGS G 401 " pdb=" C8 AGS G 401 " ideal model delta sigma weight residual 103.67 108.36 -4.69 4.26e-01 5.51e+00 1.21e+02 angle pdb=" C5 AGS B 401 " pdb=" C4 AGS B 401 " pdb=" N3 AGS B 401 " ideal model delta sigma weight residual 126.80 118.88 7.92 7.41e-01 1.82e+00 1.14e+02 angle pdb=" C5 AGS C 401 " pdb=" C4 AGS C 401 " pdb=" N3 AGS C 401 " ideal model delta sigma weight residual 126.80 118.92 7.88 7.41e-01 1.82e+00 1.13e+02 ... (remaining 83798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 20169 34.72 - 69.44: 924 69.44 - 104.16: 42 104.16 - 138.88: 3 138.88 - 173.60: 6 Dihedral angle restraints: 21144 sinusoidal: 12180 harmonic: 8964 Sorted by residual: dihedral pdb=" CA LYS I 106 " pdb=" C LYS I 106 " pdb=" N PRO I 107 " pdb=" CA PRO I 107 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" O1A AGS E 401 " pdb=" O3A AGS E 401 " pdb=" PA AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sinusoidal sigma weight residual 292.27 118.67 173.60 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS H 401 " pdb=" O3B AGS H 401 " pdb=" PB AGS H 401 " pdb=" PG AGS H 401 " ideal model delta sinusoidal sigma weight residual 68.91 -99.84 168.75 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 21141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3437 0.110 - 0.221: 135 0.221 - 0.331: 18 0.331 - 0.441: 0 0.441 - 0.552: 1 Chirality restraints: 3591 Sorted by residual: chirality pdb=" PB AGS G 401 " pdb=" O2B AGS G 401 " pdb=" O3A AGS G 401 " pdb=" O3B AGS G 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.63 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C3' AGS F 401 " pdb=" C2' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" O3' AGS F 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 3588 not shown) Planarity restraints: 6782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 134 " 0.276 9.50e-02 1.11e+02 9.38e-02 1.62e+01 pdb=" NE ARG G 134 " 0.000 2.00e-02 2.50e+03 pdb=" CZ ARG G 134 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG G 134 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 134 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG G 134 " -0.035 2.00e-02 2.50e+03 pdb="HH12 ARG G 134 " 0.014 2.00e-02 2.50e+03 pdb="HH21 ARG G 134 " -0.030 2.00e-02 2.50e+03 pdb="HH22 ARG G 134 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 106 " -0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO I 107 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO I 107 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO I 107 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 105 " -0.240 9.50e-02 1.11e+02 8.10e-02 1.03e+01 pdb=" NE ARG C 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG C 105 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 105 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 105 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 105 " 0.025 2.00e-02 2.50e+03 pdb="HH12 ARG C 105 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG C 105 " 0.021 2.00e-02 2.50e+03 pdb="HH22 ARG C 105 " -0.011 2.00e-02 2.50e+03 ... (remaining 6779 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 551 1.95 - 2.61: 53073 2.61 - 3.28: 132384 3.28 - 3.94: 167585 3.94 - 4.60: 263223 Nonbonded interactions: 616816 Sorted by model distance: nonbonded pdb=" OE2 GLU E 18 " pdb=" HZ3 LYS E 23 " model vdw 1.291 1.850 nonbonded pdb=" HB2 LYS A 19 " pdb=" HZ3 LYS A 19 " model vdw 1.320 2.270 nonbonded pdb=" HB2 LYS F 245 " pdb=" HZ3 LYS F 245 " model vdw 1.354 2.270 nonbonded pdb=" HB3 LYS F 317 " pdb=" HZ2 LYS F 317 " model vdw 1.363 2.270 nonbonded pdb=" HB3 LYS H 106 " pdb=" HZ2 LYS H 106 " model vdw 1.380 2.270 ... (remaining 616811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.950 