Starting phenix.real_space_refine on Thu Mar 5 00:09:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d82_27244/03_2026/8d82_27244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d82_27244/03_2026/8d82_27244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d82_27244/03_2026/8d82_27244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d82_27244/03_2026/8d82_27244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d82_27244/03_2026/8d82_27244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d82_27244/03_2026/8d82_27244.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 10970 2.51 5 N 2920 2.21 5 O 3390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17366 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2340 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 23, 'TRANS': 272} Chain: "D" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1358 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4719 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 553} Chain: "G" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2340 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 23, 'TRANS': 272} Chain: "H" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1358 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "E" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4719 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 553} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ARG C 101 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG C 101 " occ=0.00 residue: pdb=" N ASN C 155 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN C 155 " occ=0.00 residue: pdb=" N SER C 156 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER C 156 " occ=0.00 residue: pdb=" N ARG G 101 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 101 " occ=0.00 residue: pdb=" N ASN G 155 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN G 155 " occ=0.00 residue: pdb=" N SER G 156 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 156 " occ=0.00 residue: pdb=" C1 NAG I 2 " occ=0.50 ... (12 atoms not shown) pdb=" O7 NAG I 2 " occ=0.50 residue: pdb=" C1 NAG N 2 " occ=0.50 ... (12 atoms not shown) pdb=" O7 NAG N 2 " occ=0.50 Time building chain proxies: 4.11, per 1000 atoms: 0.24 Number of scatterers: 17366 At special positions: 0 Unit cell: (172.55, 209.95, 166.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 3390 8.00 N 2920 7.00 C 10970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 47 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS G 132 " distance=2.03 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 176 " distance=2.03 Simple disulfide: pdb=" SG CYS H 72 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 103 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 144 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 458 " - pdb=" SG CYS E 466 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 801 " - " ASN A 227 " " NAG A 802 " - " ASN A 157 " " NAG A 803 " - " ASN A 383 " " NAG A 804 " - " ASN A 379 " " NAG A 805 " - " ASN A 390 " " NAG A 806 " - " ASN A 564 " " NAG B 1 " - " ASN C 245 " " NAG C 401 " - " ASN C 221 " " NAG C 402 " - " ASN C 55 " " NAG C 403 " - " ASN C 93 " " NAG E 801 " - " ASN E 227 " " NAG E 802 " - " ASN E 157 " " NAG E 803 " - " ASN E 383 " " NAG E 804 " - " ASN E 379 " " NAG E 805 " - " ASN E 390 " " NAG E 806 " - " ASN E 564 " " NAG F 1 " - " ASN A 83 " " NAG G 401 " - " ASN G 221 " " NAG G 402 " - " ASN G 55 " " NAG G 403 " - " ASN G 93 " " NAG I 1 " - " ASN A 553 " " NAG J 1 " - " ASN A 43 " " NAG K 1 " - " ASN A 131 " " NAG L 1 " - " ASN G 245 " " NAG M 1 " - " ASN E 83 " " NAG N 1 " - " ASN E 553 " " NAG O 1 " - " ASN E 43 " " NAG P 1 " - " ASN E 131 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 636.3 milliseconds 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4028 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 46 sheets defined 13.9% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.528A pdb=" N SER C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 75 removed outlier: 3.740A pdb=" N ILE D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.714A pdb=" N GLY D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 130 removed outlier: 4.517A pdb=" N VAL D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 156 removed outlier: 3.579A pdb=" N ALA D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 179 removed outlier: 3.540A pdb=" N LEU D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 211 removed outlier: 4.076A pdb=" N GLN D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.289A pdb=" N SER A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.833A pdb=" N ALA A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 4.332A pdb=" N ASN A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.528A pdb=" N SER G 91 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 75 removed outlier: 3.745A pdb=" N ILE H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN H 73 " --> pdb=" O LYS H 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.716A pdb=" N GLY H 100 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 130 removed outlier: 4.527A pdb=" N VAL H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 156 removed outlier: 3.580A pdb=" N ALA H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL H 143 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 179 removed outlier: 3.534A pdb=" N LEU H 176 " --> pdb=" O ASN