Starting phenix.real_space_refine on Sat Jun 14 10:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwk_26834/06_2025/7uwk_26834.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwk_26834/06_2025/7uwk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uwk_26834/06_2025/7uwk_26834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwk_26834/06_2025/7uwk_26834.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwk_26834/06_2025/7uwk_26834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwk_26834/06_2025/7uwk_26834.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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, 'ASP:plan': 1, 'HIS: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: {'TYR:plan': 1, 'HIS: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: 9.72, per 1000 atoms: 0.61 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: 4.01 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.88 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: 3.88 Time building geometry restraints manager: 4.74 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.690 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- 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 : 18.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.18), 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 TRP 0.030 0.002 TRP K 34 HIS 0.004 0.001 HIS I 139 PHE 0.013 0.001 PHE L 157 TYR 0.022 0.002 TYR A 92 ARG 0.010 0.001 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.32804 ( 293) hydrogen bonds : angle 11.95805 ( 744) SS BOND : bond 0.00438 ( 41) SS BOND : angle 1.76747 ( 82) covalent geometry : bond 0.00368 (16439) covalent geometry : angle 0.80082 (22305) *********************** 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 : 1.583 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: C 249 GLN cc_start: 0.3999 (mp10) cc_final: 0.3783 (mp10) REVERT: C 262 ILE cc_start: 0.6466 (mt) cc_final: 0.6053 (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: 0.5000 (tpt) REVERT: E 130 SER cc_start: 0.6589 (t) cc_final: 0.6002 (p) REVERT: I 35 MET cc_start: 0.7541 (mtm) cc_final: 0.7211 (mtm) REVERT: I 87 CYS cc_start: 0.3727 (p) cc_final: 0.2749 (p) REVERT: K 147 ASN cc_start: 0.8405 (m110) cc_final: 0.8103 (m110) REVERT: J 35 MET cc_start: 0.6634 (ptp) cc_final: 0.5578 (tmm) REVERT: J 172 LYS cc_start: 0.8734 (tptp) cc_final: 0.8384 (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: 0.6506 (tm-30) REVERT: L 84 THR cc_start: 0.7202 (p) cc_final: 0.6963 (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: 0.7409 (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: 0.6630 (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: 0.3229 time to fit residues: 206.6209 Evaluate side-chains 415 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.0870 chunk 152 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 0.0980 chunk 117 optimal weight: 0.3980 chunk 182 optimal weight: 1.9990 overall best weight: 0.2558 ------------------------------------------------------------------------------- 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 119 GLN K 212 GLN F 123 HIS J 23 GLN J 249 GLN H 107 HIS ** 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 = 0.4825 r_free = 0.4825 target = 0.214482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.188602 restraints weight = 38272.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.188511 restraints weight = 41512.