Starting phenix.real_space_refine on Thu Feb 5 07:32:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwk_26834/02_2026/7uwk_26834.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwk_26834/02_2026/7uwk_26834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uwk_26834/02_2026/7uwk_26834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwk_26834/02_2026/7uwk_26834.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uwk_26834/02_2026/7uwk_26834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwk_26834/02_2026/7uwk_26834.map" } resolution = 4.4 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= 0.009 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 149 5.16 5 C 10088 2.51 5 N 2882 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16064 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1899 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1804 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 220} Chain breaks: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1917 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 232} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 808 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1879 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 228} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 778 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1875 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 227} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 803 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1944 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 234} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.12, per 1000 atoms: 0.19 Number of scatterers: 16064 At special positions: 0 Unit cell: (214.704, 127.8, 144.84, 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 149 16.00 O 2945 8.00 N 2882 7.00 C 10088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 102 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 102 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 261 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 170 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 102 " distance=2.04 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 99 " distance=2.04 Simple disulfide: pdb=" SG CYS I 162 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 187 " - pdb=" SG CYS I 271 " distance=2.03 Simple disulfide: pdb=" SG CYS I 257 " - pdb=" SG CYS I 261 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 168 " distance=2.04 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 170 " distance=2.03 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 102 " distance=2.04 Simple disulfide: pdb=" SG CYS K 87 " - pdb=" SG CYS K 99 " distance=2.03 Simple disulfide: pdb=" SG CYS K 162 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 187 " - pdb=" SG CYS K 271 " distance=2.03 Simple disulfide: pdb=" SG CYS K 257 " - pdb=" SG CYS K 261 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 170 " distance=2.03 Simple disulfide: pdb=" SG CYS J 24 " - pdb=" SG CYS J 102 " distance=2.04 Simple disulfide: pdb=" SG CYS J 87 " - pdb=" SG CYS J 99 " distance=2.03 Simple disulfide: pdb=" SG CYS J 162 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 187 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 257 " - pdb=" SG CYS J 261 " distance=2.03 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 168 " distance=2.04 Simple disulfide: pdb=" SG CYS H 115 " - pdb=" SG CYS H 170 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 102 " distance=2.03 Simple disulfide: pdb=" SG CYS L 87 " - pdb=" SG CYS L 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 162 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 187 " - pdb=" SG CYS L 271 " distance=2.03 Simple disulfide: pdb=" SG CYS L 257 " - pdb=" SG CYS L 261 " 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 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 829.6 milliseconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3844 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 50 sheets defined 4.8% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.661A pdb=" N MET C 35 " --> pdb=" O PRO C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.534A pdb=" N LEU C 80 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 removed outlier: 4.391A pdb=" N TYR C 169 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.928A pdb=" N CYS C 261 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 257 through 261 removed outlier: 4.028A pdb=" N CYS D 261 " --> pdb=" O GLY D 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 36 Processing helix chain 'I' and resid 170 through 176 removed outlier: 3.613A pdb=" N ALA I 176 " --> pdb=" O LYS I 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 36 Processing helix chain 'K' and resid 170 through 175 Processing helix chain 'J' and resid 31 through 36 removed outlier: 3.685A pdb=" N MET J 35 " --> pdb=" O PRO J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 168 removed outlier: 3.702A pdb=" N LYS J 168 " --> pdb=" O HIS J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 176 Processing helix chain 'L' and resid 31 through 36 Processing helix chain 'L' and resid 76 through 80 removed outlier: 3.517A pdb=" N LEU L 80 " --> pdb=" O SER L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 176 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 96 removed outlier: 3.621A pdb=" N HIS A 107 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 141 removed outlier: 6.296A pdb=" N ASN A 129 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS A 170 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU A 131 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 168 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 133 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 158 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 26 removed outlier: 4.010A pdb=" N GLN C 23 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN C 103 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 25 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 101 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS C 102 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 137 " --> pdb=" O CYS C 87 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET C 153 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 54 removed outlier: 3.701A pdb=" N LEU C 65 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE C 64 " --> pdb=" O PRO C 127 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET C 66 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 125 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.575A pdb=" N VAL C 235 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 221 through 223 removed outlier: 3.762A pdb=" N VAL C 222 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR C 207 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 263 through 264 removed outlier: 6.573A pdb=" N ARG C 263 " --> pdb=" O MET B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.552A pdb=" N LEU B 105 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.840A pdb=" N GLU B 131 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 169 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.657A pdb=" N HIS B 135 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 164 " --> pdb=" O HIS B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 26 removed outlier: 4.244A pdb=" N GLY D 25 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 101 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 83 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS D 139 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 91 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL D 133 " --> pdb=" O LYS D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.588A pdb=" N ASP D 47 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 53 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.588A pdb=" N ASP D 47 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE D 64 " --> pdb=" O PRO D 127 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET D 66 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 125 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP D 70 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE D 121 " --> pdb=" O TRP D 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 235 through 236 removed outlier: 7.013A pdb=" N ALA D 186 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 216 through 218 removed outlier: 3.640A pdb=" N ILE D 217 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE D 211 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 251 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 96 removed outlier: 4.268A pdb=" N ARG E 91 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 109 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU E 93 " --> pdb=" O HIS E 107 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS E 107 " --> pdb=" O GLU E 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP E 95 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 105 " --> pdb=" O ASP E 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 138 removed outlier: 3.883A pdb=" N ALA E 167 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS E 135 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N SER E 165 " --> pdb=" O HIS E 135 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN E 137 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG E 163 " --> pdb=" O GLN E 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 175 through 176 Processing sheet with id=AC3, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.806A pdb=" N GLY I 25 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 88 " --> pdb=" O SER I 98 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL I 100 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA I 83 " --> pdb=" O ILE I 141 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS I 85 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS I 139 " --> pdb=" O LYS I 85 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR I 89 