Starting phenix.real_space_refine on Sat Jul 4 01:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d82_27244/07_2026/8d82_27244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d82_27244/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8d82_27244/07_2026/8d82_27244.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d82_27244/07_2026/8d82_27244.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d82_27244/07_2026/8d82_27244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d82_27244/07_2026/8d82_27244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d82_27244/07_2026/8d82_27244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d82_27244/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 4.15, 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: 1.57 Conformation dependent library (CDL) restraints added in 720.1 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: 0.59 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: 4.23 Time building geometry restraints manager: 2.13 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 - 17.97: 9563 17.97 - 35.94: 709 35.94 - 53.92: 138 53.92 - 71.89: 18 71.89 - 89.86: 28 Dihedral angle restraints: 10456 sinusoidal: 4252 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 10453 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: 0.04 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: 9.150 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 13.461 89.859 6362 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/Z covalent geometry : bond 0.00288 / 0.14 (17790) covalent geometry : angle 0.52397 / 0.27 (24210) SS BOND : bond 0.00139 / 0.09 ( 22) SS BOND : angle 0.51194 / 0.40 ( 44) hydrogen bonds : bond 0.26345 / 18.26 ( 538) hydrogen bonds : angle 9.53119 / 6.54 ( 1650) link_BETA1-4 : bond 0.00453 / 0.30 ( 10) link_BETA1-4 : angle 1.72906 / 1.25 ( 30) link_NAG-ASN : bond 0.00599 / 0.43 ( 28) link_NAG-ASN : angle 2.60800 / 1.70 ( 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 : 0.641 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: 0.1556 time to fit residues: 61.6007 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 : 0.675 ------------------------------------------------------------------------------- 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... C 118 GLN C 162 GLN C 206 GLN C 215 GLN C 239 GLN D 73 ASN 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 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: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.196593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.147206 restraints weight = 28366.399| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.78 r_work: 0.3676 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 542 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 544 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1620 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= 0.130 Angle : 0.562 8.267 24368 Z= 0.281 Chirality : 0.043 0.296 2804 Planarity : 0.004 0.052 3044 Dihedral : 4.597 49.920 2300 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.01 % Allowed : 12.57 % Favored : 85.43 % 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: -1.55 (0.17), residues: 2096 helix: 1.29 (0.34), residues: 242 sheet: -0.90 (0.17), residues: 802 loop : -1.67 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 210 TYR 0.012 0.001 TYR E 513 PHE 0.018 0.002 PHE A 72 TRP 0.007 0.001 TRP E 67 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17790) covalent geometry : angle 0.53907 / 0.28 (24210) SS BOND : bond 0.00713 / 0.43 ( 22) SS BOND : angle 0.64315 / 0.45 ( 44) hydrogen bonds : bond 0.04624 / 3.21 ( 538) hydrogen bonds : angle 6.55472 / 4.52 ( 1650) link_BETA1-4 : bond 0.00677 / 0.45 ( 10) link_BETA1-4 : angle 1.44670 / 1.06 ( 30) link_NAG-ASN : bond 0.00520 / 0.37 ( 28) link_NAG-ASN : angle 2.60931 / 1.74 ( 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 207 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.672 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: 0.3656 (ttt) cc_final: 0.3313 (pmm) REVERT: D 77 MET cc_start: 0.8454 (mtm) cc_final: 0.8112 (mtm) REVERT: D 189 MET cc_start: 0.6818 (tpp) cc_final: 0.6505 (tpt) REVERT: A 557 PHE cc_start: 0.4206 (OUTLIER) cc_final: 0.3653 (p90) REVERT: G 77 MET cc_start: 0.3658 (ttt) cc_final: 0.3314 (pmm) REVERT: H 54 ASP cc_start: 0.8486 (m-30) cc_final: 0.8111 (m-30) REVERT: H 189 MET cc_start: 0.6788 (tpp) cc_final: 0.6376 (tpt) REVERT: E 557 PHE cc_start: 0.4202 (OUTLIER) cc_final: 0.3647 (p90) outliers start: 38 outliers final: 22 residues processed: 197 average time/residue: 0.1280 time to fit residues: 39.7555 