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.189576 restraints weight = 38685.137| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16480 Z= 0.122 Angle : 0.639 11.015 22387 Z= 0.326 Chirality : 0.045 0.249 2482 Planarity : 0.006 0.069 2871 Dihedral : 5.230 24.782 2241 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.39 % Allowed : 4.07 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2005 helix: -2.37 (0.64), residues: 54 sheet: -0.60 (0.18), residues: 769 loop : -1.18 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 34 HIS 0.005 0.000 HIS A 135 PHE 0.012 0.001 PHE K 135 TYR 0.014 0.001 TYR E 92 ARG 0.007 0.001 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 293) hydrogen bonds : angle 8.62147 ( 744) SS BOND : bond 0.00443 ( 41) SS BOND : angle 1.58843 ( 82) covalent geometry : bond 0.00268 (16439) covalent geometry : angle 0.63253 (22305) *********************** 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 460 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 453 time to evaluate : 1.586 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: A 105 LEU cc_start: 0.8031 (mt) cc_final: 0.7729 (mt) REVERT: A 137 GLN cc_start: 0.6967 (pm20) cc_final: 0.6424 (pm20) REVERT: A 164 VAL cc_start: 0.6390 (p) cc_final: 0.6030 (t) REVERT: A 176 MET cc_start: 0.1539 (ppp) cc_final: 0.1313 (ppp) REVERT: C 67 ASN cc_start: 0.7620 (t0) cc_final: 0.7397 (t0) REVERT: C 84 THR cc_start: 0.8207 (m) cc_final: 0.7908 (m) REVERT: C 100 VAL cc_start: 0.6501 (m) cc_final: 0.6158 (p) REVERT: C 167 MET cc_start: 0.6020 (tpp) cc_final: 0.5569 (tpp) REVERT: C 262 ILE cc_start: 0.6678 (mt) cc_final: 0.6233 (mt) REVERT: B 123 HIS cc_start: 0.7433 (m90) cc_final: 0.7179 (m90) REVERT: B 162 TYR cc_start: 0.6607 (t80) cc_final: 0.6339 (t80) REVERT: D 126 PHE cc_start: 0.5240 (m-80) cc_final: 0.4923 (m-80) REVERT: E 103 GLN cc_start: 0.8095 (mm110) cc_final: 0.7399 (mm-40) REVERT: E 124 MET cc_start: 0.6033 (tpt) cc_final: 0.5012 (tpt) REVERT: I 35 MET cc_start: 0.8184 (mtm) cc_final: 0.7844 (mtm) REVERT: I 50 VAL cc_start: 0.8664 (t) cc_final: 0.8034 (p) REVERT: I 82 LYS cc_start: 0.7188 (pttm) cc_final: 0.6744 (mtmm) REVERT: I 206 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6209 (ttp80) REVERT: G 96 ARG cc_start: 0.7229 (tpt90) cc_final: 0.6880 (tpt170) REVERT: G 114 HIS cc_start: 0.6515 (m-70) cc_final: 0.6118 (m-70) REVERT: G 176 MET cc_start: 0.5806 (mmm) cc_final: 0.5292 (tpt) REVERT: K 82 LYS cc_start: 0.6715 (pttt) cc_final: 0.6466 (pttp) REVERT: K 147 ASN cc_start: 0.8558 (m110) cc_final: 0.8085 (m-40) REVERT: K 157 PHE cc_start: 0.7883 (t80) cc_final: 0.7438 (t80) REVERT: K 198 PHE cc_start: 0.7276 (p90) cc_final: 0.6988 (p90) REVERT: F 141 TYR cc_start: 0.6976 (m-10) cc_final: 0.6632 (m-10) REVERT: J 35 MET cc_start: 0.7147 (ptp) cc_final: 0.6091 (tmm) REVERT: J 139 HIS cc_start: 0.7075 (p90) cc_final: 0.6858 (p90) REVERT: J 172 LYS cc_start: 0.9015 (tptp) cc_final: 0.8003 (tppt) REVERT: J 181 ASP cc_start: 0.7466 (t0) cc_final: 0.7020 (t0) REVERT: J 183 ASN cc_start: 0.7109 (m110) cc_final: 0.6872 (m110) REVERT: J 208 MET cc_start: 0.6055 (mpp) cc_final: 0.5483 (mpp) REVERT: H 91 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7182 (mpp-170) REVERT: H 95 ASP cc_start: 0.8124 (t0) cc_final: 0.7868 (t0) REVERT: H 99 ASN cc_start: 0.6904 (m-40) cc_final: 0.5467 (t0) REVERT: H 131 GLU cc_start: 0.6287 (pm20) cc_final: 0.5971 (pm20) REVERT: H 133 LEU cc_start: 0.7761 (mm) cc_final: 0.7268 (mm) REVERT: H 158 GLU cc_start: 0.6933 (tt0) cc_final: 0.6411 (tm-30) REVERT: L 35 MET cc_start: 0.6719 (mtm) cc_final: 0.6412 (mtm) REVERT: L 140 ASN cc_start: 0.7562 (p0) cc_final: 0.7180 (p0) REVERT: L 197 ASN cc_start: 0.7271 (t0) cc_final: 0.6581 (t0) REVERT: L 228 LYS cc_start: 0.8450 (tptm) cc_final: 0.8171 (tmmt) REVERT: L 229 LYS cc_start: 0.8846 (tptt) cc_final: 0.8553 (tptp) REVERT: L 249 GLN cc_start: 0.5683 (pm20) cc_final: 0.5313 (pm20) outliers start: 7 outliers final: 3 residues processed: 459 average time/residue: 0.3311 time to fit residues: 211.7056 Evaluate side-chains 413 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 410 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 195 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS F 103 GLN F 123 HIS J 23 GLN ** J 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.209261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.182704 restraints weight = 37547.