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE I 135 " --> pdb=" O THR I 89 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL I 133 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE I 136 " --> pdb=" O VAL I 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 45 through 52 removed outlier: 3.550A pdb=" N ASP I 47 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR I 123 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP I 70 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE I 121 " --> pdb=" O TRP I 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 235 through 238 removed outlier: 3.525A pdb=" N VAL I 196 " --> pdb=" O VAL I 235 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 216 through 223 removed outlier: 4.409A pdb=" N GLY I 218 " --> pdb=" O ILE I 211 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE I 211 " --> pdb=" O GLY I 218 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER I 220 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA I 209 " --> pdb=" O SER I 220 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG I 206 " --> pdb=" O TYR I 253 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET I 208 " --> pdb=" O THR I 251 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR I 251 " --> pdb=" O MET I 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU I 250 " --> pdb=" O HIS I 264 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS I 264 " --> pdb=" O LEU I 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 93 removed outlier: 3.502A pdb=" N ARG G 109 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU G 93 " --> pdb=" O HIS G 107 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS G 107 " --> pdb=" O GLU G 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 129 through 131 removed outlier: 3.552A pdb=" N GLU G 131 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G 169 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 134 through 136 removed outlier: 3.686A pdb=" N HIS G 135 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL G 164 " --> pdb=" O HIS G 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 139 through 141 removed outlier: 3.737A pdb=" N ARG G 160 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 25 through 26 removed outlier: 4.191A pdb=" N GLY K 25 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG K 101 " --> pdb=" O GLY K 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'K' and resid 47 through 54 removed outlier: 3.516A pdb=" N TRP K 70 " --> pdb=" O PHE K 121 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE K 121 " --> pdb=" O TRP K 70 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 95 through 97 removed outlier: 3.532A pdb=" N ALA K 83 " --> pdb=" O ILE K 141 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET K 153 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 235 through 238 removed outlier: 3.867A pdb=" N VAL K 269 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 206 through 207 removed outlier: 4.886A pdb=" N TYR K 207 " --> pdb=" O VAL K 222 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL K 222 " --> pdb=" O TYR K 207 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'K' and resid 210 through 212 removed outlier: 3.548A pdb=" N LEU K 210 " --> pdb=" O GLN K 249 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 92 through 96 removed outlier: 3.570A pdb=" N HIS F 107 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU F 105 " --> pdb=" O ASP F 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AE1, first strand: chain 'F' and resid 129 through 137 removed outlier: 3.879A pdb=" N ASN F 129 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA F 167 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS F 135 " --> pdb=" O SER F 165 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER F 165 " --> pdb=" O HIS F 135 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN F 137 " --> pdb=" O ARG F 163 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG F 163 " --> pdb=" O GLN F 137 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 175 through 176 Processing sheet with id=AE3, first strand: chain 'J' and resid 22 through 25 removed outlier: 4.648A pdb=" N GLY J 25 " --> pdb=" O ARG J 101 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG J 101 " --> pdb=" O GLY J 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 45 through 54 Processing sheet with id=AE5, first strand: chain 'J' and resid 95 through 96 removed outlier: 3.874A pdb=" N LYS J 91 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL J 133 " --> pdb=" O LYS J 91 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 187 through 188 Processing sheet with id=AE7, first strand: chain 'J' and resid 193 through 199 Processing sheet with id=AE8, first strand: chain 'J' and resid 216 through 223 removed outlier: 3.839A pdb=" N GLY J 218 " --> pdb=" O ILE J 211 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 129 through 137 removed outlier: 3.944A pdb=" N ALA H 167 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N HIS H 135 " --> pdb=" O SER H 165 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER H 165 " --> pdb=" O HIS H 135 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN H 137 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG H 163 " --> pdb=" O GLN H 137 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 22 through 25 removed outlier: 3.690A pdb=" N GLN L 23 " --> pdb=" O ASN L 103 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN L 103 " --> pdb=" O GLN L 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY L 25 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG L 101 " --> pdb=" O GLY L 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 47 through 54 removed outlier: 3.828A pdb=" N ASP L 47 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP L 70 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE L 121 " --> pdb=" O TRP L 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 95 through 97 removed outlier: 3.522A pdb=" N SER L 96 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY L 90 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 136 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL L 155 " --> pdb=" O ILE L 136 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 235 through 238 removed outlier: 6.388A pdb=" N THR L 193 " --> pdb=" O LYS L 189 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA L 186 " --> pdb=" O VAL L 269 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 216 through 223 removed outlier: 3.599A pdb=" N GLY L 218 " --> pdb=" O ILE L 211 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5288 1.35 - 1.47: 3878 1.47 - 1.59: 7076 1.59 - 1.71: 0 1.71 - 1.83: 197 Bond restraints: 16439 Sorted by residual: bond pdb=" C THR D 158 " pdb=" N SER D 159 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.46e-02 4.69e+03 1.63e+01 bond pdb=" C THR C 158 " pdb=" N SER C 159 " ideal model delta sigma weight residual 1.331 1.369 -0.038 2.07e-02 2.33e+03 3.43e+00 bond pdb=" CB PRO L 202 " pdb=" CG PRO L 202 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.85e+00 bond pdb=" C THR I 89 " pdb=" N GLY I 90 " ideal model delta sigma weight residual 1.332 1.322 0.010 6.60e-03 2.30e+04 2.42e+00 bond pdb=" CB PRO E 144 " pdb=" CG PRO E 144 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.20e+00 ... (remaining 16434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 21681 2.19 - 4.37: 550 4.37 - 6.56: 58 6.56 - 8.75: 14 8.75 - 10.93: 2 Bond angle restraints: 22305 Sorted by residual: angle pdb=" C TYR D 253 " pdb=" N PHE D 254 " pdb=" CA PHE D 254 " ideal model delta sigma weight residual 120.51 111.96 8.55 1.45e+00 4.76e-01 3.48e+01 angle pdb=" C THR J 158 " pdb=" N SER J 159 " pdb=" CA SER J 159 " ideal model delta sigma weight residual 121.48 132.41 -10.93 2.04e+00 2.40e-01 2.87e+01 angle pdb=" C PRO D 252 " pdb=" N TYR D 253 " pdb=" CA TYR D 253 " ideal model delta sigma weight residual 123.04 115.49 7.55 1.59e+00 3.96e-01 2.26e+01 angle pdb=" N ASN H 83 " pdb=" CA ASN H 83 " pdb=" C ASN H 83 " ideal model delta sigma weight residual 113.17 107.98 5.19 1.26e+00 6.30e-01 1.70e+01 angle pdb=" C LYS K 91 " pdb=" N SER K 92 " pdb=" CA SER K 92 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 ... (remaining 22300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 8961 14.89 - 29.78: 792 29.78 - 44.66: 221 44.66 - 59.55: 30 59.55 - 74.44: 17 Dihedral angle restraints: 10021 sinusoidal: 4067 harmonic: 5954 Sorted by residual: dihedral pdb=" CB CYS K 87 " pdb=" SG CYS K 87 " pdb=" SG CYS K 99 " pdb=" CB CYS K 99 " ideal model delta sinusoidal sigma weight residual -86.00 -11.56 -74.44 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS J 87 " pdb=" SG CYS J 87 " pdb=" SG CYS J 99 " pdb=" CB CYS J 99 " ideal model delta sinusoidal sigma weight residual -86.00 -18.49 -67.51 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS I 187 " pdb=" SG CYS I 187 " pdb=" SG CYS I 271 " pdb=" CB CYS I 271 " ideal model delta sinusoidal sigma weight residual 93.00 159.25 -66.25 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 10018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1502 0.033 - 0.066: 594 0.066 - 0.098: 240 0.098 - 0.131: 129 0.131 - 0.164: 17 Chirality restraints: 2482 Sorted by residual: chirality pdb=" CG LEU H 101 " pdb=" CB LEU H 101 " pdb=" CD1 LEU H 101 " pdb=" CD2 LEU H 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CB ILE K 136 " pdb=" CA ILE K 136 " pdb=" CG1 ILE K 136 " pdb=" CG2 ILE K 136 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB VAL D 269 " pdb=" CA VAL D 269 " pdb=" CG1 VAL D 269 " pdb=" CG2 VAL D 269 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2479 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 201 " 0.074 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO L 202 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO L 202 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO L 202 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 143 " -0.059 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO E 144 