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: 0.710 Extract box with map and model: 5.900 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 138.410 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.290 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:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.009 0.202 23203 Z= 0.611 Angle : 0.846 10.986 31402 Z= 0.581 Chirality : 0.051 0.552 3591 Planarity : 0.006 0.109 3940 Dihedral : 17.979 173.599 8884 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.78 % Allowed : 20.20 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2892 helix: 0.77 (0.16), residues: 1094 sheet: 0.02 (0.23), residues: 487 loop : -1.45 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 308 HIS 0.007 0.002 HIS B 97 PHE 0.014 0.002 PHE E 217 TYR 0.012 0.002 TYR G 218 ARG 0.018 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 606 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7581 (mm-30) REVERT: D 68 GLU cc_start: 0.7893 (pm20) cc_final: 0.7508 (pm20) REVERT: H 63 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: H 113 ASN cc_start: 0.7997 (p0) cc_final: 0.7747 (p0) REVERT: H 123 GLU cc_start: 0.5165 (mm-30) cc_final: 0.4756 (mm-30) REVERT: H 233 GLU cc_start: 0.7915 (pp20) cc_final: 0.7712 (pp20) REVERT: I 108 ASN cc_start: 0.7860 (m-40) cc_final: 0.7599 (m-40) REVERT: I 110 ASP cc_start: 0.8066 (m-30) cc_final: 0.7777 (m-30) REVERT: I 171 ASN cc_start: 0.8275 (t0) cc_final: 0.7914 (t0) outliers start: 18 outliers final: 13 residues processed: 618 average time/residue: 2.9614 time to fit residues: 2084.6513 Evaluate side-chains 582 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 568 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 261 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN C 97 HIS E 84 GLN F 257 GLN H 181 ASN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23203 Z= 0.223 Angle : 0.606 6.843 31402 Z= 0.322 Chirality : 0.043 0.165 3591 Planarity : 0.005 0.085 3940 Dihedral : 14.643 172.907 3542 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.00 % Allowed : 19.33 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2892 helix: 1.13 (0.16), residues: 1102 sheet: 0.26 (0.23), residues: 502 loop : -1.41 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 308 HIS 0.005 0.001 HIS G 97 PHE 0.014 0.001 PHE C 260 TYR 0.011 0.001 TYR D 65 ARG 0.010 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 591 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6026 (mt-10) cc_final: 0.3702 (tt0) REVERT: A 127 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 202 MET cc_start: 0.7238 (mmm) cc_final: 0.7023 (tmm) REVERT: A 283 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7929 (tt) REVERT: B 159 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8340 (tt) REVERT: D 16 GLN cc_start: 0.7923 (tp40) cc_final: 0.7538 (tm-30) REVERT: D 68 GLU cc_start: 0.7867 (pm20) cc_final: 0.7481 (pm20) REVERT: F 154 GLU cc_start: 0.8500 (tt0) cc_final: 0.8279 (tt0) REVERT: F 202 MET cc_start: 0.6481 (mmt) cc_final: 0.6099 (mmt) REVERT: G 16 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7750 (tp-100) REVERT: G 199 ILE cc_start: 0.7963 (tp) cc_final: 0.7697 (tt) REVERT: G 241 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7198 (mm-30) REVERT: H 63 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: H 123 GLU cc_start: 0.5002 (mm-30) cc_final: 0.4504 (mm-30) REVERT: H 155 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8452 (tt) REVERT: H 213 ASN cc_start: 0.8523 (m110) cc_final: 0.8277 (m110) REVERT: H 233 GLU cc_start: 0.7914 (pp20) cc_final: 0.7638 (pp20) REVERT: I 110 ASP cc_start: 0.8032 (m-30) cc_final: 0.7729 (m-30) REVERT: I 125 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8499 (mt) REVERT: I 151 ASP cc_start: 0.7238 (t0) cc_final: 0.6823 (t0) REVERT: I 171 ASN cc_start: 0.8238 (t0) cc_final: 0.7897 (t0) outliers start: 46 outliers final: 21 residues processed: 608 average time/residue: 2.9656 time to fit residues: 2052.1296 Evaluate side-chains 608 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 582 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 259 optimal weight: 50.0000 chunk 89 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN D 205 ASN G 213 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23203 Z= 0.292 Angle : 0.590 6.425 31402 Z= 0.316 Chirality : 0.044 0.161 3591 Planarity : 0.005 0.085 3940 Dihedral : 14.293 179.904 3527 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.61 % Allowed : 18.98 % Favored : 78.41 % 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: -0.17 (0.15), residues: 2892 helix: 1.19 (0.16), residues: 1101 sheet: 0.27 (0.23), residues: 502 loop : -1.46 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 290 HIS 0.006 0.001 HIS E 97 PHE 0.015 0.001 PHE G 270 TYR 0.013 0.001 TYR A 271 ARG 0.011 0.001 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 587 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6153 (mt-10) cc_final: 0.3756 (tt0) REVERT: A 127 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: A 202 MET cc_start: 0.7253 (mmm) cc_final: 0.7020 (tmm) REVERT: A 283 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7955 (tt) REVERT: B 159 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8357 (tt) REVERT: B 236 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8082 (m-40) REVERT: D 16 GLN cc_start: 0.7932 (tp40) cc_final: 0.7490 (tm-30) REVERT: D 68 GLU cc_start: 0.7882 (pm20) cc_final: 0.7488 (pm20) REVERT: D 243 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8301 (ttm170) REVERT: E 86 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7375 (mm-30) REVERT: F 154 GLU cc_start: 0.8501 (tt0) cc_final: 0.8240 (tt0) REVERT: F 202 MET cc_start: 0.6477 (mmt) cc_final: 0.6077 (mmt) REVERT: F 280 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7999 (ttmm) REVERT: G 16 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7779 (tp-100) REVERT: G 241 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7275 (mt-10) REVERT: H 63 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: H 123 GLU cc_start: 0.5093 (mm-30) cc_final: 0.4743 (mm-30) REVERT: H 213 ASN cc_start: 0.8583 (m110) cc_final: 0.8314 (m110) REVERT: H 233 GLU cc_start: 0.7939 (pp20) cc_final: 0.7677 (pp20) REVERT: I 110 ASP cc_start: 0.8038 (m-30) cc_final: 0.7724 (m-30) REVERT: I 125 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8487 (mt) REVERT: I 151 ASP cc_start: 0.7287 (t0) cc_final: 0.6835 (t0) REVERT: I 159 LYS cc_start: 0.8404 (tttt) cc_final: 0.8090 (tttt) REVERT: I 171 ASN cc_start: 0.8188 (t0) cc_final: 0.7902 (t0) REVERT: I 180 ASP cc_start: 0.7707 (t0) cc_final: 0.7346 (p0) outliers start: 60 outliers final: 37 residues processed: 610 average time/residue: 2.9815 time to fit residues: 2073.0394 Evaluate side-chains 614 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 569 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN F 300 GLN G 213 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 23203 Z= 0.433 Angle : 0.636 6.392 31402 Z= 0.341 Chirality : 0.046 0.166 3591 Planarity : 0.005 0.090 3940 Dihedral : 14.310 170.227 3527 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.17 % Allowed : 19.50 % Favored : 77.32 % 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: -0.46 (0.15), residues: 2892 helix: 0.94 (0.15), residues: 1101 sheet: 0.12 (0.23), residues: 502 loop : -1.60 (0.15), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 