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.182747 restraints weight = 45748.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.184223 restraints weight = 40363.838| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 16480 Z= 0.218 Angle : 0.720 13.317 22387 Z= 0.371 Chirality : 0.047 0.215 2482 Planarity : 0.006 0.064 2871 Dihedral : 5.670 27.723 2241 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.22 % Allowed : 4.01 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.18), residues: 2005 helix: -2.83 (0.54), residues: 66 sheet: -0.91 (0.19), residues: 756 loop : -1.37 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 34 HIS 0.007 0.001 HIS F 135 PHE 0.022 0.002 PHE K 94 TYR 0.021 0.002 TYR K 97 ARG 0.007 0.001 ARG F 163 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 293) hydrogen bonds : angle 8.50695 ( 744) SS BOND : bond 0.00670 ( 41) SS BOND : angle 1.99197 ( 82) covalent geometry : bond 0.00453 (16439) covalent geometry : angle 0.71123 (22305) *********************** 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: 4 poor density : 452 time to evaluate : 1.806 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: symmetry clash REVERT: A 94 LEU cc_start: 0.7827 (tp) cc_final: 0.7623 (tp) REVERT: A 105 LEU cc_start: 0.8017 (mt) cc_final: 0.7567 (mt) REVERT: A 137 GLN cc_start: 0.7117 (pm20) cc_final: 0.6302 (pm20) REVERT: A 156 CYS cc_start: 0.6211 (m) cc_final: 0.5800 (m) REVERT: C 49 ARG cc_start: 0.7072 (tpt90) cc_final: 0.6717 (tpt90) REVERT: C 66 MET cc_start: 0.6242 (mmp) cc_final: 0.5911 (mmm) REVERT: C 84 THR cc_start: 0.8273 (m) cc_final: 0.7990 (m) REVERT: C 92 SER cc_start: 0.7370 (t) cc_final: 0.7125 (p) REVERT: C 100 VAL cc_start: 0.7073 (m) cc_final: 0.6628 (p) REVERT: C 167 MET cc_start: 0.6387 (tpp) cc_final: 0.5750 (tpp) REVERT: B 92 TYR cc_start: 0.4877 (m-80) cc_final: 0.4557 (m-80) REVERT: B 96 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7498 (tpp-160) REVERT: B 123 HIS cc_start: 0.7469 (m90) cc_final: 0.7165 (m90) REVERT: B 141 TYR cc_start: 0.6281 (t80) cc_final: 0.5457 (t80) REVERT: D 126 PHE cc_start: 0.5609 (m-80) cc_final: 0.5161 (m-80) REVERT: D 146 MET cc_start: -0.1026 (mmt) cc_final: -0.1336 (mmt) REVERT: E 90 TRP cc_start: 0.7651 (p90) cc_final: 0.7175 (p90) REVERT: E 103 GLN cc_start: 0.8099 (mm110) cc_final: 0.7522 (mm-40) REVERT: E 124 MET cc_start: 0.6179 (tpt) cc_final: 0.5425 (tpt) REVERT: I 35 MET cc_start: 0.8113 (mtm) cc_final: 0.7706 (mtm) REVERT: I 82 LYS cc_start: 0.7400 (pttm) cc_final: 0.6858 (mtmm) REVERT: I 206 ARG cc_start: 0.7152 (ttp80) cc_final: 0.6229 (ttp80) REVERT: G 96 ARG cc_start: 0.7490 (tpt90) cc_final: 0.7195 (tpt170) REVERT: G 114 HIS cc_start: 0.6787 (m-70) cc_final: 0.6392 (m-70) REVERT: G 124 MET cc_start: 0.4550 (tpt) cc_final: 0.4246 (tpt) REVERT: K 67 ASN cc_start: 0.6474 (m-40) cc_final: 0.6205 (m-40) REVERT: K 72 LEU cc_start: 0.8484 (pp) cc_final: 0.8078 (pp) REVERT: K 79 ARG cc_start: 0.6850 (mmt180) cc_final: 0.6613 (mmt180) REVERT: K 145 ASN cc_start: 0.4781 (p0) cc_final: 0.4554 (p0) REVERT: K 146 MET cc_start: 0.5720 (mpp) cc_final: 0.5506 (mpp) REVERT: K 147 ASN cc_start: 0.8582 (m110) cc_final: 0.8123 (m-40) REVERT: K 198 PHE cc_start: 0.7390 (p90) cc_final: 0.7102 (p90) REVERT: K 265 LYS cc_start: 0.7981 (mppt) cc_final: 0.7762 (mptt) REVERT: F 141 TYR cc_start: 0.7056 (m-10) cc_final: 