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO E 144 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 144 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 201 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO C 202 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 202 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 202 " -0.039 5.00e-02 4.00e+02 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 481 2.68 - 3.24: 15051 3.24 - 3.79: 23705 3.79 - 4.35: 30119 4.35 - 4.90: 47937 Nonbonded interactions: 117293 Sorted by model distance: nonbonded pdb=" NH1 ARG J 49 " pdb=" O VAL J 50 " model vdw 2.131 3.120 nonbonded pdb=" NH1 ARG C 49 " pdb=" O VAL C 50 " model vdw 2.134 3.120 nonbonded pdb=" OG1 THR C 112 " pdb=" O GLY C 117 " model vdw 2.139 3.040 nonbonded pdb=" NH1 ARG I 49 " pdb=" O VAL I 50 " model vdw 2.161 3.120 nonbonded pdb=" ND1 HIS H 114 " pdb=" O GLY H 128 " model vdw 2.168 3.120 ... (remaining 117288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 82 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 through 150 or (resid 151 through 152 a \ nd (name N or name CA or name C or name O or name CB )) or resid 153 through 177 \ )) selection = (chain 'B' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 150 or (resid 151 through 152 and \ (name N or name CA or name C or name O or name CB )) or resid 153 through 173 or \ (resid 174 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 5 through 177)) selection = (chain 'E' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 150 or (resid 151 \ through 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 173 or (resid 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 through 177)) selection = (chain 'F' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 151 or (resid 152 \ and (name N or name CA or name C or name O or name CB )) or resid 153 through 17 \ 3 or (resid 174 and (name N or name CA or name C or name O or name CB )) or resi \ d 175 through 177)) selection = (chain 'G' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 150 or (resid 151 \ through 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 173 or (resid 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 through 177)) selection = (chain 'H' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 150 or (resid 151 \ through 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 173 or (resid 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 through 177)) } ncs_group { reference = (chain 'C' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 53 or (resid 54 an \ d (name N or name CA or name C or name O or name CB )) or resid 55 through 74 or \ resid 77 through 142 or (resid 143 through 144 and (name N or name CA or name C \ or name O or name CB )) or resid 145 through 162 or (resid 163 and (name N or n \ ame CA or name C or name O or name CB )) or resid 164 through 188 or resid 194 t \ hrough 200 or resid 205 through 214 or (resid 215 through 217 and (name N or nam \ e CA or name C or name O or name CB )) or resid 218 through 224 or resid 227 thr \ ough 239 or resid 245 through 258 or (resid 259 and (name N or name CA or name C \ or name O or name CB )) or resid 260 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 270)) selection = (chain 'D' and (resid 19 through 52 or (resid 53 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 62 or (resid 63 and (na \ me N or name CA or name C or name O or name CB )) or resid 64 through 74 or resi \ d 77 through 117 or (resid 118 and (name N or name CA or name C or name O or nam \ e CB )) or resid 119 through 142 or (resid 143 through 144 and (name N or name C \ A or name C or name O or name CB )) or resid 145 through 148 or resid 151 throug \ h 214 or (resid 215 through 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 239 or resid 245 through 249 or (resid 250 and (na \ me N or name CA or name C or name O or name CB )) or resid 251 through 258 or (r \ esid 259 and (name N or name CA or name C or name O or name CB )) or resid 260 t \ hrough 269 or (resid 270 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'I' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 52 or (resid 53 th \ rough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) o \ r resid 64 through 74 or resid 77 through 117 or (resid 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 through 142 or (resid 143 thro \ ugh 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 148 or resid 151 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 188 or resid 194 through 200 or r \ esid 205 through 214 or (resid 215 through 217 and (name N or name CA or name C \ or name O or name CB )) or resid 218 through 224 or resid 227 through 239 or res \ id 245 through 249 or (resid 250 and (name N or name CA or name C or name O or n \ ame CB )) or resid 251 through 258 or (resid 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 through 266 or (resid 267 and (name N or \ name CA or name C or name O or name CB )) or resid 268 through 269 or (resid 270 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 52 or (resid 53 th \ rough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) o \ r resid 64 through 148 or resid 151 through 162 or (resid 163 and (name N or nam \ e CA or name C or name O or name CB )) or resid 164 through 188 or resid 194 thr \ ough 200 or resid 205 through 214 or (resid 215 through 217 and (name N or name \ CA or name C or name O or name CB )) or resid 218 through 224 or resid 227 throu \ gh 239 or resid 245 through 249 or (resid 250 and (name N or name CA or name C o \ r name O or name CB )) or resid 251 through 258 or (resid 259 and (name N or nam \ e CA or name C or name O or name CB )) or resid 260 through 266 or (resid 267 an \ d (name N or name CA or name C or name O or name CB )) or resid 268 through 269 \ or (resid 270 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 52 or (resid 53 th \ rough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) o \ r resid 64 through 74 or resid 77 through 117 or (resid 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 through 142 or (resid 143 thro \ ugh 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 148 or resid 151 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 188 or resid 194 through 200 or r \ esid 205 through 239 or resid 245 through 249 or (resid 250 and (name N or name \ CA or name C or name O or name CB )) or resid 251 through 266 or (resid 267 and \ (name N or name CA or name C or name O or name CB )) or resid 268 through 269 or \ (resid 270 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 52 or (resid 53 th \ rough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) o \ r resid 64 through 74 or resid 77 through 117 or (resid 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 through 142 or (resid 143 thro \ ugh 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 148 or resid 151 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 188 or resid 194 through 200 or r \ esid 205 through 214 or (resid 215 through 217 and (name N or name CA or name C \ or name O or name CB )) or resid 218 through 224 or resid 227 through 239 or res \ id 245 through 249 or (resid 250 and (name N or name CA or name C or name O or n \ ame CB )) or resid 251 through 258 or (resid 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 through 266 or (resid 267 and (name N or \ name CA or name C or name O or name CB )) or resid 268 through 269 or (resid 270 \ and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.510 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.440 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 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 : 0.004 0.084 16480 Z= 0.181 Angle : 0.806 10.932 22387 Z= 0.439 Chirality : 0.046 0.164 2482 Planarity : 0.007 0.109 2871 Dihedral : 12.348 72.433 6054 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.11 % Allowed : 0.17 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.76 (0.18), residues: 2005 helix: -2.76 (0.58), residues: 64 sheet: -0.67 (0.19), residues: 744 loop : -1.41 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 127 TYR 0.022 0.002 TYR A 92 PHE 0.013 0.001 PHE L 157 TRP 0.030 0.002 TRP K 34 HIS 0.004 0.001 HIS I 139 Details of bonding type rmsd covalent geometry : bond 0.00368 (16439) covalent geometry : angle 0.80082 (22305) SS BOND : bond 0.00438 ( 41) SS BOND : angle 1.76747 ( 82) hydrogen bonds : bond 0.32804 ( 293) hydrogen bonds : angle 11.95805 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 457 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 249 GLN cc_start: 0.3999 (mp10) cc_final: 0.3786 (mp10) REVERT: C 262 ILE cc_start: 0.6466 (mt) cc_final: 0.6062 (mt) REVERT: E 103 GLN cc_start: 0.8028 (mm110) cc_final: 0.7426 (mm-40) REVERT: E 124 MET cc_start: 0.5514 (tpt) cc_final: 0.5008 (tpt) REVERT: E 130 SER cc_start: 0.6589 (t) cc_final: 0.6005 (p) REVERT: I 35 MET cc_start: 0.7541 (mtm) cc_final: 0.7220 (mtm) REVERT: I 87 CYS cc_start: 0.3728 (p) cc_final: 0.2749 (p) REVERT: I 265 LYS cc_start: 0.8419 (mmtm) cc_final: 0.7926 (tptp) REVERT: K 147 ASN cc_start: 0.8405 (m110) cc_final: 0.8102 (m110) REVERT: J 35 MET cc_start: 0.6634 (ptp) cc_final: 0.5569 (tmm) REVERT: J 152 SER cc_start: 0.6363 (t) cc_final: 0.6148 (t) REVERT: J 172 LYS cc_start: 0.8734 (tptp) cc_final: 0.8382 (tppt) REVERT: J 175 LYS cc_start: 0.7540 (mppt) cc_final: 0.7159 (ptpp) REVERT: J 181 ASP cc_start: 0.7350 (t0) cc_final: 0.6832 (t0) REVERT: H 99 ASN cc_start: 0.6746 (m-40) cc_final: 0.6065 (t0) REVERT: H 158 GLU cc_start: 0.7813 (tt0) cc_final: 0.6507 (tm-30) REVERT: L 84 THR cc_start: 0.7202 (p) cc_final: 0.6961 (p) REVERT: L 85 LYS cc_start: 0.7070 (tptp) cc_final: 0.6731 (tptt) REVERT: L 171 LYS cc_start: 0.7815 (mptt) cc_final: 0.7410 (mmtt) REVERT: L 172 LYS cc_start: 0.8595 (mppt) cc_final: 0.8348 (mppt) REVERT: L 197 ASN cc_start: 0.7556 (t0) cc_final: 0.6631 (t0) REVERT: L 228 LYS cc_start: 0.8037 (tptm) cc_final: 0.7598 (tptp) REVERT: L 262 ILE cc_start: 0.8666 (tp) cc_final: 0.8311 (tp) outliers start: 2 outliers final: 1 residues processed: 459 average time/residue: 0.1463 time to fit residues: 94.2852 Evaluate side-chains 414 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 152 HIS C 23 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN D 213 HIS ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS I 143 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN K 212 GLN F 123 HIS J 23 GLN J 249 GLN H 107 HIS ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN L 111 GLN L 213 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.212878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.186731 restraints weight = 38180.