H 172 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 211 removed outlier: 4.087A pdb=" N GLN H 211 " --> pdb=" O ARG H 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 Processing helix chain 'E' and resid 247 through 252 removed outlier: 4.287A pdb=" N SER E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 278 removed outlier: 3.833A pdb=" N ALA E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 548 removed outlier: 4.332A pdb=" N ASN E 548 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 37 removed outlier: 3.819A pdb=" N SER C 37 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.924A pdb=" N VAL C 43 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.660A pdb=" N SER C 120 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP C 134 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 166 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 159 through 163 removed outlier: 3.566A pdb=" N GLU C 159 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 152 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 161 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 150 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 187 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 159 through 163 removed outlier: 3.566A pdb=" N GLU C 159 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 152 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 161 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 150 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 187 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 220 through 226 removed outlier: 5.978A pdb=" N ASN C 221 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN C 239 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 266 through 269 Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 88 removed outlier: 7.021A pdb=" N ASP E 26 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.960A pdb=" N ASP A 26 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.598A pdb=" N TYR A 30 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.219A pdb=" N ILE A 105 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASN A 114 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 142 through 147 removed outlier: 6.807A pdb=" N ARG A 143 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS A 134 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU A 145 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 132 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 130 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS A 221 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.029A pdb=" N ASN A 157 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 201 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 195 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.029A pdb=" N ASN A 157 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 201 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 195 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 226 through 231 removed outlier: 4.272A pdb=" N LEU A 228 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR A 243 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 230 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 241 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 240 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AB8, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AB9, first strand: chain 'A' and resid 332 through 335 removed outlier: 3.740A pdb=" N VAL A 389 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 376 through 382 removed outlier: 4.044A pdb=" N HIS A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 370 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 380 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 371 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 397 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 430 through 432 removed outlier: 4.256A pdb=" N VAL A 441 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR A 480 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 469 through 474 removed outlier: 4.027A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 458 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 469 through 474 removed outlier: 4.027A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 458 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 508 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 566 through 571 removed outlier: 3.563A pdb=" N VAL A 568 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 553 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 589 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 594 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 601 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 566 through 571 removed outlier: 3.563A pdb=" N VAL A 568 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 553 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 589 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 606 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 34 through 37 removed outlier: 3.819A pdb=" N SER G 37 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 43 through 44 removed outlier: 3.924A pdb=" N VAL G 43 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.660A pdb=" N SER G 120 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP G 134 " --> pdb=" O PHE G 174 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN G 