Evaluate side-chains 178 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 0.9980 chunk 96 optimal weight: 0.0050 chunk 48 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 124 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 162 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN E 393 ASN ** E 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.195030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.145386 restraints weight = 28935.729| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 3.86 r_work: 0.3647 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 544 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 544 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2050 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= 0.109 Angle : 0.548 8.803 24368 Z= 0.271 Chirality : 0.042 0.308 2804 Planarity : 0.004 0.038 3044 Dihedral : 4.619 51.785 2298 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.43 % Allowed : 14.41 % Favored : 83.16 % 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: -1.09 (0.18), residues: 2096 helix: 1.67 (0.34), residues: 246 sheet: -0.56 (0.18), residues: 790 loop : -1.42 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 210 TYR 0.021 0.001 TYR E 513 PHE 0.013 0.001 PHE E 72 TRP 0.005 0.001 TRP C 268 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17790) covalent geometry : angle 0.52523 / 0.27 (24210) SS BOND : bond 0.00357 / 0.22 ( 22) SS BOND : angle 0.82101 / 0.50 ( 44) hydrogen bonds : bond 0.03853 / 2.68 ( 538) hydrogen bonds : angle 5.66803 / 3.91 ( 1650) link_BETA1-4 : bond 0.00574 / 0.38 ( 10) link_BETA1-4 : angle 1.41367 / 1.03 ( 30) link_NAG-ASN : bond 0.00584 / 0.41 ( 28) link_NAG-ASN : angle 2.58207 / 1.72 ( 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 215 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.678 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: 0.8523 (mtm) cc_final: 0.8201 (mtm) REVERT: D 189 MET cc_start: 0.7095 (tpp) cc_final: 0.6806 (tpt) REVERT: A 386 LYS cc_start: 0.7604 (mmmm) cc_final: 0.6849 (mmtm) REVERT: A 499 VAL cc_start: 0.6697 (t) cc_final: 0.6436 (p) REVERT: A 557 PHE cc_start: 0.4241 (OUTLIER) cc_final: 0.3642 (p90) REVERT: H 54 ASP cc_start: 0.8508 (m-30) cc_final: 0.8179 (m-30) REVERT: H 189 MET cc_start: 0.7099 (tpp) cc_final: 0.6698 (tpt) REVERT: E 499 VAL cc_start: 0.6672 (t) cc_final: 0.6415 (p) REVERT: E 557 PHE cc_start: 0.4238 (OUTLIER) cc_final: 0.3642 (p90) outliers start: 46 outliers final: 33 residues processed: 203 average time/residue: 0.1271 time to fit residues: 40.6426 Evaluate side-chains 193 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 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 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 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 283 SER 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: 30.0000 chunk 5 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN E 393 ASN ** E 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.194312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144626 restraints weight = 28949.104| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.69 r_work: 0.3633 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 544 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 548 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17850 Z= 0.098 Angle : 0.537 9.278 24368 Z= 0.261 Chirality : 0.042 0.310 2804 Planarity : 0.003 0.036 3044 Dihedral : 4.638 52.592 2298 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.75 % Allowed : 14.68 % Favored : 82.58 % 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: -0.78 (0.18), residues: 2096 helix: 1.96 (0.35), residues: 246 sheet: -0.36 (0.18), residues: 788 loop : -1.23 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 210 TYR 0.016 0.001 TYR A 492 PHE 0.014 0.001 PHE A 108 TRP 0.007 0.001 TRP A 269 HIS 0.003 0.000 HIS G 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (17790) covalent geometry : angle 0.51175 / 0.26 (24210) SS BOND : bond 0.00254 / 0.17 ( 22) SS BOND : angle 0.72498 / 0.50 ( 44) hydrogen bonds : bond 0.03348 / 2.32 ( 538) hydrogen bonds : angle 5.27392 / 3.65 ( 1650) link_BETA1-4 : bond 0.00586 / 0.38 ( 10) link_BETA1-4 : angle 1.39357 / 1.01 ( 30) link_NAG-ASN : bond 0.00593 / 0.41 ( 28) link_NAG-ASN : angle 2.66309 / 1.83 ( 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 210 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.673 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: 0.8520 (mtm) cc_final: 0.8169 (mtm) REVERT: D 189 MET cc_start: 0.7090 (tpp) cc_final: 0.6823 (tpt) REVERT: A 557 PHE cc_start: 0.4172 (OUTLIER) cc_final: 0.3654 (p90) REVERT: H 77 MET cc_start: 0.8502 (mtm) cc_final: 0.8228 (mtm) REVERT: H 189 MET cc_start: 0.7066 (tpp) cc_final: 0.6694 (tpt) REVERT: E 557 PHE cc_start: 0.4169 (OUTLIER) cc_final: 0.3650 (p90) outliers start: 52 outliers final: 33 residues processed: 198 average time/residue: 0.1299 time to fit residues: 40.3476 Evaluate side-chains 182 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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: 1.9990 chunk 24 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 GLN D 45 GLN A 226 HIS A 348 GLN G 87 GLN E 226 HIS E 348 GLN E 393 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.187005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135849 restraints weight = 28230.936| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.43 r_work: 0.3509 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 548 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17850 Z= 0.218 Angle : 0.706 12.411 24368 Z= 0.350 Chirality : 0.049 0.316 2804 Planarity : 0.005 0.040 3044 Dihedral : 5.426 55.873 2296 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.33 % Allowed : 16.47 % Favored : 80.20 % 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: -0.92 (0.18), residues: 2096 helix: 1.67 (0.34), residues: 248 sheet: -0.36 (0.17), residues: 798 loop : -1.36 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 210 TYR 0.026 0.002 TYR D 59 PHE 0.028 0.003 PHE A 91 TRP 0.015 0.001 TRP C 244 HIS 0.008 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (17790) covalent geometry : angle 0.67909 / 0.34 (24210) SS BOND : bond 0.00508 / 0.35 ( 22) SS BOND : angle 1.35450 / 0.94 ( 44) hydrogen bonds : bond 0.05082 / 3.54 ( 538) hydrogen bonds : angle 5.37237 / 3.75 ( 1650) link_BETA1-4 : bond 0.00586 / 0.39 ( 10) link_BETA1-4 : angle 1.26649 / 0.90 ( 30) link_NAG-ASN : bond 0.00660 / 0.42 ( 28) link_NAG-ASN : angle 3.18971 / 2.12 ( 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 227 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.656 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: 0.8677 (m-30) cc_final: 0.8321 (m-30) REVERT: D 77 MET cc_start: 0.8658 (mtm) cc_final: 0.8319 (mtt) REVERT: A 470 TRP cc_start: 0.7269 (p-90) cc_final: 0.6908 (p-90) REVERT: H 54 ASP cc_start: 0.8542 (m-30) cc_final: 0.8161 (m-30) REVERT: H 77 MET cc_start: 0.8711 (mtm) cc_final: 0.8347 (mtm) REVERT: E 470 TRP cc_start: 0.7273 (p-90) cc_final: 0.6915 (p-90) outliers start: 63 outliers final: 51 residues processed: 211 average time/residue: 0.1295 time to fit residues: 42.8530 Evaluate side-chains 196 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 D residue 212 MET 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 344 TYR 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 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 H residue 212 MET Chi-restraints excluded: chain E residue 49 VAL 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 344 TYR 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 564 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 15 optimal weight: 0.0770 chunk 150 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 5 optimal weight: 40.0000 chunk 37 optimal weight: 0.3980 chunk 138 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN E 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.189731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140531 restraints weight = 27783.473| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.39 r_work: 0.3573 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 549 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 550 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17850 Z= 0.106 Angle : 0.588 10.906 24368 Z= 0.290 Chirality : 0.043 0.304 2804 Planarity : 0.003 0.036 3044 Dihedral : 5.199 58.993 2296 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.27 % Allowed : 18.43 % Favored : 79.30 % 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: -0.70 (0.18), residues: 2096 helix: 1.97 (0.34), residues: 248 sheet: -0.27 (0.18), residues: 794 loop : -1.19 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 229 TYR 0.014 0.001 TYR A 492 PHE 0.011 0.001 PHE G 161 TRP 0.010 0.001 TRP A 333 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (17790) covalent geometry : angle 0.55781 / 0.28 (24210) SS BOND : bond 0.00182 / 0.12 ( 22) SS BOND : angle 1.08621 / 0.68 ( 44) hydrogen bonds : bond 0.03676 / 2.56 ( 538) hydrogen bonds : angle 5.04624 / 3.50 ( 1650) link_BETA1-4 : bond 0.00596 / 0.39 ( 10) link_BETA1-4 : angle 1.36909 / 1.00 ( 30) link_NAG-ASN : bond 0.00656 / 0.45 ( 28) link_NAG-ASN : angle 