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.186334 restraints weight = 39566.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.187484 restraints weight = 37565.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.188163 restraints weight = 25605.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.188739 restraints weight = 23305.960| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16480 Z= 0.136 Angle : 0.649 9.808 22387 Z= 0.332 Chirality : 0.045 0.225 2482 Planarity : 0.006 0.070 2871 Dihedral : 5.351 25.607 2241 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.45 % Allowed : 4.12 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.58 (0.18), residues: 2005 helix: -2.33 (0.65), residues: 54 sheet: -0.70 (0.19), residues: 736 loop : -1.21 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 79 TYR 0.016 0.001 TYR E 92 PHE 0.013 0.001 PHE K 94 TRP 0.018 0.002 TRP C 34 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00304 (16439) covalent geometry : angle 0.64217 (22305) SS BOND : bond 0.00446 ( 41) SS BOND : angle 1.65653 ( 82) hydrogen bonds : bond 0.04316 ( 293) hydrogen bonds : angle 8.72998 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 458 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8029 (mt) cc_final: 0.7685 (mt) REVERT: A 137 GLN cc_start: 0.7094 (pm20) cc_final: 0.6504 (pm20) REVERT: A 162 TYR cc_start: 0.6252 (t80) cc_final: 0.5997 (t80) REVERT: A 164 VAL cc_start: 0.6354 (p) cc_final: 0.6027 (t) REVERT: C 67 ASN cc_start: 0.7606 (t0) cc_final: 0.7380 (t0) REVERT: C 84 THR cc_start: 0.8231 (m) cc_final: 0.7907 (m) REVERT: C 100 VAL cc_start: 0.6622 (m) cc_final: 0.6238 (p) REVERT: C 167 MET cc_start: 0.6068 (tpp) cc_final: 0.5592 (tpp) REVERT: C 262 ILE cc_start: 0.6721 (mt) cc_final: 0.6248 (mt) REVERT: B 123 HIS cc_start: 0.7503 (m90) cc_final: 0.7228 (m90) REVERT: B 162 TYR cc_start: 0.6805 (t80) cc_final: 0.6455 (t80) REVERT: D 126 PHE cc_start: 0.5323 (m-80) cc_final: 0.4958 (m-80) REVERT: E 103 GLN cc_start: 0.8200 (mm110) cc_final: 0.7528 (mm-40) REVERT: E 124 MET cc_start: 0.6010 (tpt) cc_final: 0.4992 (tpt) REVERT: I 35 MET cc_start: 0.8291 (mtm) cc_final: 0.7834 (mtm) REVERT: I 50 VAL cc_start: 0.8713 (t) cc_final: 0.8092 (p) REVERT: I 82 LYS cc_start: 0.7108 (pttm) cc_final: 0.6722 (mtmm) REVERT: I 148 GLU cc_start: 0.6179 (mp0) cc_final: 0.5944 (mp0) REVERT: I 206 ARG cc_start: 0.7143 (ttp80) cc_final: 0.6217 (ttp80) REVERT: G 96 ARG cc_start: 0.7375 (tpt90) cc_final: 0.7050 (tpt170) REVERT: G 109 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7435 (mmm-85) REVERT: G 114 HIS cc_start: 0.6550 (m-70) cc_final: 0.6164 (m-70) REVERT: G 176 MET cc_start: 0.5856 (mmm) cc_final: 0.5339 (tpt) REVERT: K 82 LYS cc_start: 0.6747 (pttt) cc_final: 0.6515 (pttp) REVERT: K 84 THR cc_start: 0.6920 (m) cc_final: 0.6617 (m) REVERT: K 147 ASN cc_start: 0.8589 (m110) cc_final: 0.8162 (m-40) REVERT: K 157 PHE cc_start: 0.7885 (t80) cc_final: 0.7491 (t80) REVERT: K 198 PHE cc_start: 0.7344 (p90) cc_final: 0.7042 (p90) REVERT: F 141 TYR cc_start: 0.6639 (m-10) cc_final: 0.6259 (m-10) REVERT: J 35 MET cc_start: 0.7052 (ptp) cc_final: 0.5512 (tmm) REVERT: J 124 ILE cc_start: 0.8475 (mp) cc_final: 0.8272 (mp) REVERT: J 139 HIS cc_start: 0.7016 (p-80) cc_final: 0.6668 (p90) REVERT: J 172 LYS cc_start: 0.9021 (tptp) cc_final: 0.8022 (tppt) REVERT: J 181 ASP cc_start: 0.7569 (t0) cc_final: 0.7097 (t0) REVERT: J 208 MET cc_start: 0.6174 (mpp) cc_final: 0.5541 (mpp) REVERT: H 91 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7280 (mpp-170) REVERT: H 105 LEU cc_start: 0.7527 (mt) cc_final: 0.7184 (mm) REVERT: H 131 GLU cc_start: 0.6311 (pm20) cc_final: 0.5956 (pm20) REVERT: H 158 GLU cc_start: 0.7204 (tt0) cc_final: 0.6677 (tm-30) REVERT: H 162 TYR cc_start: 0.7033 (t80) cc_final: 0.6123 (t80) REVERT: L 47 ASP cc_start: 0.6592 (t0) cc_final: 0.4493 (t0) REVERT: L 49 ARG cc_start: 0.6749 (mmp-170) cc_final: 0.6379 (mmp80) REVERT: L 140 ASN cc_start: 0.7650 (p0) cc_final: 0.7232 (p0) REVERT: L 197 ASN cc_start: 0.7165 (t0) cc_final: 0.6365 (t0) REVERT: L 229 LYS cc_start: 0.8849 (tptt) cc_final: 0.8543 (tptp) outliers start: 8 outliers final: 4 residues processed: 465 average time/residue: 0.1391 time to fit residues: 91.2685 Evaluate side-chains 417 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 413 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 39 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 chunk 135 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 168 optimal weight: 0.0970 chunk 129 optimal weight: 5.9990 chunk 127 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS C 23 GLN C 95 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS F 123 HIS J 23 GLN J 212 GLN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS L 213 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.212633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.185930 restraints weight = 38744.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.185937 restraints weight = 40814.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.187294 restraints weight = 38442.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.187836 restraints weight = 26053.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.188481 restraints weight = 23962.991| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16480 Z= 0.140 Angle : 0.644 10.763 22387 Z= 0.327 Chirality : 0.045 0.195 2482 Planarity : 0.006 0.063 2871 Dihedral : 5.207 25.651 2241 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.56 (0.18), residues: 2005 helix: -2.70 (0.57), residues: 60 sheet: -0.68 (0.19), residues: 744 loop : -1.16 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 109 TYR 0.017 0.001 TYR H 134 PHE 0.016 0.001 PHE K 94 TRP 0.019 0.001 TRP C 34 HIS 0.004 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00308 (16439) covalent geometry : angle 0.63617 (22305) SS BOND : bond 0.00428 ( 41) SS BOND : angle 1.75662 ( 82) hydrogen bonds : bond 0.03763 ( 293) hydrogen bonds : angle 8.07183 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 453 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.7598 (m-80) cc_final: 0.7380 (m-80) REVERT: A 105 LEU cc_start: 0.8072 (mt) cc_final: 0.7644 (mt) REVERT: A 137 GLN cc_start: 0.6865 (pm20) cc_final: 0.6431 (pm20) REVERT: A 156 CYS cc_start: 0.6023 (m) cc_final: 0.5543 (m) REVERT: C 67 ASN cc_start: 0.7567 (t0) cc_final: 0.7365 (t0) REVERT: C 84 THR cc_start: 0.8295 (m) cc_final: 0.8012 (m) REVERT: C 92 SER cc_start: 0.7234 (t) cc_final: 0.7002 (p) REVERT: C 95 GLN cc_start: 0.7180 (tp40) cc_final: 0.6835 (tm-30) REVERT: C 100 VAL cc_start: 0.6922 (m) cc_final: 0.6501 (p) REVERT: C 167 MET cc_start: 0.6124 (tpp) cc_final: 0.5667 (tpp) REVERT: B 96 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7546 (tpp80) REVERT: B 123 HIS cc_start: 0.7435 (m90) cc_final: 0.7133 (m90) REVERT: B 141 TYR cc_start: 0.6268 (t80) cc_final: 0.5449 (t80) REVERT: D 126 PHE cc_start: 0.5577 (m-80) cc_final: 0.5176 (m-80) REVERT: E 103 GLN cc_start: 0.8037 (mm110) cc_final: 0.7385 (mm-40) REVERT: E 124 MET cc_start: 0.6012 (tpt) cc_final: 0.5075 (tpt) REVERT: E 133 LEU cc_start: 0.6256 (mp) cc_final: 0.6040 (mp) REVERT: I 35 MET cc_start: 0.8207 (mtm) cc_final: 0.7826 (mtm) REVERT: I 82 LYS cc_start: 0.7207 (pttm) cc_final: 0.6713 (mtmm) REVERT: I 139 HIS cc_start: 0.7643 (p90) cc_final: 0.7349 (p90) REVERT: I 206 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6237 (ttp80) REVERT: G 96 ARG cc_start: 0.7308 (tpt90) cc_final: 0.7070 (tpt170) REVERT: G 114 HIS cc_start: 0.6744 (m-70) cc_final: 0.6351 (m-70) REVERT: G 123 HIS cc_start: 0.7328 (m90) cc_final: 0.7104 (m-70) REVERT: G 124 MET cc_start: 0.4295 (tpt) cc_final: 0.3969 (tpt) REVERT: K 82 LYS cc_start: 0.6754 (pttt) cc_final: 0.6511 (pttt) REVERT: K 147 ASN cc_start: 0.8568 (m110) cc_final: 0.8117 (m-40) REVERT: K 157 PHE cc_start: 0.7806 (t80) cc_final: 0.7563 (t80) REVERT: K 198 PHE cc_start: 0.7369 (p90) cc_final: 0.7084 (p90) REVERT: K 265 LYS cc_start: 0.7979 (mppt) cc_final: 0.7745 (mptt) REVERT: F 141 TYR cc_start: 0.7110 (m-10) cc_final: 0.6481 (m-10) REVERT: J 35 MET cc_start: 0.7129 (ptp) cc_final: 0.6260 (tmm) REVERT: J 56 SER cc_start: 0.8521 (p) cc_final: 0.8274 (t) REVERT: J 134 TYR cc_start: 0.5811 (m-80) cc_final: 0.5580 (m-80) REVERT: J 172 LYS cc_start: 0.8681 (tptp) cc_final: 0.8232 (tppt) REVERT: J 175 LYS cc_start: 0.7514 (ptpp) cc_final: 0.7240 (pttm) REVERT: J 181 ASP cc_start: 0.7653 (t0) cc_final: 0.7143 (t0) REVERT: J 208 MET cc_start: 0.6367 (mpp) cc_final: 0.5337 (mpp) REVERT: J 215 THR cc_start: 0.5922 (p) cc_final: 0.4768 (p) REVERT: H 91 ARG cc_start: 0.7203 (mpp-170) cc_final: 0.6864 (mtm-85) REVERT: H 95 ASP cc_start: 0.8156 (t0) cc_final: 0.7622 (t0) REVERT: H 105 LEU cc_start: 0.7692 (mt) cc_final: 0.7349 (mm) REVERT: H 131 GLU cc_start: 0.6365 (pm20) cc_final: 0.6001 (pm20) REVERT: H 157 LEU cc_start: 0.7360 (tp) cc_final: 0.7062 (tp) REVERT: H 158 GLU cc_start: 0.7335 (tt0) cc_final: 0.6906 (tm-30) REVERT: H 162 TYR cc_start: 0.7009 (t80) cc_final: 0.6160 (t80) REVERT: L 91 LYS cc_start: 0.7388 (tptm) cc_final: 0.7084 (tptm) REVERT: L 106 GLU cc_start: 0.6292 (mt-10) cc_final: 0.5985 (mt-10) REVERT: L 140 ASN cc_start: 0.7815 (p0) cc_final: 0.7363 (p0) REVERT: L 171 LYS cc_start: 0.8098 (mptt) cc_final: 0.7851 (mmtt) REVERT: L 197 ASN cc_start: 0.7214 (t0) cc_final: 0.6403 (t0) REVERT: L 228 LYS cc_start: 0.8275 (pptt) cc_final: 0.7761 (mmmm) REVERT: L 229 LYS cc_start: 0.8755 (tptt) cc_final: 0.8412 (tptp) outliers start: 3 outliers final: 0 residues processed: 455 average time/residue: 0.1436 time to fit residues: 92.2679 Evaluate side-chains 419 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 10 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 76 optimal weight: 0.0980 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN G 103 GLN F 123 HIS J 23 GLN J 249 GLN H 103 GLN L 213 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.212354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.185676 restraints weight = 38545.