166 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 159 through 163 removed outlier: 3.563A pdb=" N GLU G 159 " --> pdb=" O LYS G 152 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS G 152 " --> pdb=" O GLU G 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 161 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 150 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 187 " --> pdb=" O PHE G 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 159 through 163 removed outlier: 3.563A pdb=" N GLU G 159 " --> pdb=" O LYS G 152 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS G 152 " --> pdb=" O GLU G 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 161 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 150 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 187 " --> pdb=" O PHE G 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 220 through 226 removed outlier: 5.978A pdb=" N ASN G 221 " --> pdb=" O GLN G 239 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN G 239 " --> pdb=" O ASN G 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 266 through 269 Processing sheet with id=AD5, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.587A pdb=" N TYR E 30 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 66 through 68 removed outlier: 6.217A pdb=" N ILE E 105 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASN E 114 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 142 through 147 removed outlier: 6.807A pdb=" N ARG E 143 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS E 134 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU E 145 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU E 132 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS E 130 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS E 221 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 136 " --> pdb=" O LYS E 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 172 through 173 removed outlier: 4.029A pdb=" N ASN E 157 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU E 201 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 195 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 172 through 173 removed outlier: 4.029A pdb=" N ASN E 157 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU E 201 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 195 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 226 through 231 removed outlier: 4.272A pdb=" N LEU E 228 " --> pdb=" O THR E 243 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR E 243 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL E 230 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS E 241 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU E 240 " --> pdb=" O VAL E 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 255 through 257 Processing sheet with id=AE3, first strand: chain 'E' and resid 270 through 271 Processing sheet with id=AE4, first strand: chain 'E' and resid 332 through 335 removed outlier: 3.740A pdb=" N VAL E 389 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 387 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 376 through 382 removed outlier: 4.044A pdb=" N HIS E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 370 " --> pdb=" O GLN E 378 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR E 380 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP E 365 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 371 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU E 397 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 430 through 432 removed outlier: 4.256A pdb=" N VAL E 441 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR E 480 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 469 through 474 removed outlier: 4.027A pdb=" N LYS E 452 " --> pdb=" O VAL E 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS E 458 " --> pdb=" O LEU E 493 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E 503 " --> pdb=" O TYR E 500 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 469 through 474 removed outlier: 4.027A pdb=" N LYS E 452 " --> pdb=" O VAL E 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS E 458 " --> pdb=" O LEU E 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU E 508 " --> pdb=" O VAL E 496 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 566 through 571 removed outlier: 3.563A pdb=" N VAL E 568 " --> pdb=" O ILE E 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 553 " --> pdb=" O TYR E 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET E 589 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA E 594 " --> pdb=" O LYS E 601 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS E 601 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 566 through 571 removed outlier: 3.563A pdb=" N VAL E 568 " --> pdb=" O ILE E 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 553 " --> pdb=" O TYR E 595 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET E 589 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 606 " --> pdb=" O VAL E 590 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1650 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: 2.89 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5528 1.34 - 1.46: 4317 1.46 - 1.58: 7827 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 17790 Sorted by residual: bond pdb=" C1 NAG A 804 " pdb=" O5 NAG A 804 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C1 