3.07476 / 2.01 ( 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 202 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.680 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: 0.8566 (m-30) cc_final: 0.8196 (m-30) REVERT: D 77 MET cc_start: 0.8503 (mtm) cc_final: 0.8210 (mtm) REVERT: D 196 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8155 (ttp80) REVERT: A 470 TRP cc_start: 0.7271 (p-90) cc_final: 0.6840 (p-90) REVERT: H 54 ASP cc_start: 0.8466 (m-30) cc_final: 0.8068 (m-30) REVERT: H 77 MET cc_start: 0.8554 (mtm) cc_final: 0.8183 (mtm) REVERT: H 196 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8182 (ttp80) REVERT: E 470 TRP cc_start: 0.7273 (p-90) cc_final: 0.6843 (p-90) outliers start: 43 outliers final: 33 residues processed: 188 average time/residue: 0.1325 time to fit residues: 38.5240 Evaluate side-chains 181 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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 205 THR Chi-restraints excluded: chain E residue 54 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 83 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.186883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136253 restraints weight = 28278.245| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 4.21 r_work: 0.3511 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 550 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 550 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17850 Z= 0.181 Angle : 0.655 11.566 24368 Z= 0.328 Chirality : 0.046 0.304 2804 Planarity : 0.004 0.034 3044 Dihedral : 5.459 59.285 2296 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.90 % Allowed : 18.37 % Favored : 78.72 % 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: -0.70 (0.18), residues: 2096 helix: 1.97 (0.34), residues: 248 sheet: -0.33 (0.18), residues: 798 loop : -1.14 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 281 TYR 0.019 0.001 TYR A 492 PHE 0.020 0.002 PHE A 91 TRP 0.011 0.001 TRP E 333 HIS 0.006 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (17790) covalent geometry : angle 0.62416 / 0.32 (24210) SS BOND : bond 0.00311 / 0.21 ( 22) SS BOND : angle 1.35522 / 0.79 ( 44) hydrogen bonds : bond 0.04687 / 3.28 ( 538) hydrogen bonds : angle 5.05228 / 3.52 ( 1650) link_BETA1-4 : bond 0.00641 / 0.44 ( 10) link_BETA1-4 : angle 1.25853 / 0.91 ( 30) link_NAG-ASN : bond 0.00570 / 0.40 ( 28) link_NAG-ASN : angle 3.25722 / 2.19 ( 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: 55 poor density : 152 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: D 54 ASP cc_start: 0.8647 (m-30) cc_final: 0.8311 (m-30) REVERT: D 77 MET cc_start: 0.8594 (mtm) cc_final: 0.8229 (mtm) REVERT: A 155 GLU cc_start: 0.8059 (pp20) cc_final: 0.7789 (pp20) REVERT: A 470 TRP cc_start: 0.7280 (p-90) cc_final: 0.6818 (p-90) REVERT: A 474 ASP cc_start: 0.6784 (t0) cc_final: 0.6022 (p0) REVERT: A 481 TYR cc_start: 0.7365 (p90) cc_final: 0.7127 (p90) REVERT: H 77 MET cc_start: 0.8580 (mtm) cc_final: 0.8169 (mtm) REVERT: E 155 GLU cc_start: 0.8057 (pp20) cc_final: 0.7784 (pp20) REVERT: E 470 TRP cc_start: 0.7288 (p-90) cc_final: 0.6827 (p-90) REVERT: E 474 ASP cc_start: 0.6782 (t0) cc_final: 0.6020 (p0) REVERT: E 481 TYR cc_start: 0.7368 (p90) cc_final: 0.7129 (p90) outliers start: 55 outliers final: 40 residues processed: 191 average time/residue: 0.1296 time to fit residues: 39.0805 Evaluate side-chains 185 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 D residue 212 MET 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 344 TYR 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 205 THR 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 292 PHE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 344 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 189 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 60 optimal weight: 0.0070 chunk 160 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.188418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.138853 restraints weight = 27714.177| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.75 r_work: 0.3532 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 550 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3519 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= 0.115 Angle : 0.629 11.751 24368 Z= 0.307 Chirality : 0.045 0.309 2804 Planarity : 0.004 0.034 3044 Dihedral : 5.342 58.494 2296 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.64 % Allowed : 19.11 % Favored : 78.25 % 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: -0.52 (0.18), residues: 2096 helix: 2.10 (0.34), residues: 248 sheet: -0.23 (0.18), residues: 