308 HIS 0.006 0.001 HIS E 97 PHE 0.014 0.002 PHE E 191 TYR 0.019 0.002 TYR A 103 ARG 0.013 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 568 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: A 202 MET cc_start: 0.7256 (mmm) cc_final: 0.7021 (tmm) REVERT: B 159 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8380 (tt) REVERT: B 236 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8159 (m-40) REVERT: D 16 GLN cc_start: 0.7980 (tp40) cc_final: 0.7539 (tm-30) REVERT: D 68 GLU cc_start: 0.7880 (pm20) cc_final: 0.7513 (pm20) REVERT: E 32 ASP cc_start: 0.8141 (t0) cc_final: 0.7858 (t0) REVERT: E 86 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7402 (mm-30) REVERT: E 321 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7261 (mmtt) REVERT: F 202 MET cc_start: 0.6487 (mmt) cc_final: 0.6086 (mmt) REVERT: F 280 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7985 (ttmm) REVERT: G 282 LYS cc_start: 0.8287 (mmtm) cc_final: 0.8032 (mmtm) REVERT: H 63 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: H 123 GLU cc_start: 0.5211 (mm-30) cc_final: 0.4899 (mm-30) REVERT: H 213 ASN cc_start: 0.8596 (m110) cc_final: 0.8319 (m110) REVERT: H 233 GLU cc_start: 0.7974 (pp20) cc_final: 0.7620 (pp20) REVERT: I 110 ASP cc_start: 0.8045 (m-30) cc_final: 0.7770 (m-30) REVERT: I 125 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8489 (mt) REVERT: I 151 ASP cc_start: 0.7326 (t0) cc_final: 0.6850 (t0) REVERT: I 159 LYS cc_start: 0.8411 (tttt) cc_final: 0.8052 (tttt) REVERT: I 180 ASP cc_start: 0.7696 (t0) cc_final: 0.7357 (p0) outliers start: 73 outliers final: 46 residues processed: 599 average time/residue: 2.9050 time to fit residues: 1982.8722 Evaluate side-chains 609 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 557 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 116 CYS Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN G 194 GLN G 213 ASN ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23203 Z= 0.205 Angle : 0.558 5.608 31402 Z= 0.298 Chirality : 0.042 0.163 3591 Planarity : 0.005 0.087 3940 Dihedral : 14.041 166.512 3527 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.56 % Allowed : 20.07 % Favored : 77.37 % 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: -0.12 (0.15), residues: 2892 helix: 1.29 (0.16), residues: 1101 sheet: 0.24 (0.23), residues: 502 loop : -1.46 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 308 HIS 0.004 0.001 HIS B 97 PHE 0.015 0.001 PHE G 270 TYR 0.012 0.001 TYR A 293 ARG 0.011 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 565 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6144 (mt-10) cc_final: 0.3912 (tt0) REVERT: A 202 MET cc_start: 0.7205 (mmm) cc_final: 0.6968 (tmm) REVERT: A 283 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7985 (tt) REVERT: B 159 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8350 (tt) REVERT: B 236 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8054 (m-40) REVERT: D 16 GLN cc_start: 0.7997 (tp40) cc_final: 0.7546 (tm-30) REVERT: D 68 GLU cc_start: 0.7873 (pm20) cc_final: 0.7461 (pm20) REVERT: E 32 ASP cc_start: 0.8074 (t0) cc_final: 0.7817 (t0) REVERT: E 86 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7261 (mm-30) REVERT: E 308 TRP cc_start: 0.7283 (t60) cc_final: 0.6976 (t60) REVERT: F 26 ILE cc_start: 0.8360 (mt) cc_final: 0.8150 (tt) REVERT: F 202 MET cc_start: 0.6470 (mmt) cc_final: 0.6070 (mmt) REVERT: F 280 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7963 (ttmm) REVERT: G 16 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7794 (tp-100) REVERT: G 282 LYS cc_start: 0.8287 (mmtm) cc_final: 0.8038 (mmtm) REVERT: H 63 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: H 123 GLU cc_start: 