NAG E 804 " pdb=" O5 NAG E 804 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 ... (remaining 17785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 23345 1.33 - 2.66: 717 2.66 - 3.98: 128 3.98 - 5.31: 16 5.31 - 6.64: 4 Bond angle restraints: 24210 Sorted by residual: angle pdb=" N VAL A 546 " pdb=" CA VAL A 546 " pdb=" C VAL A 546 " ideal model delta sigma weight residual 113.20 109.77 3.43 9.60e-01 1.09e+00 1.28e+01 angle pdb=" N VAL E 546 " pdb=" CA VAL E 546 " pdb=" C VAL E 546 " ideal model delta sigma weight residual 113.20 109.77 3.43 9.60e-01 1.09e+00 1.28e+01 angle pdb=" C PRO A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.06e+00 angle pdb=" C PRO E 434 " pdb=" N LYS E 435 " pdb=" CA LYS E 435 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.06e+00 angle pdb=" N LYS E 76 " pdb=" CA LYS E 76 " pdb=" C LYS E 76 " ideal model delta sigma weight residual 111.30 114.49 -3.19 1.36e+00 5.41e-01 5.50e+00 ... (remaining 24205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 10355 22.00 - 44.00: 575 44.00 - 66.01: 152 66.01 - 88.01: 62 88.01 - 110.01: 110 Dihedral angle restraints: 11254 sinusoidal: 5050 harmonic: 6204 Sorted by residual: dihedral pdb=" CB CYS H 72 " pdb=" SG CYS H 72 " pdb=" SG CYS H 78 " pdb=" CB CYS H 78 " ideal model delta sinusoidal sigma weight residual -86.00 -28.34 -57.66 1 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" CB CYS D 72 " pdb=" SG CYS D 72 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual -86.00 -28.41 -57.59 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CA ASP E 436 " pdb=" C ASP E 436 " pdb=" N ASN E 437 " pdb=" CA ASN E 437 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 11251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2441 0.059 - 0.118: 338 0.118 - 0.177: 19 0.177 - 0.236: 4 0.236 - 0.295: 2 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C1 NAG E 803 " pdb=" ND2 ASN E 383 " pdb=" C2 NAG E 803 " pdb=" O5 NAG E 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 383 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN G 245 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2801 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 325 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO E 326 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 326 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 326 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 325 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 326 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 337 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO E 338 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 338 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 338 " -0.021 5.00e-02 4.00e+02 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2830 2.77 - 3.30: 15548 3.30 - 3.84: 27162 3.84 - 4.37: 30064 4.37 - 4.90: 52907 Nonbonded interactions: 128511 Sorted by model distance: nonbonded pdb=" O LEU E 364 " pdb=" O3 NAG E 803 " model vdw 2.239 3.040 nonbonded pdb=" O LEU A 364 " pdb=" O3 NAG A 803 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 596 " pdb=" O GLY A 599 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR E 596 " pdb=" O GLY E 599 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR G 257 " pdb=" OD1 ASP G 281 " model vdw 2.292 3.040 ... (remaining 128506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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=0.00 max=1.00 mean=0.97 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: 6.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.990 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 : 0.003 0.047 17850 Z= 0.144 Angle : 0.548 8.933 24368 Z= 0.277 Chirality : 0.042 0.295 2804 Planarity : 0.003 0.039 3044 Dihedral : 19.913 110.011 7160 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.95 % Allowed : 9.50 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.16), residues: 2096 helix: -0.32 (0.31), residues: 252 sheet: -1.60 (0.16), residues: 806 loop : -2.19 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 79 TYR 0.004 0.001 TYR A 334 PHE 0.009 0.001 PHE E 108 TRP 0.006 0.000 TRP E 333 HIS 0.001 0.000 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00288 (17790) covalent geometry : angle 0.52397 (24210) SS BOND : bond 0.00139 ( 22) SS BOND : angle 0.51194 ( 44) hydrogen bonds : bond 0.26345 ( 538) hydrogen bonds : angle 9.53119 ( 1650) link_BETA1-4 : bond 0.00453 ( 10) link_BETA1-4 : angle 1.72906 ( 30) link_NAG-ASN : bond 0.00599 ( 28) link_NAG-ASN : angle 2.60800 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 0.598 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: C 77 MET cc_start: 0.3044 (ttt) cc_final: 0.2803 (pmm) REVERT: D 189 MET cc_start: 0.6403 (tpp) cc_final: 0.6064 (tpt) REVERT: A 360 ASN cc_start: 0.5259 (m-40) cc_final: 0.4611 (m110) REVERT: A 458 CYS cc_start: 0.5990 (p) cc_final: 0.5420 (p) REVERT: A 592 MET cc_start: 0.2043 (ptp) cc_final: -0.0051 (ttm) REVERT: G 77 MET cc_start: 0.3050 (ttt) cc_final: 0.2808 (pmm) REVERT: H 189 MET cc_start: 0.6458 (tpp) cc_final: 0.6059 (tpt) REVERT: E 360 ASN cc_start: 0.5260 (m-40) cc_final: 0.4611 (m110) REVERT: E 458 CYS cc_start: 0.5998 (p) cc_final: 0.5428 (p) REVERT: E 592 MET cc_start: 0.2053 (ptp) cc_final: -0.0047 (ttm) outliers start: 18 outliers final: 16 residues processed: 269 average time/residue: 0.1477 time to fit residues: 58.4586 Evaluate side-chains 181 