798 loop : -1.00 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 210 TYR 0.016 0.001 TYR A 492 PHE 0.012 0.001 PHE E 332 TRP 0.011 0.001 TRP A 333 HIS 0.004 0.000 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17790) covalent geometry : angle 0.59381 / 0.30 (24210) SS BOND : bond 0.00206 / 0.13 ( 22) SS BOND : angle 1.47358 / 0.95 ( 44) hydrogen bonds : bond 0.03843 / 2.68 ( 538) hydrogen bonds : angle 4.89973 / 3.41 ( 1650) link_BETA1-4 : bond 0.00598 / 0.40 ( 10) link_BETA1-4 : angle 1.39514 / 1.03 ( 30) link_NAG-ASN : bond 0.00645 / 0.44 ( 28) link_NAG-ASN : angle 3.37522 / 2.29 ( 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 198 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.593 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: 0.8591 (m-30) cc_final: 0.8265 (m-30) REVERT: A 155 GLU cc_start: 0.8083 (pp20) cc_final: 0.7841 (pp20) REVERT: A 470 TRP cc_start: 0.7345 (p-90) cc_final: 0.6928 (p-90) REVERT: A 481 TYR cc_start: 0.7384 (p90) cc_final: 0.7142 (p90) REVERT: H 77 MET cc_start: 0.8619 (mtm) cc_final: 0.8224 (mtm) REVERT: E 155 GLU cc_start: 0.8078 (pp20) cc_final: 0.7836 (pp20) REVERT: E 470 TRP cc_start: 0.7350 (p-90) cc_final: 0.6932 (p-90) outliers start: 50 outliers final: 41 residues processed: 181 average time/residue: 0.1314 time to fit residues: 37.3306 Evaluate side-chains 185 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 311 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 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 TYR 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 202 PHE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain H residue 166 THR 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 344 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 GLN G 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.189104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.138454 restraints weight = 28238.802| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 4.18 r_work: 0.3544 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3604 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= 0.125 Angle : 0.644 13.018 24368 Z= 0.317 Chirality : 0.045 0.399 2804 Planarity : 0.004 0.034 3044 Dihedral : 5.364 58.054 2296 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.27 % Allowed : 18.85 % Favored : 78.88 % 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: -0.48 (0.18), residues: 2096 helix: 2.15 (0.34), residues: 248 sheet: -0.18 (0.18), residues: 798 loop : -1.00 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 229 TYR 0.014 0.001 TYR A 492 PHE 0.016 0.001 PHE E 433 TRP 0.011 0.001 TRP E 333 HIS 0.004 0.000 HIS H 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (17790) covalent geometry : angle 0.60434 / 0.31 (24210) SS BOND : bond 0.00232 / 0.15 ( 22) SS BOND : angle 1.60990 / 1.09 ( 44) hydrogen bonds : bond 0.03904 / 2.72 ( 538) hydrogen bonds : angle 4.87046 / 3.39 ( 1650) link_BETA1-4 : bond 0.00585 / 0.39 ( 10) link_BETA1-4 : angle 1.36493 / 1.01 ( 30) link_NAG-ASN : bond 0.00628 / 0.45 ( 28) link_NAG-ASN : angle 3.62737 / 2.50 ( 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 194 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.694 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: 0.8602 (m-30) cc_final: 0.8246 (m-30) REVERT: D 77 MET cc_start: 0.8556 (mtm) cc_final: 0.8293 (mtm) REVERT: A 155 GLU cc_start: 0.8049 (pp20) cc_final: 0.7828 (pp20) REVERT: A 457 TRP cc_start: 0.7368 (p90) cc_final: 0.6959 (p90) REVERT: A 470 TRP cc_start: 0.7245 (p-90) cc_final: 0.6703 (p-90) REVERT: A 481 TYR cc_start: 0.7328 (p90) cc_final: 0.7118 (p90) REVERT: H 54 ASP cc_start: 0.8513 (m-30) cc_final: 0.8090 (m-30) REVERT: E 155 GLU cc_start: 0.8039 (pp20) cc_final: 0.7815 (pp20) REVERT: E 457 TRP cc_start: 0.7367 (p90) cc_final: 0.6959 (p90) REVERT: E 470 TRP cc_start: 0.7249 (p-90) cc_final: 0.6706 (p-90) REVERT: E 481 TYR cc_start: 0.7327 (p90) cc_final: 0.7116 (p90) outliers start: 43 outliers final: 39 residues processed: 180 average time/residue: 0.1346 time to fit residues: 37.7348 Evaluate side-chains 188 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS 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 263 THR Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 TYR 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 202 PHE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 166 THR 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 344 TYR 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: 30.0000 chunk 183 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 78 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 1 optimal weight: 50.0000 chunk 81 optimal weight: 7.