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.184973 restraints weight = 41832.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.186364 restraints weight = 36770.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.187249 restraints weight = 25432.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.187573 restraints weight = 23694.662| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16480 Z= 0.134 Angle : 0.635 10.259 22387 Z= 0.323 Chirality : 0.045 0.216 2482 Planarity : 0.005 0.058 2871 Dihedral : 5.106 28.465 2241 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.17 % Allowed : 3.57 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.58 (0.18), residues: 2005 helix: -2.54 (0.59), residues: 60 sheet: -0.76 (0.19), residues: 736 loop : -1.14 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 73 TYR 0.018 0.001 TYR B 106 PHE 0.015 0.001 PHE K 94 TRP 0.018 0.001 TRP C 34 HIS 0.005 0.001 HIS E 135 Details of bonding type rmsd covalent geometry : bond 0.00297 (16439) covalent geometry : angle 0.62849 (22305) SS BOND : bond 0.00476 ( 41) SS BOND : angle 1.62926 ( 82) hydrogen bonds : bond 0.03414 ( 293) hydrogen bonds : angle 7.61118 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 459 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8051 (mt) cc_final: 0.7687 (mt) REVERT: A 129 ASN cc_start: 0.6663 (p0) cc_final: 0.6371 (p0) REVERT: A 162 TYR cc_start: 0.6397 (t80) cc_final: 0.6171 (t80) REVERT: C 49 ARG cc_start: 0.6707 (tpt90) cc_final: 0.6411 (tpt90) REVERT: C 67 ASN cc_start: 0.7659 (t0) cc_final: 0.7412 (t0) REVERT: C 84 THR cc_start: 0.8262 (m) cc_final: 0.7987 (m) REVERT: C 92 SER cc_start: 0.7453 (t) cc_final: 0.7100 (p) REVERT: C 95 GLN cc_start: 0.7237 (tp40) cc_final: 0.7001 (tp-100) REVERT: C 100 VAL cc_start: 0.6670 (m) cc_final: 0.6269 (p) REVERT: C 167 MET cc_start: 0.6240 (tpp) cc_final: 0.5610 (tpp) REVERT: C 262 ILE cc_start: 0.6600 (mt) cc_final: 0.6048 (mt) REVERT: B 92 TYR cc_start: 0.4859 (m-80) cc_final: 0.4619 (m-80) REVERT: B 96 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7048 (tpp-160) REVERT: B 141 TYR cc_start: 0.6466 (t80) cc_final: 0.5595 (t80) REVERT: D 126 PHE cc_start: 0.5611 (m-80) cc_final: 0.5185 (m-80) REVERT: E 103 GLN cc_start: 0.8103 (mm110) cc_final: 0.7481 (mm-40) REVERT: E 124 MET cc_start: 0.6205 (tpt) cc_final: 0.5409 (tpt) REVERT: I 35 MET cc_start: 0.8202 (mtm) cc_final: 0.7855 (mtm) REVERT: I 82 LYS cc_start: 0.7214 (pttm) cc_final: 0.6650 (mtmm) REVERT: I 139 HIS cc_start: 0.7638 (p90) cc_final: 0.7351 (p90) REVERT: I 206 ARG cc_start: 0.7359 (ttp80) cc_final: 0.6370 (ttp80) REVERT: G 96 ARG cc_start: 0.7317 (tpt90) cc_final: 0.7034 (tpt170) REVERT: G 109 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7276 (mmm-85) REVERT: G 114 HIS cc_start: 0.6713 (m-70) cc_final: 0.6322 (m-70) REVERT: G 124 MET cc_start: 0.4671 (tpt) cc_final: 0.4413 (tpt) REVERT: K 147 ASN cc_start: 0.8547 (m110) cc_final: 0.8105 (m-40) REVERT: K 198 PHE cc_start: 0.7434 (p90) cc_final: 0.7117 (p90) REVERT: K 265 LYS cc_start: 0.7967 (mppt) cc_final: 0.7722 (mptt) REVERT: J 35 MET cc_start: 0.7554 (ptp) cc_final: 0.6969 (tmm) REVERT: J 139 HIS cc_start: 0.7206 (p-80) cc_final: 0.6965 (p90) REVERT: J 172 LYS cc_start: 0.8724 (tptp) cc_final: 0.8193 (tppt) REVERT: J 175 LYS cc_start: 0.7544 (ptpp) cc_final: 0.7279 (pttm) REVERT: J 181 ASP cc_start: 0.7566 (t0) cc_final: 0.7063 (t0) REVERT: J 208 MET cc_start: 0.6141 (mpp) cc_final: 0.4899 (mpp) REVERT: H 91 ARG cc_start: 0.7097 (mpp-170) cc_final: 0.6781 (mtm-85) REVERT: H 95 ASP cc_start: 0.8132 (t0) cc_final: 0.7613 (t0) REVERT: H 105 LEU cc_start: 0.7625 (mt) cc_final: 0.7393 (mm) REVERT: H 131 GLU cc_start: 0.6590 (pm20) cc_final: 0.6053 (pm20) REVERT: H 157 LEU cc_start: 0.7571 (tp) cc_final: 0.7325 (tp) REVERT: H 159 ARG cc_start: 0.6904 (tpt90) cc_final: 0.6671 (tpt170) REVERT: L 35 MET cc_start: 0.6666 (mtm) cc_final: 0.6432 (mtm) REVERT: L 85 LYS cc_start: 0.8396 (tppt) cc_final: 0.7675 (tppt) REVERT: L 106 GLU cc_start: 0.6277 (mt-10) cc_final: 0.6019 (mt-10) REVERT: L 140 ASN cc_start: 0.7816 (p0) cc_final: 0.7454 (p0) REVERT: L 171 LYS cc_start: 0.8087 (mptt) cc_final: 0.7781 (mmtt) REVERT: L 172 LYS cc_start: 0.8757 (mppt) cc_final: 0.8520 (mppt) REVERT: L 197 ASN cc_start: 0.7231 (t0) cc_final: 0.6401 (t0) REVERT: L 213 HIS cc_start: 0.6278 (t70) cc_final: 0.5810 (t-90) REVERT: L 228 LYS cc_start: 0.8294 (pptt) cc_final: 0.7712 (mmmm) REVERT: L 229 LYS cc_start: 0.8693 (tptt) cc_final: 0.8215 (tptp) outliers start: 3 outliers final: 0 residues processed: 462 average time/residue: 0.1369 time to fit residues: 89.6669 Evaluate side-chains 424 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 110 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 195 optimal weight: 0.0670 chunk 30 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 123 HIS J 23 GLN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.210178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.182798 restraints weight = 38159.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.181660 restraints weight = 45982.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.183428 restraints weight = 38959.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.184382 restraints weight = 25986.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.184883 restraints weight = 24448.475| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16480 Z= 0.176 Angle : 0.678 11.625 22387 Z= 0.346 Chirality : 0.046 0.243 2482 Planarity : 0.005 0.054 2871 Dihedral : 5.370 26.768 2241 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.17 % Allowed : 2.79 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.84 (0.18), residues: 2005 helix: -2.72 (0.54), residues: 68 sheet: -0.97 (0.18), residues: 798 loop : -1.27 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 142 TYR 0.019 0.002 TYR H 92 PHE 0.019 0.001 PHE K 94 TRP 0.022 0.002 TRP C 34 HIS 0.005 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00376 (16439) covalent geometry : angle 0.66997 (22305) SS BOND : bond 0.00474 ( 41) SS BOND : angle 1.84693 ( 82) hydrogen bonds : bond 0.03647 ( 293) hydrogen bonds : angle 7.66348 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 452 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7329 (tp) cc_final: 0.7009 (tp) REVERT: A 94 LEU cc_start: 0.7934 (tp) cc_final: 0.7673 (tp) REVERT: A 105 LEU cc_start: 0.7985 (mt) cc_final: 0.7630 (mt) REVERT: A 129 ASN cc_start: 0.6709 (p0) cc_final: 0.6431 (p0) REVERT: A 137 GLN cc_start: 0.7245 (pm20) cc_final: 0.6871 (pm20) REVERT: A 156 CYS cc_start: 0.5745 (m) cc_final: 0.5441 (m) REVERT: A 162 TYR cc_start: 0.6544 (t80) cc_final: 0.6198 (t80) REVERT: C 49 ARG cc_start: 0.7090 (tpt90) cc_final: 0.6781 (tpt90) REVERT: C 84 THR cc_start: 0.8237 (m) cc_final: 0.7920 (m) REVERT: C 92 SER cc_start: 0.7042 (t) cc_final: 0.6637 (p) REVERT: C 100 VAL cc_start: 0.6553 (m) cc_final: 0.6306 (p) REVERT: C 167 MET cc_start: 0.6704 (tpp) cc_final: 0.6133 (tpp) REVERT: C 219 PHE cc_start: 0.6859 (p90) cc_final: 0.6624 (p90) REVERT: C 262 ILE cc_start: 0.6617 (mt) cc_final: 0.6085 (mt) REVERT: B 96 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7113 (tpp-160) REVERT: B 105 LEU cc_start: 0.8119 (mt) cc_final: 0.7913 (mt) REVERT: B 123 HIS cc_start: 0.7581 (m90) cc_final: 0.7266 (m90) REVERT: B 141 TYR cc_start: 0.6609 (t80) cc_final: 0.5724 (t80) REVERT: B 176 MET cc_start: 0.3864 (ptm) cc_final: 0.3626 (ptm) REVERT: D 126 PHE cc_start: 0.6155 (m-80) cc_final: 0.5506 (m-80) REVERT: D 146 MET cc_start: -0.1071 (mmt) cc_final: -0.1332 (mmt) REVERT: E 103 GLN cc_start: 0.8094 (mm110) cc_final: 0.7493 (mm-40) REVERT: E 124 MET cc_start: 0.6269 (tpt) cc_final: 0.5497 (tpt) REVERT: I 35 MET cc_start: 0.8152 (mtm) cc_final: 0.7803 (mtm) REVERT: I 50 VAL cc_start: 0.8310 (m) cc_final: 0.7676 (p) REVERT: I 82 LYS cc_start: 0.7309 (pttm) cc_final: 0.6717 (mtmm) REVERT: G 96 ARG cc_start: 0.7582 (tpt90) cc_final: 0.7163 (tpt170) REVERT: G 109 ARG cc_start: 0.7788 (mmt90) cc_final: 0.7260 (mmm-85) REVERT: G 114 HIS cc_start: 0.6719 (m-70) cc_final: 0.6337 (m-70) REVERT: K 33 GLU cc_start: 0.7821 (pp20) cc_final: 0.6775 (tm-30) REVERT: K 147 ASN cc_start: 0.8500 (m110) cc_final: 0.8007 (m-40) REVERT: K 157 PHE cc_start: 0.7820 (t80) cc_final: 0.7580 (t80) REVERT: K 198 PHE cc_start: 0.7501 (p90) cc_final: 0.7173 (p90) REVERT: F 98 LEU cc_start: 0.8826 (mt) cc_final: 0.8376 (mt) REVERT: F 160 ARG cc_start: 0.8198 (mpt180) cc_final: 0.7905 (mmt180) REVERT: J 35 MET cc_start: 0.7444 (ptp) cc_final: 0.6722 (tmm) REVERT: J 172 LYS cc_start: 0.8739 (tptp) cc_final: 0.8226 (tppt) REVERT: J 175 LYS cc_start: 0.7594 (ptpp) cc_final: 0.7300 (pttm) REVERT: J 181 ASP cc_start: 0.7772 (t0) cc_final: 0.7516 (t0) REVERT: J 208 MET cc_start: 0.5806 (mpp) cc_final: 0.4808 (mpp) REVERT: H 91 ARG cc_start: 0.7158 (mpp-170) cc_final: 0.6807 (mtm-85) REVERT: H 95 ASP cc_start: 0.8306 (t0) cc_final: 0.7813 (t70) REVERT: H 103 GLN cc_start: 0.7291 (pt0) cc_final: 0.6812 (mt0) REVERT: H 109 ARG cc_start: 0.7600 (mmt-90) cc_final: 0.7306 (mmt-90) REVERT: H 131 GLU cc_start: 0.6737 (pm20) cc_final: 0.6143 (pm20) REVERT: H 159 ARG cc_start: 0.7272 (tpt90) cc_final: 0.7005 (tpt170) REVERT: L 35 MET cc_start: 0.6624 (mtm) cc_final: 0.6409 (mtm) REVERT: L 85 LYS cc_start: 0.8316 (tppt) cc_final: 0.7598 (tppt) REVERT: L 106 GLU cc_start: 0.6303 (mt-10) cc_final: 0.6067 (mt-10) REVERT: L 140 ASN cc_start: 0.7982 (p0) cc_final: 0.7574 (p0) REVERT: L 171 LYS cc_start: 0.8094 (mptt) cc_final: 0.7776 (mptt) REVERT: L 197 ASN cc_start: 0.7026 (t0) cc_final: 0.6352 (t0) REVERT: L 210 LEU cc_start: 0.7336 (mm) cc_final: 0.7118 (mm) REVERT: L 213 HIS cc_start: 0.6459 (t70) cc_final: 0.5944 (t-90) REVERT: L 228 LYS cc_start: 0.8280 (pptt) cc_final: 0.7707 (mmmm) REVERT: L 229 LYS cc_start: 0.8769 (tptt) cc_final: 0.8388 (tptp) outliers start: 3 outliers final: 1 residues processed: 455 average time/residue: 0.1371 time to fit residues: 88.1774 Evaluate side-chains 414 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 123 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 116 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 ASN I 249 GLN G 119 GLN K 212 GLN F 123 HIS J 23 GLN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.211229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.184434 restraints weight = 38128.