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN C 162 GLN C 206 GLN C 215 GLN C 239 GLN D 76 ASN D 131 ASN D 144 GLN D 172 ASN D 211 GLN A 104 ASN A 153 HIS A 342 GLN A 404 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 547 GLN A 548 ASN A 569 ASN A 574 HIS G 118 GLN G 162 GLN G 206 GLN G 215 GLN ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 131 ASN H 144 GLN H 172 ASN H 211 GLN E 104 ASN E 153 HIS E 342 GLN E 404 ASN ** E 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 GLN E 547 GLN E 548 ASN E 569 ASN E 574 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.195972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.147742 restraints weight = 28265.240| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 4.06 r_work: 0.3665 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 542 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 544 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17850 Z= 0.132 Angle : 0.637 8.526 24368 Z= 0.300 Chirality : 0.047 0.316 2804 Planarity : 0.004 0.052 3044 Dihedral : 17.103 90.268 3098 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.01 % Allowed : 12.78 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2096 helix: 1.21 (0.34), residues: 246 sheet: -0.93 (0.17), residues: 802 loop : -1.61 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 210 TYR 0.015 0.001 TYR E 513 PHE 0.019 0.002 PHE A 72 TRP 0.008 0.001 TRP E 67 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00303 (17790) covalent geometry : angle 0.61409 (24210) SS BOND : bond 0.00536 ( 22) SS BOND : angle 0.75896 ( 44) hydrogen bonds : bond 0.04161 ( 538) hydrogen bonds : angle 6.33728 ( 1650) link_BETA1-4 : bond 0.00753 ( 10) link_BETA1-4 : angle 1.86001 ( 30) link_NAG-ASN : bond 0.00634 ( 28) link_NAG-ASN : angle 2.71415 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.492 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: D 77 MET cc_start: 0.8471 (mtm) cc_final: 0.8161 (mtm) REVERT: D 189 MET cc_start: 0.6880 (tpp) cc_final: 0.6574 (tpt) REVERT: A 557 PHE cc_start: 0.4095 (OUTLIER) cc_final: 0.3462 (p90) REVERT: H 54 ASP cc_start: 0.8451 (m-30) cc_final: 0.8075 (m-30) REVERT: H 189 MET cc_start: 0.6789 (tpp) cc_final: 0.6382 (tpt) REVERT: E 557 PHE cc_start: 0.4099 (OUTLIER) cc_final: 0.3465 (p90) outliers start: 38 outliers final: 22 residues processed: 201 average time/residue: 0.1246 time to fit residues: 39.2612 Evaluate side-chains 176 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 157 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN A 393 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN G 239 GLN E 393 ASN ** E 471 GLN ** 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 = 0.4486 r_free = 0.4486 target = 0.193206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143026 restraints weight = 28817.602| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 4.02 r_work: 0.3619 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 544 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 545 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17850 Z= 0.129 Angle : 0.626 8.852 24368 Z= 0.294 Chirality : 0.045 0.343 2804 Planarity : 0.004 0.038 3044 Dihedral : 13.647 80.095 3096 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.53 % Allowed : 14.78 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 2096 helix: 1.67 (0.34), residues: 246 sheet: -0.58 (0.18), residues: 802 loop : -1.38 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 559 TYR 0.020 0.001 TYR E 513 PHE 0.013 0.002 PHE E 433 TRP 0.006 0.001 TRP G 268 HIS 0.004 0.001 HIS E 153 Details of bonding type rmsd covalent geometry : bond 0.00297 (17790) covalent geometry : angle 0.60311 (24210) SS BOND : bond 0.00242 ( 22) SS BOND : angle 0.89843 ( 44) hydrogen bonds : bond 0.04142 ( 538) hydrogen bonds : angle 5.56532 ( 1650) link_BETA1-4 : bond 0.00740 ( 10) link_BETA1-4 : angle 1.92896 ( 30) link_NAG-ASN : bond 0.00630 ( 28) link_NAG-ASN : angle 2.65084 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 MET cc_start: 0.8554 (mtm) cc_final: 0.8208 (mtm) REVERT: D 189 MET cc_start: 0.7077 (tpp) cc_final: 0.6694 (tpt) REVERT: A 499 VAL cc_start: 0.6732 (t) cc_final: 0.6477 (p) REVERT: A 557 PHE cc_start: 0.4145 (OUTLIER) cc_final: 0.3593 (p90) REVERT: H 54 ASP cc_start: 0.8521 (m-30) cc_final: 0.8196 (m-30) REVERT: H 77 MET cc_start: 0.8509 (mtm) cc_final: 0.8301 (mtm) REVERT: H 189 MET cc_start: 0.7105 (tpp) cc_final: 0.6720 (tpt) REVERT: E 499 VAL cc_start: 0.6715 (t) cc_final: 0.6462 (p) REVERT: E 557 PHE cc_start: 0.4146 (OUTLIER) cc_final: 0.3586 (p90) outliers start: 48 outliers final: 32 residues processed: 207 average time/residue: 0.1213 time to fit residues: 39.3698 Evaluate side-chains 185 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 201 optimal weight: 40.0000 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN ** E 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.191755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.143061 restraints weight = 28312.786| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.50 r_work: 0.3624 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 545 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 548 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17850 Z= 0.114 Angle : 0.618 8.484 24368 Z= 0.289 Chirality : 0.045 0.318 2804 Planarity : 0.004 0.036 3044 Dihedral : 11.816 71.716 3096 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.12 % Allowed : 15.26 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2096 helix: 1.99 (0.35), residues: 246 sheet: -0.40 (0.18), residues: 796 loop : -1.22 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 210 TYR 0.010 0.001 TYR H 59 PHE 0.018 0.001 PHE E 433 TRP 0.009 0.001 TRP A 333 HIS 0.004 0.001 HIS E 478 Details of bonding type rmsd covalent geometry : bond 0.00258 (17790) covalent geometry : angle 0.59335 (24210) SS BOND : bond 0.00285 ( 22) SS BOND : angle 0.84010 ( 44) hydrogen bonds : bond 0.03530 ( 538) hydrogen bonds : angle 5.25143 ( 1650) link_BETA1-4 : bond 0.00795 ( 10) link_BETA1-4 : angle 2.01041 ( 30) link_NAG-ASN : bond 0.00655 ( 28) link_NAG-ASN : angle 2.70902 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 0.626 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: D 54 ASP cc_start: 0.8587 (m-30) cc_final: 0.8255 (m-30) REVERT: D 77 MET cc_start: 0.8547 (mtm) cc_final: 0.8194 (mtm) REVERT: A 470 TRP cc_start: 0.7408 (p-90) cc_final: 0.6904 (p-90) REVERT: A 513 TYR cc_start: 0.3557 (t80) cc_final: 0.3266 (t80) REVERT: A 557 PHE cc_start: 0.4091 (OUTLIER) cc_final: 0.3440 (p90) REVERT: H 77 MET cc_start: 0.8501 (mtm) cc_final: 0.8095 (mtm) REVERT: H 189 MET cc_start: 0.7093 (tpp) cc_final: 0.6729 (tpt) REVERT: E 470 TRP cc_start: 0.7399 (p-90) cc_final: 0.6896 (p-90) REVERT: E 513 TYR cc_start: 0.3567 (t80) cc_final: 0.3271 (t80) REVERT: E 557 PHE cc_start: 0.4091 (OUTLIER) cc_final: 0.3437 (p90) outliers start: 59 outliers final: 38 residues processed: 204 average time/residue: 0.1243 time to fit residues: 39.8615 Evaluate side-chains 190 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 204 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.188171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.137507 restraints weight = 28349.543| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 4.03 r_work: 0.3527 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 548 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 548 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17850 Z= 0.190 Angle : 0.707 12.370 24368 Z= 0.336 Chirality : 0.047 0.298 2804 Planarity : 0.004 0.037 3044 Dihedral : 10.795 64.926 3094 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.96 % Allowed : 17.00 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2096 helix: 1.84 (0.34), residues: 248 sheet: -0.37 (0.18), residues: 800 loop : -1.22 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 210 TYR 0.019 0.001 TYR D 59 PHE 0.021 0.002 PHE A 91 TRP 0.009 0.001 TRP G 244 HIS 0.006 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00466 (17790) covalent geometry : angle 0.67678 (24210) SS BOND : bond 0.00401 ( 22) SS BOND : angle 1.06832 ( 44) hydrogen bonds : bond 0.04525 ( 538) hydrogen bonds : angle 5.16665 ( 1650) link_BETA1-4 : bond 0.00864 ( 10) link_BETA1-4 : angle 1.95486 ( 30) link_NAG-ASN : bond 0.00704 ( 28) link_NAG-ASN : angle 3.32886 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.644 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: D 54 ASP cc_start: 0.8555 (m-30) cc_final: 0.8214 (m-30) REVERT: D 77 MET cc_start: 0.8536 (mtm) cc_final: 0.8179 (mtt) REVERT: A 121 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8455 (tp) REVERT: A 470 TRP cc_start: 0.7317 (p-90) cc_final: 0.6850 (p-90) REVERT: A 513 TYR cc_start: 0.3612 (t80) cc_final: 0.3260 (t80) REVERT: A 557 PHE cc_start: 0.3981 (OUTLIER) cc_final: 0.3260 (p90) REVERT: H 54 ASP cc_start: 0.8470 (m-30) cc_final: 0.8115 (m-30) REVERT: H 77 MET cc_start: 0.8537 (mtm) cc_final: 0.8122 (mtt) REVERT: E 470 TRP cc_start: 0.7314 (p-90) cc_final: 0.6850 (p-90) REVERT: E 513 TYR cc_start: 0.3606 (t80) cc_final: 0.3255 (t80) REVERT: E 557 PHE cc_start: 0.3978 (OUTLIER) cc_final: 0.3260 (p90) outliers start: 56 outliers final: 45 residues processed: 205 average time/residue: 0.1238 time to fit residues: 39.9577 Evaluate side-chains 194 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 15 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 5 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN C 239 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN G 239 GLN G 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.190204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139075 restraints weight = 28396.093| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.92 r_work: 0.3564 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 548 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17850 Z= 0.120 Angle : 0.643 9.860 24368 Z= 0.306 Chirality : 0.044 0.296 2804 Planarity : 0.004 0.035 3044 Dihedral : 9.832 56.627 3094 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.06 % Allowed : 17.11 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2096 helix: 2.01 (0.34), residues: 248 sheet: -0.28 (0.18), residues: 798 loop : -1.07 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 210 TYR 0.011 0.001 TYR H 59 PHE 0.013 0.001 PHE G 161 TRP 0.010 0.001 TRP E 333 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00267 (17790) covalent geometry : angle 0.61049 (24210) SS BOND : bond 0.00284 ( 22) SS BOND : angle 1.09785 ( 44) hydrogen bonds : bond 0.03786 ( 538) hydrogen bonds : angle 4.96956 ( 1650) link_BETA1-4 : bond 0.00803 ( 10) link_BETA1-4 : angle 2.05004 ( 30) link_NAG-ASN : bond 0.00835 ( 28) link_NAG-ASN : angle 3.21497 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.467 