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 56 GLN A 437 ASN E 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.186427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.135038 restraints weight = 28148.024| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.91 r_work: 0.3501 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | 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: 552 | |-----------------------------------------------------------------------------| |-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: 552 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17850 Z= 0.180 Angle : 0.690 14.176 24368 Z= 0.343 Chirality : 0.047 0.307 2804 Planarity : 0.004 0.035 3044 Dihedral : 5.598 57.251 2296 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.38 % Allowed : 18.69 % Favored : 78.93 % 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: -0.59 (0.18), residues: 2096 helix: 2.05 (0.33), residues: 248 sheet: -0.26 (0.18), residues: 802 loop : -1.08 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 229 TYR 0.013 0.001 TYR H 59 PHE 0.018 0.002 PHE E 91 TRP 0.014 0.001 TRP E 333 HIS 0.006 0.001 HIS H 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (17790) covalent geometry : angle 0.65151 / 0.33 (24210) SS BOND : bond 0.00254 / 0.17 ( 22) SS BOND : angle 1.85814 / 1.24 ( 44) hydrogen bonds : bond 0.04651 / 3.25 ( 538) hydrogen bonds : angle 4.95981 / 3.47 ( 1650) link_BETA1-4 : bond 0.00618 / 0.41 ( 10) link_BETA1-4 : angle 1.35253 / 0.99 ( 30) link_NAG-ASN : bond 0.00678 / 0.45 ( 28) link_NAG-ASN : angle 3.65711 / 2.50 ( 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 199 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.609 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: D 54 ASP cc_start: 0.8660 (m-30) cc_final: 0.8322 (m-30) REVERT: D 77 MET cc_start: 0.8693 (mtm) cc_final: 0.8446 (mtm) REVERT: A 457 TRP cc_start: 0.7444 (p90) cc_final: 0.7080 (p90) REVERT: A 470 TRP cc_start: 0.7274 (p-90) cc_final: 0.6713 (p-90) REVERT: A 474 ASP cc_start: 0.6805 (t0) cc_final: 0.6042 (p0) REVERT: H 54 ASP cc_start: 0.8565 (m-30) cc_final: 0.8166 (m-30) REVERT: H 77 MET cc_start: 0.8601 (mtm) cc_final: 0.8318 (mtm) REVERT: E 457 TRP cc_start: 0.7445 (p90) cc_final: 0.7080 (p90) REVERT: E 470 TRP cc_start: 0.7262 (p-90) cc_final: 0.6708 (p-90) REVERT: E 474 ASP cc_start: 0.6809 (t0) cc_final: 0.6040 (p0) outliers start: 45 outliers final: 41 residues processed: 185 average time/residue: 0.1323 time to fit residues: 37.8033 Evaluate side-chains 192 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 HIS 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 263 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 TYR 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 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 263 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 344 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 153 optimal weight: 0.0030 chunk 127 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 148 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.188066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.138380 restraints weight = 27722.476| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.81 r_work: 0.3524 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- 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: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 554 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17850 Z= 0.119 Angle : 0.644 12.753 24368 Z= 0.319 Chirality : 0.044 0.310 2804 Planarity : 0.004 0.036 3044 Dihedral : 5.178 56.744 2292 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.11 % Allowed : 19.38 % Favored : 78.51 % 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: -0.48 (0.18), residues: 2096 helix: 2.18 (0.33), residues: 248 sheet: -0.25 (0.18), residues: 802 loop : -0.96 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 229 TYR 0.011 0.001 TYR E 492 PHE 0.017 0.001 PHE A 292 TRP 0.023 0.001 TRP A 333 HIS 0.003 0.000 HIS H 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17790) covalent geometry : angle 0.60779 / 0.31 (24210) SS BOND : bond 0.00221 / 0.14 ( 22) SS BOND : angle 1.37932 / 0.89 ( 44) hydrogen bonds : bond 0.03963 / 2.77 ( 538) hydrogen bonds : angle 4.84522 / 3.40 ( 1650) link_BETA1-4 : bond 0.00596 / 0.39 ( 10) link_BETA1-4 : angle 1.37916 / 1.02 ( 30) link_NAG-ASN : bond 0.00662 / 0.46 ( 28) link_NAG-ASN : angle 3.49252 / 2.40 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7667.85 seconds wall clock time: 131 minutes 18.14 seconds (7878.14 seconds total)