0.5118 (mm-30) cc_final: 0.4815 (mm-30) REVERT: H 213 ASN cc_start: 0.8562 (m110) cc_final: 0.8287 (m110) REVERT: H 233 GLU cc_start: 0.7982 (pp20) cc_final: 0.7582 (pp20) REVERT: I 110 ASP cc_start: 0.8028 (m-30) cc_final: 0.7723 (m-30) REVERT: I 125 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8465 (mt) REVERT: I 151 ASP cc_start: 0.7293 (t0) cc_final: 0.6815 (t0) REVERT: I 159 LYS cc_start: 0.8376 (tttt) cc_final: 0.8027 (tttt) REVERT: I 180 ASP cc_start: 0.7625 (t0) cc_final: 0.7370 (p0) outliers start: 59 outliers final: 39 residues processed: 587 average time/residue: 2.9374 time to fit residues: 1966.9946 Evaluate side-chains 593 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 548 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 231 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN E 205 ASN G 213 ASN I 198 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23203 Z= 0.197 Angle : 0.546 6.271 31402 Z= 0.290 Chirality : 0.042 0.158 3591 Planarity : 0.005 0.093 3940 Dihedral : 13.880 165.466 3527 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.43 % Allowed : 20.94 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 2892 helix: 1.50 (0.16), residues: 1102 sheet: 0.23 (0.22), residues: 516 loop : -1.37 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 290 HIS 0.004 0.001 HIS F 163 PHE 0.017 0.001 PHE C 270 TYR 0.011 0.001 TYR G 271 ARG 0.014 0.000 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 557 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6154 (mt-10) cc_final: 0.4096 (pm20) REVERT: A 202 MET cc_start: 0.7195 (mmm) cc_final: 0.6951 (tmm) REVERT: A 210 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8466 (p) REVERT: A 283 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7968 (tt) REVERT: B 159 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8163 (tt) REVERT: B 236 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8043 (m-40) REVERT: C 271 TYR cc_start: 0.7923 (m-80) cc_final: 0.7501 (m-80) REVERT: D 16 GLN cc_start: 0.7998 (tp40) cc_final: 0.7543 (tm-30) REVERT: D 68 GLU cc_start: 0.7867 (pm20) cc_final: 0.7455 (pm20) REVERT: D 105 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7740 (ttm110) REVERT: E 86 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7274 (mm-30) REVERT: E 308 TRP cc_start: 0.7285 (t60) cc_final: 0.6999 (t60) REVERT: E 321 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7416 (mmtt) REVERT: F 26 ILE cc_start: 0.8360 (mt) cc_final: 0.8087 (tt) REVERT: F 202 MET cc_start: 0.6466 (mmt) cc_final: 0.6073 (mmt) REVERT: F 280 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7874 (ttmm) REVERT: G 16 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7766 (tp-100) REVERT: G 282 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8044 (mmtm) REVERT: H 10 LEU cc_start: 0.7938 (mt) cc_final: 0.7520 (mt) REVERT: H 63 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: H 123 GLU cc_start: 0.4871 (mm-30) cc_final: 0.4573 (mm-30) REVERT: H 213 ASN cc_start: 0.8558 (m110) cc_final: 0.8293 (m110) REVERT: H 233 GLU cc_start: 0.7934 (pp20) cc_final: 0.7636 (pp20) REVERT: I 110 ASP cc_start: 0.8041 (m-30) cc_final: 0.7733 (m-30) REVERT: I 125 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8461 (mt) REVERT: I 151 ASP cc_start: 0.7330 (t0) cc_final: 0.6832 (t0) REVERT: I 159 LYS cc_start: 0.8363 (tttt) cc_final: 0.8013 (tttt) REVERT: I 180 ASP cc_start: 0.7572 (t0) cc_final: 0.7348 (p0) outliers start: 56 outliers final: 42 residues processed: 581 average time/residue: 2.9890 time to fit residues: 1984.5510 Evaluate side-chains 595 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 545 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 277 