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: D 54 ASP cc_start: 0.8593 (m-30) cc_final: 0.8262 (m-30) REVERT: D 196 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8160 (ttp80) REVERT: A 470 TRP cc_start: 0.7330 (p-90) cc_final: 0.6885 (p-90) REVERT: A 557 PHE cc_start: 0.4225 (OUTLIER) cc_final: 0.3660 (p90) REVERT: H 54 ASP cc_start: 0.8466 (m-30) cc_final: 0.8095 (m-30) REVERT: H 77 MET cc_start: 0.8468 (mtm) cc_final: 0.8091 (mtm) REVERT: E 121 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8533 (tp) REVERT: E 470 TRP cc_start: 0.7321 (p-90) cc_final: 0.6876 (p-90) REVERT: E 557 PHE cc_start: 0.4227 (OUTLIER) cc_final: 0.3655 (p90) outliers start: 58 outliers final: 42 residues processed: 203 average time/residue: 0.1217 time to fit residues: 38.4876 Evaluate side-chains 203 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 83 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.187588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.137880 restraints weight = 28394.597| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 4.29 r_work: 0.3506 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17850 Z= 0.157 Angle : 0.685 13.659 24368 Z= 0.325 Chirality : 0.046 0.392 2804 Planarity : 0.004 0.033 3044 Dihedral : 9.169 59.977 3094 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.75 % Allowed : 18.16 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2096 helix: 2.04 (0.34), residues: 248 sheet: -0.27 (0.18), residues: 798 loop : -1.07 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 210 TYR 0.014 0.001 TYR D 59 PHE 0.016 0.002 PHE A 91 TRP 0.011 0.001 TRP E 333 HIS 0.005 0.001 HIS H 192 Details of bonding type rmsd covalent geometry : bond 0.00378 (17790) covalent geometry : angle 0.64312 (24210) SS BOND : bond 0.00219 ( 22) SS BOND : angle 1.26384 ( 44) hydrogen bonds : bond 0.04277 ( 538) hydrogen bonds : angle 4.92837 ( 1650) link_BETA1-4 : bond 0.00854 ( 10) link_BETA1-4 : angle 2.06705 ( 30) link_NAG-ASN : bond 0.00750 ( 28) link_NAG-ASN : angle 3.79325 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 0.668 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: D 54 ASP cc_start: 0.8676 (m-30) cc_final: 0.8342 (m-30) REVERT: D 77 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: A 155 GLU cc_start: 0.8073 (pp20) cc_final: 0.7798 (pp20) REVERT: A 470 TRP cc_start: 0.7279 (p-90) cc_final: 0.6796 (p-90) REVERT: A 557 PHE cc_start: 0.4210 (OUTLIER) cc_final: 0.3590 (p90) REVERT: E 155 GLU cc_start: 0.8057 (pp20) cc_final: 0.7796 (pp20) REVERT: E 470 TRP cc_start: 0.7281 (p-90) cc_final: 0.6801 (p-90) REVERT: E 557 PHE cc_start: 0.4223 (OUTLIER) cc_final: 0.3599 (p90) outliers start: 52 outliers final: 43 residues processed: 191 average time/residue: 0.1282 time to fit residues: 38.2729 Evaluate side-chains 189 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 189 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.186468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137122 restraints weight = 27695.757| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.92 r_work: 0.3520 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 547 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17850 Z= 0.163 Angle : 0.685 12.212 24368 Z= 0.329 Chirality : 0.046 0.356 2804 Planarity : 0.004 0.034 3044 Dihedral : 8.485 58.606 3094 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.96 % Allowed : 18.32 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2096 helix: 2.06 (0.33), residues: 246 sheet: -0.25 (0.18), residues: 800 loop : -1.07 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 229 TYR 0.012 0.001 TYR H 59 PHE 0.015 0.002 PHE A 292 TRP 0.013 0.001 TRP A 333 HIS 0.005 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00393 (17790) covalent geometry : angle 0.64361 (24210) SS BOND : bond 0.00307 ( 22) SS BOND : angle 1.40405 ( 44) hydrogen bonds : bond 0.04381 ( 538) hydrogen bonds : angle 4.93358 ( 1650) link_BETA1-4 : bond 0.00873 ( 10) link_BETA1-4 : angle 2.11136 ( 30) link_NAG-ASN : bond 0.00673 ( 28) link_NAG-ASN : angle 3.74177 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 0.652 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: D 54 ASP cc_start: 0.8656 (m-30) cc_final: 0.8347 (m-30) REVERT: D 77 MET cc_start: 0.8613 (mtm) cc_final: 0.8369 (mtm) REVERT: A 155 GLU cc_start: 0.8030 (pp20) cc_final: 0.7820 (pp20) REVERT: A 470 TRP cc_start: 0.7322 (p-90) cc_final: 0.6861 (p-90) REVERT: A 474 ASP cc_start: 0.6800 (t0) cc_final: 0.6069 (p0) REVERT: H 77 MET cc_start: 0.8564 (mtm) cc_final: 0.8304 (mtm) REVERT: E 155 GLU cc_start: 0.8025 (pp20) cc_final: 0.7813 (pp20) REVERT: E 470 TRP cc_start: 0.7323 (p-90) cc_final: 0.6861 (p-90) REVERT: E 474 ASP cc_start: 0.6801 (t0) cc_final: 0.6068 (p0) outliers start: 56 outliers final: 45 residues processed: 194 average time/residue: 0.1323 time to fit residues: 39.8294 Evaluate side-chains 196 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.186875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137643 restraints weight = 27768.269| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.87 r_work: 0.3528 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 547 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17850 Z= 0.142 Angle : 0.672 13.827 24368 Z= 0.323 Chirality : 0.045 0.382 2804 Planarity : 0.004 0.035 3044 Dihedral : 7.969 58.953 3094 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.64 % Allowed : 18.32 