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.183193 restraints weight = 43848.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.185063 restraints weight = 39138.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.185492 restraints weight = 27030.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.186106 restraints weight = 25841.211| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16480 Z= 0.142 Angle : 0.655 10.555 22387 Z= 0.331 Chirality : 0.046 0.248 2482 Planarity : 0.005 0.055 2871 Dihedral : 5.225 27.391 2241 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.17 % Allowed : 1.56 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.78 (0.18), residues: 2005 helix: -2.62 (0.56), residues: 66 sheet: -0.88 (0.18), residues: 799 loop : -1.28 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 143 TYR 0.012 0.001 TYR E 92 PHE 0.016 0.001 PHE K 94 TRP 0.021 0.001 TRP C 34 HIS 0.005 0.001 HIS E 135 Details of bonding type rmsd covalent geometry : bond 0.00314 (16439) covalent geometry : angle 0.64655 (22305) SS BOND : bond 0.00463 ( 41) SS BOND : angle 1.80555 ( 82) hydrogen bonds : bond 0.03281 ( 293) hydrogen bonds : angle 7.36218 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 450 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7860 (mp0) cc_final: 0.6925 (mp0) REVERT: A 105 LEU cc_start: 0.8062 (mt) cc_final: 0.7587 (mt) REVERT: A 129 ASN cc_start: 0.6709 (p0) cc_final: 0.6372 (p0) REVERT: A 137 GLN cc_start: 0.7239 (pm20) cc_final: 0.6995 (mp10) REVERT: A 143 ARG cc_start: 0.6362 (tmm160) cc_final: 0.5997 (tmt170) REVERT: A 156 CYS cc_start: 0.5226 (m) cc_final: 0.1310 (m) REVERT: A 162 TYR cc_start: 0.6484 (t80) cc_final: 0.6230 (t80) REVERT: C 84 THR cc_start: 0.8192 (m) cc_final: 0.7933 (m) REVERT: C 92 SER cc_start: 0.6818 (t) cc_final: 0.6462 (p) REVERT: C 98 SER cc_start: 0.6654 (t) cc_final: 0.6417 (p) REVERT: C 100 VAL cc_start: 0.6766 (m) cc_final: 0.6338 (p) REVERT: C 126 PHE cc_start: 0.7614 (m-10) cc_final: 0.7362 (m-10) REVERT: C 146 MET cc_start: 0.7779 (ppp) cc_final: 0.7243 (ppp) REVERT: C 167 MET cc_start: 0.6797 (tpp) cc_final: 0.6101 (tpp) REVERT: C 219 PHE cc_start: 0.6842 (p90) cc_final: 0.6593 (p90) REVERT: C 262 ILE cc_start: 0.6570 (mt) cc_final: 0.6012 (mt) REVERT: B 96 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7569 (tpp-160) REVERT: B 123 HIS cc_start: 0.7570 (m90) cc_final: 0.7263 (m90) REVERT: B 141 TYR cc_start: 0.6689 (t80) cc_final: 0.5761 (t80) REVERT: B 176 MET cc_start: 0.3885 (ptm) cc_final: 0.3644 (ptm) REVERT: D 126 PHE cc_start: 0.5995 (m-80) cc_final: 0.5498 (m-80) REVERT: D 146 MET cc_start: -0.1072 (mmt) cc_final: -0.1289 (mmt) REVERT: E 103 GLN cc_start: 0.8136 (mm110) cc_final: 0.7609 (mm-40) REVERT: E 124 MET cc_start: 0.6284 (tpt) cc_final: 0.5834 (tpt) REVERT: I 35 MET cc_start: 0.8114 (mtm) cc_final: 0.7796 (mtm) REVERT: I 50 VAL cc_start: 0.8336 (m) cc_final: 0.7659 (p) REVERT: I 82 LYS cc_start: 0.7336 (pttm) cc_final: 0.6722 (mtmm) REVERT: G 96 ARG cc_start: 0.7463 (tpt90) cc_final: 0.7030 (tpt170) REVERT: G 109 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7535 (mmt90) REVERT: G 114 HIS cc_start: 0.6487 (m-70) cc_final: 0.5871 (m-70) REVERT: G 124 MET cc_start: 0.5837 (tpt) cc_final: 0.5159 (tpt) REVERT: K 33 GLU cc_start: 0.7739 (pp20) cc_final: 0.6722 (tm-30) REVERT: K 67 ASN cc_start: 0.5872 (p0) cc_final: 0.5448 (p0) REVERT: K 73 ARG cc_start: 0.8013 (tpm170) cc_final: 0.7706 (tpp-160) REVERT: K 91 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7567 (mtmm) REVERT: K 147 ASN cc_start: 0.8453 (m110) cc_final: 0.7937 (m-40) REVERT: K 157 PHE cc_start: 0.7939 (t80) cc_final: 0.7682 (t80) REVERT: K 198 PHE cc_start: 0.7445 (p90) cc_final: 0.7116 (p90) REVERT: K 265 LYS cc_start: 0.8024 (mptt) cc_final: 0.7610 (mptt) REVERT: F 98 LEU cc_start: 0.8793 (mt) cc_final: 0.8403 (mt) REVERT: F 160 ARG cc_start: 0.8216 (mpt180) cc_final: 0.7690 (mmp80) REVERT: J 23 GLN cc_start: 0.1517 (OUTLIER) cc_final: 0.1236 (pp30) REVERT: J 35 MET cc_start: 0.7381 (ptp) cc_final: 0.6740 (tmm) REVERT: J 172 LYS cc_start: 0.8748 (tptp) cc_final: 0.8138 (tppt) REVERT: J 175 LYS cc_start: 0.7293 (ptpp) cc_final: 0.7049 (pttm) REVERT: J 181 ASP cc_start: 0.8524 (t0) cc_final: 0.7896 (t0) REVERT: J 208 MET cc_start: 0.5562 (mpp) cc_final: 0.4735 (mpp) REVERT: H 91 ARG cc_start: 0.7159 (mpp-170) cc_final: 0.6681 (mtm-85) REVERT: H 95 ASP cc_start: 0.8342 (t0) cc_final: 0.7901 (t70) REVERT: H 105 LEU cc_start: 0.8211 (tp) cc_final: 0.7767 (tp) REVERT: H 131 GLU cc_start: 0.6622 (pm20) cc_final: 0.6031 (pm20) REVERT: H 142 ARG cc_start: 0.8261 (ptp-110) cc_final: 0.7518 (ptp-170) REVERT: H 157 LEU cc_start: 0.7962 (tp) cc_final: 0.7734 (tp) REVERT: H 158 GLU cc_start: 0.7898 (tt0) cc_final: 0.6921 (tm-30) REVERT: L 85 LYS cc_start: 0.8304 (tppt) cc_final: 0.7599 (tppt) REVERT: L 106 GLU cc_start: 0.6475 (mt-10) cc_final: 0.6194 (mt-10) REVERT: L 140 ASN cc_start: 0.7912 (p0) cc_final: 0.7498 (p0) REVERT: L 171 LYS cc_start: 0.8081 (mptt) cc_final: 0.7751 (mptt) REVERT: L 172 LYS cc_start: 0.8799 (mppt) cc_final: 0.8493 (mppt) REVERT: L 197 ASN cc_start: 0.7525 (t0) cc_final: 0.7191 (t0) REVERT: L 213 HIS cc_start: 0.6425 (t70) cc_final: 0.5997 (t70) REVERT: L 228 LYS cc_start: 0.8293 (pptt) cc_final: 0.7705 (mmmm) REVERT: L 229 LYS cc_start: 0.8763 (tptt) cc_final: 0.8341 (tptp) REVERT: L 249 GLN cc_start: 0.6139 (pm20) cc_final: 0.5926 (pm20) outliers start: 3 outliers final: 0 residues processed: 452 average time/residue: 0.1447 time to fit residues: 91.7164 Evaluate side-chains 429 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 428 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 177 optimal weight: 0.2980 chunk 183 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS J 212 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.209642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.182877 restraints weight = 41497.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.181630 restraints weight = 49370.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.184342 restraints weight = 42279.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.184751 restraints weight = 27810.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.185713 restraints weight = 26818.627| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 16480 Z= 0.210 Angle : 0.717 12.834 22387 Z= 0.368 Chirality : 0.047 0.258 2482 Planarity : 0.006 0.058 2871 Dihedral : 5.594 27.418 2241 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.00 (0.18), residues: 2005 helix: -2.54 (0.57), residues: 66 sheet: -1.18 (0.18), residues: 775 loop : -1.32 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 109 TYR 0.016 0.002 TYR H 92 PHE 0.021 0.001 PHE K 94 TRP 0.027 0.002 TRP C 34 HIS 0.015 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00436 (16439) covalent geometry : angle 0.70966 (22305) SS BOND : bond 0.00526 ( 41) SS BOND : angle 1.83248 ( 82) hydrogen bonds : bond 0.03851 ( 293) hydrogen bonds : angle 7.80522 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.7938 (mt) cc_final: 0.7528 (mt) REVERT: A 129 ASN cc_start: 0.6729 (p0) cc_final: 0.6388 (p0) REVERT: A 143 ARG cc_start: 0.6039 (tmm160) cc_final: 0.5757 (tmt170) REVERT: A 156 CYS cc_start: 0.5790 (m) cc_final: 0.2131 (m) REVERT: A 162 TYR cc_start: 0.6681 (t80) cc_final: 0.6345 (t80) REVERT: C 84 THR cc_start: 0.8191 (m) cc_final: 0.7929 (m) REVERT: C 100 VAL cc_start: 0.6923 (m) cc_final: 0.6512 (p) REVERT: C 146 MET cc_start: 0.7951 (ppp) cc_final: 0.7394 (ppp) REVERT: C 153 MET cc_start: 0.5051 (mpp) cc_final: 0.4797 (mpp) REVERT: C 167 MET cc_start: 0.6525 (tpp) cc_final: 0.5916 (tpp) REVERT: C 262 ILE cc_start: 0.6584 (mt) cc_final: 0.6095 (mt) REVERT: B 96 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7579 (tpp-160) REVERT: B 141 TYR cc_start: 0.6956 (t80) cc_final: 0.5989 (t80) REVERT: B 176 MET cc_start: 0.4486 (ptm) cc_final: 0.4156 (ptm) REVERT: D 35 MET cc_start: 0.7373 (mmm) cc_final: 0.6475 (mpp) REVERT: D 126 PHE cc_start: 0.6321 (m-80) cc_final: 0.5685 (m-80) REVERT: D 146 MET cc_start: -0.1399 (mmt) cc_final: -0.1633 (mmt) REVERT: E 103 GLN cc_start: 0.8046 (mm110) cc_final: 0.7497 (mm-40) REVERT: E 124 MET cc_start: 0.6357 (tpt) cc_final: 0.5503 (tpt) REVERT: I 50 VAL cc_start: 0.8365 (m) cc_final: 0.7661 (p) REVERT: I 66 MET cc_start: 0.3848 (ttp) cc_final: 0.3621 (ttp) REVERT: I 67 ASN cc_start: 0.7021 (m-40) cc_final: 0.6639 (t0) REVERT: I 82 LYS cc_start: 0.7462 (pttm) cc_final: 0.6809 (mtmm) REVERT: I 128 VAL cc_start: 0.8509 (t) cc_final: 0.8119 (m) REVERT: I 198 PHE cc_start: 0.8154 (p90) cc_final: 0.7697 (p90) REVERT: G 96 ARG cc_start: 0.7688 (tpt90) cc_final: 0.7086 (tpt170) REVERT: G 109 ARG cc_start: 0.7849 (mmt90) cc_final: 0.7638 (mmt90) REVERT: G 114 HIS cc_start: 0.6859 (m-70) cc_final: 0.6254 (m-70) REVERT: G 124 MET cc_start: 0.5996 (tpt) cc_final: 0.5351 (tpt) REVERT: G 158 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6176 (mm-30) REVERT: G 160 ARG cc_start: 0.7407 (mpp-170) cc_final: 0.6940 (mpp-170) REVERT: K 33 GLU cc_start: 0.7758 (pp20) cc_final: 0.6841 (tm-30) REVERT: K 91 LYS cc_start: 0.8005 (ptpt) cc_final: 0.7565 (mtmm) REVERT: K 146 MET cc_start: 0.5808 (mpp) cc_final: 0.5518 (mpp) REVERT: K 147 ASN cc_start: 0.8528 (m110) cc_final: 0.8068 (m-40) REVERT: K 198 PHE cc_start: 0.7710 (p90) cc_final: 0.7290 (p90) REVERT: K 265 LYS cc_start: 0.8093 (mptt) cc_final: 0.7508 (mptt) REVERT: F 98 LEU cc_start: 0.8897 (mt) cc_final: 0.8589 (mt) REVERT: F 160 ARG cc_start: 0.8292 (mpt180) cc_final: 0.8087 (mmp80) REVERT: J 35 MET cc_start: 0.7589 (ptp) cc_final: 0.6841 (tmm) REVERT: J 139 HIS cc_start: 0.7397 (p-80) cc_final: 0.7078 (p90) REVERT: J 172 LYS cc_start: 0.8689 (tptp) cc_final: 0.8136 (tppt) REVERT: J 175 LYS cc_start: 0.7354 (ptpp) cc_final: 0.7149 (pttm) REVERT: J 181 ASP cc_start: 0.8354 (t0) cc_final: 0.7966 (t0) REVERT: J 208 MET cc_start: 0.5842 (mpp) cc_final: 0.5024 (mpp) REVERT: H 91 ARG cc_start: 0.7158 (mpp-170) cc_final: 0.6713 (mtm-85) REVERT: H 95 ASP cc_start: 0.8288 (t0) cc_final: 0.7855 (t70) REVERT: H 105 LEU cc_start: 0.8213 (tp) cc_final: 0.7970 (tp) REVERT: H 131 GLU cc_start: 0.6764 (pm20) cc_final: 0.6146 (pm20) REVERT: H 133 LEU cc_start: 0.7909 (mm) cc_final: 0.7576 (mm) REVERT: H 157 LEU cc_start: 0.8240 (tp) cc_final: 0.8028 (tp) REVERT: H 158 GLU cc_start: 0.8112 (tt0) cc_final: 0.7017 (tm-30) REVERT: L 82 LYS cc_start: 0.7604 (pttm) cc_final: 0.7114 (pttm) REVERT: L 85 LYS cc_start: 0.8131 (tppt) cc_final: 0.7643 (tppt) REVERT: L 106 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6262 (mt-10) REVERT: L 140 ASN cc_start: 0.7994 (p0) cc_final: 0.7495 (p0) REVERT: L 172 LYS cc_start: 0.8849 (mppt) cc_final: 0.8361 (mppt) REVERT: L 197 ASN cc_start: 0.7772 (t0) cc_final: 0.7465 (t0) REVERT: L 213 HIS cc_start: 0.6636 (t70) cc_final: 0.6171 (t70) REVERT: L 228 LYS cc_start: 0.8318 (pptt) cc_final: 0.7728 (mmmm) REVERT: L 229 LYS cc_start: 0.8577 (tptt) cc_final: 0.8101 (tptp) REVERT: L 249 GLN cc_start: 0.5716 (pm20) cc_final: 0.5042 (pm20) outliers start: 1 outliers final: 0 residues processed: 456 average time/residue: 0.1327 time to fit residues: 85.5560 Evaluate side-chains 420 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 135 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 157 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 158 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS C 23 GLN C 95 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN F 123 HIS ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.211660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.185159 restraints weight = 41525.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.185788 restraints weight = 44625.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.187312 restraints weight = 39964.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.187652 restraints weight = 27085.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.188966 restraints weight = 24723.396| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16480 Z= 0.148 Angle : 0.680 10.720 22387 Z= 0.343 Chirality : 0.046 0.269 2482 Planarity : 0.005 0.054 2871 Dihedral : 5.378 26.632 2241 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.06 % Allowed : 0.72 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.85 (0.18), residues: 2005 helix: -2.80 (0.54), residues: 66 sheet: -0.98 (0.19), residues: 732 loop : -1.28 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 73 TYR 0.015 0.001 TYR I 253 PHE 0.016 0.001 PHE K 94 TRP 0.022 0.001 TRP C 34 HIS 0.010 0.001 HIS H 135 Details of bonding type rmsd covalent geometry : bond 0.00327 (16439) covalent geometry : angle 0.67258 (22305) SS BOND : bond 0.00490 ( 41) SS BOND : angle 1.82026 ( 82) hydrogen bonds : bond 0.03261 ( 293) hydrogen bonds : angle 7.55938 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8026 (mt) cc_final: 0.7646 (mt) REVERT: A 129 ASN cc_start: 0.6733 (p0) cc_final: 0.6372 (p0) REVERT: A 143 ARG cc_start: 0.6266 (tmm160) cc_final: 0.5888 (tmt170) REVERT: A 156 CYS cc_start: 0.5663 (m) cc_final: 0.1956 (m) REVERT: A 162 TYR cc_start: 0.6669 (t80) cc_final: 0.6416 (t80) REVERT: C 49 ARG cc_start: 0.6852 (tpt90) cc_final: 0.6462 (tpt90) REVERT: C 146 MET cc_start: 0.7612 (ppp) cc_final: 0.7019 (ppp) REVERT: C 153 MET cc_start: 0.5129 (mpp) cc_final: 0.4837 (mpp) REVERT: C 167 MET cc_start: 0.6560 (tpp) cc_final: 0.5890 (tpp) REVERT: C 219 PHE cc_start: 0.7087 (p90) cc_final: 0.6797 (p90) REVERT: C 262 ILE cc_start: 0.6705 (mt) cc_final: 0.6199 (mt) REVERT: B 96 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7535 (tpp-160) REVERT: B 123 HIS cc_start: 0.7568 (m90) cc_final: 0.7318 (m90) REVERT: B 176 MET cc_start: 0.4403 (ptm) cc_final: 0.4034 (ptm) REVERT: D 35 MET cc_start: 0.7242 (mmm) cc_final: 0.6301 (mpp) REVERT: D 126 PHE cc_start: 0.6148 (m-80) cc_final: 0.5563 (m-80) REVERT: E 103 GLN cc_start: 0.8152 (mm110) cc_final: 0.7622 (mm-40) REVERT: E 124 MET cc_start: 0.6316 (tpt) cc_final: 0.5476 (tpt) REVERT: I 35 MET cc_start: 0.8017 (mtm) cc_final: 0.7667 (mtm) REVERT: I 50 VAL cc_start: 0.8329 (m) cc_final: 0.7628 (p) REVERT: I 82 LYS cc_start: 0.7361 (pttm) cc_final: 0.6791 (mtmm) REVERT: I 89 THR cc_start: 0.8546 (m) cc_final: 0.8115 (p) REVERT: I 128 VAL cc_start: 0.8442 (t) cc_final: 0.8097 (m) REVERT: G 96 ARG cc_start: 0.7681 (tpt90) cc_final: 0.7136 (tpt170) REVERT: G 109 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7396 (mpt-90) REVERT: G 114 HIS cc_start: 0.6753 (m-70) cc_final: 0.6171 (m-70) REVERT: G 124 MET cc_start: 0.5885 (tpt) cc_final: 0.5255 (tpt) REVERT: K 33 GLU cc_start: 0.7702 (pp20) cc_final: 0.6663 (tm-30) REVERT: K 73 ARG cc_start: 0.7119 (tpp-160) cc_final: 0.6800 (tpp-160) REVERT: K 91 LYS cc_start: 0.8072 (ptpt) cc_final: 0.7464 (mtmm) REVERT: K 147 ASN cc_start: 0.8487 (m110) cc_final: 0.8085 (m-40) REVERT: K 198 PHE cc_start: 0.7529 (p90) cc_final: 0.7096 (p90) REVERT: J 35 MET cc_start: 0.7479 (ptp) cc_final: 0.6819 (tmm) REVERT: J 172 LYS cc_start: 0.8716 (tptp) cc_final: 0.8115 (tppt) REVERT: J 175 LYS cc_start: 0.7287 (ptpp) cc_final: 0.7054 (pttm) REVERT: J 181 ASP cc_start: 0.8641 (t0) cc_final: 0.8140 (t0) REVERT: J 208 MET cc_start: 0.6041 (mpp) cc_final: 0.5576 (mpp) REVERT: J 215 THR cc_start: 0.6042 (p) cc_final: 0.4740 (p) REVERT: H 91 ARG cc_start: 0.7003 (mpp-170) cc_final: 0.6631 (mtm-85) REVERT: H 95 ASP cc_start: 0.8380 (t0) cc_final: 0.7923 (t70) REVERT: H 105 LEU cc_start: 0.8193 (tp) cc_final: 0.7902 (tp) REVERT: H 131 GLU cc_start: 0.6705 (pm20) cc_final: 0.6191 (pm20) REVERT: H 157 LEU cc_start: 0.8240 (tp) cc_final: 0.7926 (tp) REVERT: H 158 GLU cc_start: 0.8217 (tt0) cc_final: 0.7072 (tm-30) REVERT: L 82 LYS cc_start: 0.7701 (pttm) cc_final: 0.7187 (pttm) REVERT: L 85 LYS cc_start: 0.8176 (tppt) cc_final: 0.7494 (tppt) REVERT: L 106 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6182 (mt-10) REVERT: L 140 ASN cc_start: 0.7807 (p0) cc_final: 0.7278 (p0) REVERT: L 171 LYS cc_start: 0.7966 (mptt) cc_final: 0.7671 (mmtt) REVERT: L 172 LYS cc_start: 0.8763 (mppt) cc_final: 0.8506 (mppt) REVERT: L 197 ASN cc_start: 0.7740 (t0) cc_final: 0.7476 (t0) REVERT: L 213 HIS cc_start: 0.6500 (t70) cc_final: 0.5870 (t-170) REVERT: L 228 LYS cc_start: 0.8319 (pptt) cc_final: 0.7728 (mmmm) REVERT: L 229 LYS cc_start: 0.8696 (tptt) cc_final: 0.8222 (tptp) REVERT: L 249 GLN cc_start: 0.6036 (pm20) cc_final: 0.5537 (pm20) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.1287 time to fit residues: 83.3899 Evaluate side-chains 429 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 105 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 0.0570 chunk 184 optimal weight: 0.8980 chunk 194 optimal weight: 0.0570 chunk 32 optimal weight: 0.0020 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 95 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN I 249 GLN F 123 HIS ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.212573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.186126 restraints weight = 41866.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.185390 restraints weight = 45580.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.187016 restraints weight = 39112.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.188238 restraints weight = 26673.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.188645 restraints weight = 25133.090| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16480 Z= 0.121 Angle : 0.663 10.676 22387 Z= 0.332 Chirality : 0.046 0.253 2482 Planarity : 0.005 0.056 2871 Dihedral : 5.162 24.793 2241 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.06 % Allowed : 0.72 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.73 (0.18), residues: 2005 helix: -2.83 (0.55), residues: 66 sheet: -0.88 (0.19), residues: 728 loop : -1.21 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 159 TYR 0.014 0.001 TYR F 141 PHE 0.013 0.001 PHE K 94 TRP 0.019 0.001 TRP C 34 HIS 0.007 0.001 HIS K 264 Details of bonding type rmsd covalent geometry : bond 0.00275 (16439) covalent geometry : angle 0.65680 (22305) SS BOND : bond 0.00464 ( 41) SS BOND : angle 1.68716 ( 82) hydrogen bonds : bond 0.03152 ( 293) hydrogen bonds : angle 7.20248 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 447 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8034 (mt) cc_final: 0.7671 (mt) REVERT: A 129 ASN cc_start: 0.6340 (p0) cc_final: 0.6009 (p0) REVERT: A 143 ARG cc_start: 0.6226 (tmm160) cc_final: 0.5841 (tmt170) REVERT: A 156 CYS cc_start: 0.5398 (m) cc_final: 0.1715 (m) REVERT: A 162 TYR cc_start: 0.6928 (t80) cc_final: 0.6451 (t80) REVERT: C 23 GLN cc_start: 0.4699 (OUTLIER) cc_final: 0.4278 (mp10) REVERT: C 49 ARG cc_start: 0.6965 (tpt90) cc_final: 0.6553 (tpt90) REVERT: C 146 MET cc_start: 0.7601 (ppp) cc_final: 0.7008 (ppp) REVERT: C 167 MET cc_start: 0.6946 (tpp) cc_final: 0.6278 (tpp) REVERT: C 219 PHE cc_start: 0.6910 (p90) cc_final: 0.6604 (p90) REVERT: C 262 ILE cc_start: 0.6685 (mt) cc_final: 0.6222 (mt) REVERT: B 96 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7566 (tpp-160) REVERT: B 123 HIS cc_start: 0.7581 (m90) cc_final: 0.7276 (m90) REVERT: B 164 VAL cc_start: 0.7463 (t) cc_final: 0.7237 (p) REVERT: B 176 MET cc_start: 0.4693 (ptm) cc_final: 0.4257 (ptm) REVERT: D 35 MET cc_start: 0.7269 (mmm) cc_final: 0.6233 (mpp) REVERT: D 126 PHE cc_start: 0.6077 (m-80) cc_final: 0.5503 (m-80) REVERT: D 146 MET cc_start: -0.0290 (mmt) cc_final: -0.0771 (mmm) REVERT: E 96 ARG cc_start: 0.6384 (tmm160) cc_final: 0.6046 (tmm160) REVERT: E 103 GLN cc_start: 0.8055 (mm110) cc_final: 0.7517 (mm-40) REVERT: E 124 MET cc_start: 0.6398 (tpt) cc_final: 0.5536 (tpt) REVERT: I 35 MET cc_start: 0.8035 (mtm) cc_final: 0.7668 (mtm) REVERT: I 50 VAL cc_start: 0.8382 (m) cc_final: 0.7733 (p) REVERT: I 82 LYS cc_start: 0.7358 (pttm) cc_final: 0.6772 (mtmm) REVERT: I 89 THR cc_start: 0.8539 (m) cc_final: 0.8131 (p) REVERT: I 91 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7940 (tttm) REVERT: G 96 ARG cc_start: 0.7450 (tpt90) cc_final: 0.6966 (tpt170) REVERT: G 114 HIS cc_start: 0.6789 (m-70) cc_final: 0.6229 (m-70) REVERT: G 124 MET cc_start: 0.5914 (tpt) cc_final: 0.5317 (tpt) REVERT: G 132 LEU cc_start: 0.7949 (mp) cc_final: 0.7710 (mt) REVERT: K 33 GLU cc_start: 0.7782 (pp20) cc_final: 0.6690 (tm-30) REVERT: K 73 ARG cc_start: 0.7286 (tpp-160) cc_final: 0.6924 (tpp-160) REVERT: K 147 ASN cc_start: 0.8507 (m110) cc_final: 0.7978 (m-40) REVERT: K 157 PHE cc_start: 0.7835 (t80) cc_final: 0.7559 (t80) REVERT: K 198 PHE cc_start: 0.7496 (p90) cc_final: 0.7132 (p90) REVERT: K 219 PHE cc_start: 0.6519 (t80) cc_final: 0.6197 (t80) REVERT: J 35 MET cc_start: 0.7520 (ptp) cc_final: 0.6881 (tmm) REVERT: J 170 LYS cc_start: 0.8392 (tmmt) cc_final: 0.8160 (tmmt) REVERT: J 172 LYS cc_start: 0.8740 (tptp) cc_final: 0.8189 (tppt) REVERT: J 175 LYS cc_start: 0.7275 (ptpp) cc_final: 0.7024 (pttm) REVERT: J 181 ASP cc_start: 0.8679 (t0) cc_final: 0.8223 (t0) REVERT: J 208 MET cc_start: 0.6100 (mpp) cc_final: 0.5574 (mpp) REVERT: H 91 ARG cc_start: 0.7061 (mpp-170) cc_final: 0.6657 (mtm-85) REVERT: H 95 ASP cc_start: 0.8324 (t0) cc_final: 0.7937 (t70) REVERT: H 105 LEU cc_start: 0.8312 (tp) cc_final: 0.7993 (tp) REVERT: H 112 CYS cc_start: 0.8513 (m) cc_final: 0.8311 (m) REVERT: H 131 GLU cc_start: 0.6626 (pm20) cc_final: 0.6023 (pm20) REVERT: H 133 LEU cc_start: 0.7774 (mm) cc_final: 0.7391 (mm) REVERT: H 135 HIS cc_start: 0.8669 (p90) cc_final: 0.8440 (p90) REVERT: H 157 LEU cc_start: 0.8168 (tp) cc_final: 0.7855 (tp) REVERT: H 158 GLU cc_start: 0.8168 (tt0) cc_final: 0.7133 (tm-30) REVERT: H 162 TYR cc_start: 0.6802 (t80) cc_final: 0.6552 (t80) REVERT: L 85 LYS cc_start: 0.8208 (tppt) cc_final: 0.7397 (tppt) REVERT: L 106 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6288 (mt-10) REVERT: L 140 ASN cc_start: 0.7884 (p0) cc_final: 0.7373 (p0) REVERT: L 171 LYS cc_start: 0.7952 (mptt) cc_final: 0.7295 (mmtt) REVERT: L 172 LYS cc_start: 0.8733 (mppt) cc_final: 0.8276 (mppt) REVERT: L 197 ASN cc_start: 0.7488 (t0) cc_final: 0.7168 (t0) REVERT: L 213 HIS cc_start: 0.6523 (t70) cc_final: 0.5902 (t-170) REVERT: L 228 LYS cc_start: 0.8305 (pptt) cc_final: 0.7699 (mmmm) REVERT: L 229 LYS cc_start: 0.8672 (tptt) cc_final: 0.8191 (tptp) REVERT: L 249 GLN cc_start: 0.5997 (pm20) cc_final: 0.5589 (pm20) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.1278 time to fit residues: 81.3098 Evaluate side-chains 418 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 189 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 116 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.214489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.186846 restraints weight = 48137.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.186410 restraints weight = 58011.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.188611 restraints weight = 46689.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.188505 restraints weight = 33862.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.189381 restraints weight = 31820.855| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16480 Z= 0.129 Angle : 0.677 10.477 22387 Z= 0.337 Chirality : 0.046 0.226 2482 Planarity : 0.005 0.054 2871 Dihedral : 5.120 24.184 2241 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.63 (0.18), residues: 2005 helix: -2.82 (0.59), residues: 60 sheet: -0.84 (0.19), residues: 725 loop : -1.12 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 160 TYR 0.012 0.001 TYR J 253 PHE 0.034 0.001 PHE C 157 TRP 0.019 0.001 TRP I 34 HIS 0.004 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00292 (16439) covalent geometry : angle 0.66929 (22305) SS BOND : bond 0.00481 ( 41) SS BOND : angle 1.79123 ( 82) hydrogen bonds : bond 0.03120 ( 293) hydrogen bonds : angle 7.16155 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8115 (mt) cc_final: 0.7653 (mt) REVERT: A 129 ASN cc_start: 0.6399 (p0) cc_final: 0.6053 (p0) REVERT: A 156 CYS cc_start: 0.5438 (m) cc_final: 0.2022 (m) REVERT: A 162 TYR cc_start: 0.6999 (t80) cc_final: 0.6471 (t80) REVERT: C 49 ARG cc_start: 0.6947 (tpt90) cc_final: 0.6556 (tpt90) REVERT: C 146 MET cc_start: 0.7662 (ppp) cc_final: 0.7065 (ppp) REVERT: C 167 MET cc_start: 0.6987 (tpp) cc_final: 0.6340 (tpp) REVERT: C 219 PHE cc_start: 0.6946 (p90) cc_final: 0.6624 (p90) REVERT: C 262 ILE cc_start: 0.6525 (mt) cc_final: 0.6051 (mt) REVERT: B 123 HIS cc_start: 0.7753 (m90) cc_final: 0.7384 (m90) REVERT: B 176 MET cc_start: 0.4727 (ptm) cc_final: 0.4299 (ptm) REVERT: D 35 MET cc_start: 0.7496 (mmm) cc_final: 0.6665 (mpp) REVERT: D 126 PHE cc_start: 0.6134 (m-80) cc_final: 0.5541 (m-80) REVERT: E 103 GLN cc_start: 0.8065 (mm110) cc_final: 0.7528 (mm-40) REVERT: E 124 MET cc_start: 0.6387 (tpt) cc_final: 0.5527 (tpt) REVERT: I 35 MET cc_start: 0.8124 (mtm) cc_final: 0.7721 (mtm) REVERT: I 50 VAL cc_start: 0.8380 (m) cc_final: 0.7466 (p) REVERT: I 82 LYS cc_start: 0.7474 (pttm) cc_final: 0.6858 (mtmm) REVERT: I 89 THR cc_start: 0.8406 (m) cc_final: 0.7986 (p) REVERT: I 91 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7870 (tttm) REVERT: I 146 MET cc_start: 0.7099 (pmm) cc_final: 0.6495 (pmm) REVERT: I 219 PHE cc_start: 0.7384 (t80) cc_final: 0.6996 (t80) REVERT: G 96 ARG cc_start: 0.7353 (tpt90) cc_final: 0.6756 (tpt170) REVERT: G 109 ARG cc_start: 0.7477 (mmt90) cc_final: 0.7267 (mmm-85) REVERT: G 114 HIS cc_start: 0.6765 (m-70) cc_final: 0.6235 (m-70) REVERT: G 124 MET cc_start: 0.5833 (tpt) cc_final: 0.5249 (tpt) REVERT: G 132 LEU cc_start: 0.7952 (mp) cc_final: 0.7731 (mt) REVERT: K 33 GLU cc_start: 0.7632 (pp20) cc_final: 0.6546 (tm-30) REVERT: K 73 ARG cc_start: 0.7349 (tpp-160) cc_final: 0.6950 (tpp-160) REVERT: K 91 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7165 (mtmm) REVERT: K 147 ASN cc_start: 0.8534 (m110) cc_final: 0.7977 (m-40) REVERT: K 157 PHE cc_start: 0.7798 (t80) cc_final: 0.7544 (t80) REVERT: K 198 PHE cc_start: 0.7617 (p90) cc_final: 0.7230 (p90) REVERT: K 219 PHE cc_start: 0.6617 (t80) cc_final: 0.6310 (t80) REVERT: K 265 LYS cc_start: 0.8049 (mptt) cc_final: 0.7618 (mppt) REVERT: J 35 MET cc_start: 0.7469 (ptp) cc_final: 0.6735 (tmm) REVERT: J 49 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8064 (mmm-85) REVERT: J 148 GLU cc_start: 0.7886 (mp0) cc_final: 0.7677 (mp0) REVERT: J 170 LYS cc_start: 0.8358 (tmmt) cc_final: 0.8141 (tmmt) REVERT: J 172 LYS cc_start: 0.8765 (tptp) cc_final: 0.8153 (tppt) REVERT: J 175 LYS cc_start: 0.7283 (ptpp) cc_final: 0.7081 (pttm) REVERT: J 181 ASP cc_start: 0.8659 (t0) cc_final: 0.8239 (t0) REVERT: J 208 MET cc_start: 0.6027 (mpp) cc_final: 0.5693 (mpp) REVERT: J 248 VAL cc_start: 0.7557 (m) cc_final: 0.7313 (p) REVERT: J 253 TYR cc_start: 0.7004 (m-10) cc_final: 0.6790 (m-10) REVERT: H 91 ARG cc_start: 0.7169 (mpp-170) cc_final: 0.6800 (mtm-85) REVERT: H 95 ASP cc_start: 0.8296 (t0) cc_final: 0.7950 (t70) REVERT: H 105 LEU cc_start: 0.8272 (tp) cc_final: 0.7961 (tp) REVERT: H 131 GLU cc_start: 0.6486 (pm20) cc_final: 0.5988 (pm20) REVERT: H 157 LEU cc_start: 0.8190 (tp) cc_final: 0.7870 (tp) REVERT: H 158 GLU cc_start: 0.7922 (tt0) cc_final: 0.7241 (tm-30) REVERT: L 82 LYS cc_start: 0.7702 (pttm) cc_final: 0.7279 (pttm) REVERT: L 85 LYS cc_start: 0.8082 (tppt) cc_final: 0.7595 (tppt) REVERT: L 106 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6177 (mt-10) REVERT: L 140 ASN cc_start: 0.7933 (p0) cc_final: 0.7436 (p0) REVERT: L 171 LYS cc_start: 0.7976 (mptt) cc_final: 0.7774 (mmtt) REVERT: L 172 LYS cc_start: 0.8771 (mppt) cc_final: 0.8501 (mppt) REVERT: L 210 LEU cc_start: 0.7093 (mm) cc_final: 0.6845 (mm) REVERT: L 213 HIS cc_start: 0.6637 (t70) cc_final: 0.5993 (t-170) REVERT: L 228 LYS cc_start: 0.8356 (pptt) cc_final: 0.7807 (mmmm) REVERT: L 229 LYS cc_start: 0.8699 (tptt) cc_final: 0.8187 (tptp) REVERT: L 249 GLN cc_start: 0.6023 (pm20) cc_final: 0.5572 (pm20) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.1275 time to fit residues: 81.8992 Evaluate side-chains 412 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 102 optimal weight: 0.8980 chunk 194 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS J 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.199954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.151708 restraints weight = 33224.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.152021 restraints weight = 19299.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.154634 restraints weight = 15899.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.154713 restraints weight = 12860.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.155451 restraints weight = 12290.168| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 16480 Z= 0.254 Angle : 0.800 12.876 22387 Z= 0.408 Chirality : 0.050 0.236 2482 Planarity : 0.006 0.056 2871 Dihedral : 5.963 26.065 2241 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.06 (0.18), residues: 2005 helix: -2.90 (0.56), residues: 60 sheet: -1.34 (0.18), residues: 763 loop : -1.26 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 109 TYR 0.021 0.002 TYR H 92 PHE 0.023 0.002 PHE K 94 TRP 0.060 0.003 TRP I 34 HIS 0.013 0.001 HIS H 135 Details of bonding type rmsd covalent geometry : bond 0.00527 (16439) covalent geometry : angle 0.79145 (22305) SS BOND : bond 0.00509 ( 41) SS BOND : angle 2.11753 ( 82) hydrogen bonds : bond 0.04279 ( 293) hydrogen bonds : angle 8.15271 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2726.64 seconds wall clock time: 47 minutes 55.66 seconds (2875.66 seconds total)