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN G 213 ASN I 198 ASN J 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23203 Z= 0.418 Angle : 0.632 6.207 31402 Z= 0.337 Chirality : 0.046 0.161 3591 Planarity : 0.005 0.101 3940 Dihedral : 14.165 167.559 3527 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.91 % Allowed : 20.63 % Favored : 76.46 % 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: -0.30 (0.15), residues: 2892 helix: 1.16 (0.16), residues: 1099 sheet: 0.03 (0.22), residues: 511 loop : -1.53 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 290 HIS 0.006 0.002 HIS E 97 PHE 0.021 0.002 PHE C 270 TYR 0.013 0.002 TYR A 271 ARG 0.016 0.001 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 559 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7233 (mmm) cc_final: 0.6987 (tmm) REVERT: A 283 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8037 (tt) REVERT: B 159 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8395 (tt) REVERT: B 191 PHE cc_start: 0.8789 (m-80) cc_final: 0.8406 (m-80) REVERT: B 236 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8058 (m-40) REVERT: C 68 GLU cc_start: 0.7627 (pm20) cc_final: 0.7425 (pm20) REVERT: D 16 GLN cc_start: 0.7978 (tp40) cc_final: 0.7550 (tm-30) REVERT: D 68 GLU cc_start: 0.7903 (pm20) cc_final: 0.7539 (pm20) REVERT: D 105 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7493 (ttt180) REVERT: E 308 TRP cc_start: 0.7487 (t60) cc_final: 0.7119 (t60) REVERT: F 26 ILE cc_start: 0.8364 (mt) cc_final: 0.8126 (tt) REVERT: F 202 MET cc_start: 0.6487 (mmt) cc_final: 0.6091 (mmt) REVERT: F 280 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7944 (ttmm) REVERT: G 16 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7815 (tp-100) REVERT: G 282 LYS cc_start: 0.8328 (mmtm) cc_final: 0.8056 (mmtm) REVERT: H 10 LEU cc_start: 0.7965 (mt) cc_final: 0.7596 (mt) REVERT: H 123 GLU cc_start: 0.5225 (mm-30) cc_final: 0.4935 (mm-30) REVERT: H 213 ASN cc_start: 0.8591 (m110) cc_final: 0.8299 (m110) REVERT: H 233 GLU cc_start: 0.8047 (pp20) cc_final: 0.7629 (pp20) REVERT: I 110 ASP cc_start: 0.8040 (m-30) cc_final: 0.7767 (m-30) REVERT: I 151 ASP cc_start: 0.7361 (t0) cc_final: 0.6860 (t0) REVERT: I 159 LYS cc_start: 0.8386 (tttt) cc_final: 0.8038 (tttt) REVERT: I 180 ASP cc_start: 0.7636 (t0) cc_final: 0.7403 (p0) outliers start: 67 outliers final: 52 residues processed: 590 average time/residue: 2.9325 time to fit residues: 1973.0070 Evaluate side-chains 615 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 558 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 116 CYS Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN E 205 ASN F 257 GLN G 213 ASN I 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23203 Z= 0.192 Angle : 0.556 8.496 31402 Z= 0.294 Chirality : 0.042 0.158 3591 Planarity : 0.005 0.108 3940 Dihedral : 13.845 163.353 3524 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.26 % Allowed : 21.89 % Favored : 75.85 % 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: 0.07 (0.15), residues: 2892 helix: 1.53 (0.16), residues: 1099 sheet: 0.18 (0.22), residues: 517 loop : -1.37 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 290 HIS 0.003 0.001 HIS B 97 PHE 0.022 0.001 PHE C 270 TYR 0.019 0.001 TYR A 293 ARG 0.015 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 567 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6168 (mt-10) cc_final: 0.4097 (tt0) REVERT: A 127 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7604 (mm-30) REVERT: A 202 MET cc_start: 0.7185 (mmm) cc_final: 0.6942 (tmm) REVERT: A 283 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 236 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8022 (m-40) REVERT: C 68 GLU cc_start: 0.7627 (pm20) cc_final: 0.7427 (pm20) REVERT: D 16 GLN cc_start: 0.7990 (tp40) cc_final: 0.7554 (tm-30) REVERT: D 44 SER cc_start: 0.7844 (p) cc_final: 0.7609 (t) REVERT: D 68 GLU cc_start: 0.7895 (pm20) cc_final: 0.7524 (pm20) REVERT: D 110 ASP cc_start: 0.8291 (t0) cc_final: 0.8086 (t0) REVERT: E 86 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7326 (mm-30) REVERT: E 308 TRP cc_start: 0.7300 (t60) cc_final: 0.6989 (t60) REVERT: E 321 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7410 (mmtt) REVERT: F 26 ILE cc_start: 0.8378 (mt) cc_final: 0.8067 (tt) REVERT: F 202 MET cc_start: 0.6486 (mmt) cc_final: 0.6109 (mmt) REVERT: F 280 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7955 (ttmm) REVERT: G 16 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7777 (tp-100) REVERT: G 282 LYS cc_start: 0.8312 (mmtm) cc_final: 0.8052 (mmtm) REVERT: H 10 LEU cc_start: 0.7945 (mt) cc_final: 0.7536 (mt) REVERT: H 213 ASN cc_start: 0.8530 (m110) cc_final: 0.8260 (m110) REVERT: H 233 GLU cc_start: 0.8019 (pp20) cc_final: 0.7673 (pp20) REVERT: I 110 ASP cc_start: 0.8042 (m-30) cc_final: 0.7746 (m-30) REVERT: I 151 ASP cc_start: 0.7347 (t0) cc_final: 0.6847 (t0) REVERT: I 159 LYS cc_start: 0.8298 (tttt) cc_final: 0.7940 (tttt) REVERT: J 137 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7566 (mm110) outliers start: 52 outliers final: 45 residues processed: 591 average time/residue: 2.9881 time to fit residues: 2015.0304 Evaluate side-chains 602 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 554 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 79 optimal weight: 0.0030 chunk 233 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 257 optimal weight: 0.4980 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN F 257 GLN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23203 Z= 0.231 Angle : 0.566 7.501 31402 Z= 0.298 Chirality : 0.042 0.155 3591 Planarity : 0.005 0.115 3940 Dihedral : 13.821 164.201 3522 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.30 % Allowed : 22.50 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 2892 helix: 1.59 (0.16), residues: 1101 sheet: 0.19 (0.22), residues: 517 loop : -1.37 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 290 HIS 0.004 0.001 HIS E 97 PHE 0.026 0.001 PHE C 270 TYR 0.013 0.001 TYR A 103 ARG 0.018 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 557 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6201 (mt-10) cc_final: 0.4122 (tt0) REVERT: A 127 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7610 (mm-30) REVERT: A 202 MET cc_start: 0.7175 (mmm) cc_final: 0.6761 (tpp) REVERT: A 210 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 283 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7979 (tt) REVERT: D 16 GLN cc_start: 0.7989 (tp40) cc_final: 0.7560 (tm-30) REVERT: D 44 SER cc_start: 0.7847 (p) cc_final: 0.7612 (t) REVERT: D 68 GLU cc_start: 0.7889 (pm20) cc_final: 0.7531 (pm20) REVERT: E 86 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7322 (mm-30) REVERT: E 154 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: E 308 TRP cc_start: 0.7413 (t60) cc_final: 0.7060 (t60) REVERT: F 26 ILE cc_start: 0.8355 (mt) cc_final: 0.8117 (tt) REVERT: F 202 MET cc_start: 0.6494 (mmt) cc_final: 0.6119 (mmt) REVERT: F 280 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7869 (ttmm) REVERT: G 16 GLN cc_start: 0.8090 (tp-100) cc_final: 0.7782 (tp-100) REVERT: H 10 LEU cc_start: 0.7969 (mt) cc_final: 0.7569 (mt) REVERT: H 213 ASN cc_start: 0.8542 (m110) cc_final: 0.8279 (m110) REVERT: H 233 GLU cc_start: 0.8019 (pp20) cc_final: 0.7654 (pp20) REVERT: H 241 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7231 (mt-10) REVERT: I 110 ASP cc_start: 0.8045 (m-30) cc_final: 0.7766 (m-30) REVERT: I 151 ASP cc_start: 0.7365 (t0) cc_final: 0.6835 (t0) REVERT: I 159 LYS cc_start: 0.8304 (tttt) cc_final: 0.7943 (tttt) REVERT: J 137 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7560 (mm110) outliers start: 53 outliers final: 44 residues processed: 581 average time/residue: 3.0273 time to fit residues: 2026.3166 Evaluate side-chains 603 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 555 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 176 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN D 312 ASN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23203 Z= 0.186 Angle : 0.556 7.347 31402 Z= 0.291 Chirality : 0.042 0.154 3591 Planarity : 0.005 0.117 3940 Dihedral : 13.696 163.941 3522 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.13 % Allowed : 22.98 % Favored : 74.89 % 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: 0.25 (0.15), residues: 2892 helix: 1.73 (0.16), residues: 1101 sheet: 0.27 (0.22), residues: 516 loop : -1.33 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 290 HIS 0.003 0.001 HIS F 163 PHE 0.028 0.001 PHE C 270 TYR 0.024 0.001 TYR A 293 ARG 0.018 0.001 ARG G 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 559 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6050 (mt-10) cc_final: 0.4142 (tt0) REVERT: A 202 MET cc_start: 0.7170 (mmm) cc_final: 0.6755 (tpp) REVERT: A 210 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8498 (p) REVERT: A 283 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7974 (tt) REVERT: C 271 TYR cc_start: 0.7918 (m-80) cc_final: 0.7486 (m-80) REVERT: D 16 GLN cc_start: 0.7992 (tp40) cc_final: 0.7571 (tm-30) REVERT: D 68 GLU cc_start: 0.7890 (pm20) cc_final: 0.7517 (pm20) REVERT: E 86 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7314 (mm-30) REVERT: E 308 TRP cc_start: 0.7407 (t60) cc_final: 0.7052 (t60) REVERT: F 26 ILE cc_start: 0.8368 (mt) cc_final: 0.8079 (tt) REVERT: F 202 MET cc_start: 0.6490 (mmt) cc_final: 0.6115 (mmt) REVERT: F 280 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7864 (ttmm) REVERT: G 16 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7731 (tp-100) REVERT: H 10 LEU cc_start: 0.7961 (mt) cc_final: 0.7577 (mt) REVERT: H 213 ASN cc_start: 0.8526 (m110) cc_final: 0.8266 (m110) REVERT: H 233 GLU cc_start: 0.7961 (pp20) cc_final: 0.7648 (pp20) REVERT: H 241 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7334 (mt-10) REVERT: I 151 ASP cc_start: 0.7351 (t0) cc_final: 0.6840 (t0) REVERT: I 159 LYS cc_start: 0.8301 (tttt) cc_final: 0.7943 (tttt) outliers start: 49 outliers final: 41 residues processed: 580 average time/residue: 2.9732 time to fit residues: 1964.5921 Evaluate side-chains 598 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 554 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN E 205 ASN F 257 GLN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108551 restraints weight = 96044.246| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.81 r_work: 0.3257 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23203 Z= 0.244 Angle : 0.571 7.203 31402 Z= 0.301 Chirality : 0.043 0.153 3591 Planarity : 0.005 0.116 3940 Dihedral : 13.749 163.841 3522 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.09 % Allowed : 23.11 % Favored : 74.80 % 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: 0.20 (0.15), residues: 2892 helix: 1.70 (0.16), residues: 1101 sheet: 0.24 (0.22), residues: 516 loop : -1.36 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 290 HIS 0.005 0.001 HIS E 97 PHE 0.028 0.001 PHE C 270 TYR 0.013 0.001 TYR G 271 ARG 0.018 0.001 ARG G 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25633.83 seconds wall clock time: 444 minutes 9.37 seconds (26649.37 seconds total)