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2096 helix: 2.09 (0.34), residues: 248 sheet: -0.24 (0.18), residues: 804 loop : -1.01 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 229 TYR 0.012 0.001 TYR H 59 PHE 0.014 0.001 PHE E 292 TRP 0.013 0.001 TRP E 333 HIS 0.005 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00337 (17790) covalent geometry : angle 0.62711 (24210) SS BOND : bond 0.00286 ( 22) SS BOND : angle 1.86336 ( 44) hydrogen bonds : bond 0.04174 ( 538) hydrogen bonds : angle 4.92043 ( 1650) link_BETA1-4 : bond 0.00820 ( 10) link_BETA1-4 : angle 2.00776 ( 30) link_NAG-ASN : bond 0.00649 ( 28) link_NAG-ASN : angle 3.77871 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.669 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: D 54 ASP cc_start: 0.8644 (m-30) cc_final: 0.8320 (m-30) REVERT: A 457 TRP cc_start: 0.7392 (p90) cc_final: 0.6987 (p90) REVERT: A 470 TRP cc_start: 0.7199 (p-90) cc_final: 0.6660 (p-90) REVERT: A 474 ASP cc_start: 0.6803 (t0) cc_final: 0.6064 (p0) REVERT: H 54 ASP cc_start: 0.8547 (m-30) cc_final: 0.8142 (m-30) REVERT: E 457 TRP cc_start: 0.7390 (p90) cc_final: 0.6985 (p90) REVERT: E 470 TRP cc_start: 0.7208 (p-90) cc_final: 0.6659 (p-90) REVERT: E 474 ASP cc_start: 0.6803 (t0) cc_final: 0.6061 (p0) outliers start: 50 outliers final: 44 residues processed: 190 average time/residue: 0.1370 time to fit residues: 40.2157 Evaluate side-chains 196 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 292 PHE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 96 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 149 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 1 optimal weight: 50.0000 chunk 81 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN E 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.187973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.138584 restraints weight = 27680.100| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.70 r_work: 0.3544 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17850 Z= 0.119 Angle : 0.649 14.269 24368 Z= 0.311 Chirality : 0.044 0.316 2804 Planarity : 0.004 0.034 3044 Dihedral : 7.493 57.192 3094 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.38 % Allowed : 18.74 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2096 helix: 2.20 (0.34), residues: 248 sheet: -0.21 (0.18), residues: 804 loop : -0.95 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 229 TYR 0.011 0.001 TYR H 59 PHE 0.015 0.001 PHE E 433 TRP 0.013 0.001 TRP E 333 HIS 0.004 0.000 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00276 (17790) covalent geometry : angle 0.60555 (24210) SS BOND : bond 0.00231 ( 22) SS BOND : angle 1.71215 ( 44) hydrogen bonds : bond 0.03773 ( 538) hydrogen bonds : angle 4.80268 ( 1650) link_BETA1-4 : bond 0.00760 ( 10) link_BETA1-4 : angle 1.83543 ( 30) link_NAG-ASN : bond 0.00670 ( 28) link_NAG-ASN : angle 3.70002 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.636 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: C 77 MET cc_start: 0.2880 (ptt) cc_final: 0.2551 (ttt) REVERT: D 54 ASP cc_start: 0.8598 (m-30) cc_final: 0.8251 (m-30) REVERT: A 386 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7344 (mmtm) REVERT: A 457 TRP cc_start: 0.7345 (p90) cc_final: 0.6980 (p90) REVERT: A 470 TRP cc_start: 0.7081 (p-90) cc_final: 0.6573 (p-90) REVERT: A 474 ASP cc_start: 0.6585 (t0) cc_final: 0.5870 (p0) REVERT: G 77 MET cc_start: 0.2874 (ptt) cc_final: 0.2548 (ttt) REVERT: H 54 ASP cc_start: 0.8478 (m-30) cc_final: 0.8033 (m-30) REVERT: E 457 TRP cc_start: 0.7350 (p90) cc_final: 0.6986 (p90) REVERT: E 470 TRP cc_start: 0.7090 (p-90) cc_final: 0.6569 (p-90) REVERT: E 474 ASP cc_start: 0.6580 (t0) cc_final: 0.5865 (p0) outliers start: 45 outliers final: 41 residues processed: 192 average time/residue: 0.1310 time to fit residues: 38.5382 Evaluate side-chains 196 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 352 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 564 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 177 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN G 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.188705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138316 restraints weight = 28316.852| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 4.68 r_work: 0.3480 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 551 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17850 Z= 0.120 Angle : 0.627 12.007 24368 Z= 0.304 Chirality : 0.044 0.303 2804 Planarity : 0.004 0.034 3044 Dihedral : 6.992 55.832 3090 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.22 % Allowed : 18.74 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 2096 helix: 2.28 (0.34), residues: 248 sheet: -0.18 (0.18), residues: 804 loop : -0.90 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 229 TYR 0.011 0.001 TYR D 59 PHE 0.019 0.001 PHE A 292 TRP 0.013 0.001 TRP E 333 HIS 0.004 0.000 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00278 (17790) covalent geometry : angle 0.58921 (24210) SS BOND : bond 0.00256 ( 22) SS BOND : angle 1.40304 ( 44) hydrogen bonds : bond 0.03701 ( 538) hydrogen bonds : angle 4.71165 ( 1650) link_BETA1-4 : bond 0.00741 ( 10) link_BETA1-4 : angle 1.65483 ( 30) link_NAG-ASN : bond 0.00639 ( 28) link_NAG-ASN : angle 3.44997 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7161.32 seconds wall clock time: 122 minutes 18.50 seconds (7338.50 seconds total)