0.6554 (m-10) REVERT: J 35 MET cc_start: 0.7345 (ptp) cc_final: 0.6528 (tmm) REVERT: J 172 LYS cc_start: 0.8674 (tptp) cc_final: 0.8156 (tppt) REVERT: J 175 LYS cc_start: 0.7627 (ptpp) cc_final: 0.7361 (pttm) REVERT: J 180 TRP cc_start: 0.5585 (t60) cc_final: 0.5297 (t60) REVERT: J 181 ASP cc_start: 0.7813 (t0) cc_final: 0.7100 (t0) REVERT: J 208 MET cc_start: 0.6026 (mpp) cc_final: 0.5022 (mpp) REVERT: H 91 ARG cc_start: 0.7180 (mpp-170) cc_final: 0.6773 (mtm-85) REVERT: H 95 ASP cc_start: 0.8270 (t0) cc_final: 0.7673 (t0) REVERT: H 131 GLU cc_start: 0.6447 (pm20) cc_final: 0.6084 (pm20) REVERT: L 35 MET cc_start: 0.6671 (mtm) cc_final: 0.6470 (mtm) REVERT: L 85 LYS cc_start: 0.8240 (tptt) cc_final: 0.7337 (tptt) REVERT: L 86 ILE cc_start: 0.7261 (tp) cc_final: 0.6642 (tp) REVERT: L 140 ASN cc_start: 0.7929 (p0) cc_final: 0.7495 (p0) REVERT: L 197 ASN cc_start: 0.7496 (t0) cc_final: 0.6778 (t0) REVERT: L 228 LYS cc_start: 0.8534 (tptm) cc_final: 0.8078 (mmmm) REVERT: L 229 LYS cc_start: 0.8925 (tptt) cc_final: 0.8444 (tptp) outliers start: 4 outliers final: 1 residues processed: 455 average time/residue: 0.3263 time to fit residues: 207.3926 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 : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 109 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 198 optimal weight: 0.0000 chunk 186 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS J 23 GLN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** L 213 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.210288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.183242 restraints weight = 37752.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.183184 restraints weight = 45015.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.184549 restraints weight = 41803.287| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16480 Z= 0.165 Angle : 0.669 11.514 22387 Z= 0.341 Chirality : 0.046 0.220 2482 Planarity : 0.006 0.071 2871 Dihedral : 5.420 29.339 2241 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.18), residues: 2005 helix: -2.60 (0.56), residues: 66 sheet: -1.03 (0.18), residues: 786 loop : -1.37 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 34 HIS 0.007 0.001 HIS G 107 PHE 0.018 0.001 PHE K 94 TYR 0.017 0.002 TYR L 97 ARG 0.011 0.001 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 293) hydrogen bonds : angle 7.91201 ( 744) SS BOND : bond 0.00431 ( 41) SS BOND : angle 1.72901 ( 82) covalent geometry : bond 0.00353 (16439) covalent geometry : angle 0.66201 (22305) *********************** 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 457 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 455 time to evaluate : 1.615 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: A 92 TYR cc_start: 0.8114 (m-80) cc_final: 0.7815 (m-10) REVERT: A 105 LEU cc_start: 0.8008 (mt) cc_final: 0.7684 (mt) REVERT: A 129 ASN cc_start: 0.6685 (p0) cc_final: 0.6404 (p0) REVERT: A 137 GLN cc_start: 0.7349 (pm20) cc_final: 0.7004 (pm20) REVERT: A 156 CYS cc_start: 0.5834 (m) cc_final: 0.5470 (m) REVERT: A 162 TYR cc_start: 0.6533 (t80) cc_final: 0.6252 (t80) REVERT: C 84 THR cc_start: 0.8207 (m) cc_final: 0.7942 (m) REVERT: C 92 SER cc_start: 0.7319 (t) cc_final: 0.6906 (p) REVERT: C 100 VAL cc_start: 0.6851 (m) cc_final: 0.6253 (p) REVERT: C 167 MET cc_start: 0.6601 (tpp) cc_final: 0.5923 (tpp) REVERT: C 262 ILE cc_start: 0.6655 (mt) cc_final: 0.6162 (mt) REVERT: B 96 ARG cc_start: 0.7866 (tpp80) cc_final: 0.7121 (tpp-160) REVERT: B 141 TYR cc_start: 0.6502 (t80) cc_final: 0.5629 (t80) REVERT: B 162 TYR cc_start: 0.7031 (t80) cc_final: 0.6637 (t80) REVERT: D 126 PHE cc_start: 0.5616 (m-80) cc_final: 0.5180 (m-80) REVERT: D 146 MET cc_start: -0.0966 (mmt) cc_final: -0.1240 (mmt) REVERT: E 103 GLN cc_start: 0.8114 (mm110) cc_final: 0.7555 (mm-40) REVERT: E 114 HIS cc_start: 0.8144 (m-70) cc_final: 0.7939 (m-70) REVERT: E 124 MET cc_start: 0.6296 (tpt) cc_final: 0.5460 (tpt) REVERT: I 35 MET cc_start: 0.8111 (mtm) cc_final: 0.7797 (mtm) REVERT: I 82 LYS cc_start: 0.7377 (pttm) cc_final: 0.6737 (mtmm) REVERT: I 139 HIS cc_start: 0.7583 (p90) cc_final: 0.7237 (p90) REVERT: I 206 ARG cc_start: 0.7260 (ttp80) cc_final: 0.6270 (ttp80) REVERT: G 96 ARG cc_start: 0.7487 (tpt90) cc_final: 0.7166 (tpt170) REVERT: G 114 HIS cc_start: 0.6639 (m-70) cc_final: 0.6259 (m-70) REVERT: K 68 VAL cc_start: 0.7002 (p) cc_final: 0.6625 (m) REVERT: K 91 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7657 (ptmm) REVERT: K 147 ASN cc_start: 0.8516 (m110) cc_final: 0.7962 (m-40) REVERT: K 198 PHE cc_start: 0.7417 (p90) cc_final: 0.7102 (p90) REVERT: F 98 LEU cc_start: 0.8849 (mt) cc_final: 0.8409 (mt) REVERT: F 160 ARG cc_start: 0.8441 (mpt180) cc_final: 0.7826 (mmp80) REVERT: J 35 MET cc_start: 0.7454 (ptp) cc_final: 0.6718 (tmm) REVERT: J 56 SER cc_start: 0.8549 (p) cc_final: 0.8327 (t) REVERT: J 172 LYS cc_start: 0.8724 (tptp) cc_final: 0.8220 (tppt) REVERT: J 175 LYS cc_start: 0.7626 (ptpp) cc_final: 0.7304 (pttm) REVERT: J 181 ASP cc_start: 0.7794 (t0) cc_final: 0.7267 (t0) REVERT: J 208 MET cc_start: 0.5875 (mpp) cc_final: 0.4831 (mpp) REVERT: H 95 ASP cc_start: 0.8334 (t0) cc_final: 0.7719 (t0) REVERT: H 105 LEU cc_start: 0.7752 (mt) cc_final: 0.7519 (mt) REVERT: H 131 GLU cc_start: 0.6540 (pm20) cc_final: 0.6004 (pm20) REVERT: L 35 MET cc_start: 0.6712 (mtm) cc_final: 0.6467 (mtm) REVERT: L 85 LYS cc_start: 0.8301 (tptt) cc_final: 0.7317 (tptt) REVERT: L 91 LYS cc_start: 0.7238 (mttm) cc_final: 0.6775 (mttt) REVERT: L 140 ASN cc_start: 0.7845 (p0) cc_final: 0.7496 (p0) REVERT: L 171 LYS cc_start: 0.8103 (mptt) cc_final: 0.7877 (mmtt) REVERT: L 172 LYS cc_start: 0.8793 (mppt) cc_final: 0.8556 (mppt) REVERT: L 197 ASN cc_start: 0.7486 (t0) cc_final: 0.6709 (t0) REVERT: L 213 HIS cc_start: 0.6349 (t70) cc_final: 0.5889 (t-90) REVERT: L 228 LYS cc_start: 0.8535 (tptm) cc_final: 0.7959 (tptp) REVERT: L 229 LYS cc_start: 0.8865 (tptt) cc_final: 0.8563 (tptp) outliers start: 2 outliers final: 0 residues processed: 457 average time/residue: 0.3891 time to fit residues: 251.0571 Evaluate side-chains 413 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 9 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 167 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 156 optimal weight: 0.4980 chunk 170 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 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 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 GLN ** 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 = 0.4836 r_free = 0.4836 target = 0.214629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.187525 restraints weight = 48473.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.187657 restraints weight = 62680.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.189368 restraints weight = 51709.283| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.3076 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= 0.142 Angle : 0.652 10.242 22387 Z= 0.332 Chirality : 0.046 0.222 2482 Planarity : 0.005 0.057 2871 Dihedral : 5.275 28.009 2241 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.18), residues: 2005 helix: -2.58 (0.57), residues: 66 sheet: -0.97 (0.18), residues: 788 loop : -1.33 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 119 HIS 0.005 0.001 HIS G 135 PHE 0.015 0.001 PHE K 94 TYR 0.012 0.001 TYR K 97 ARG 0.008 0.001 ARG H 142 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 293) hydrogen bonds : angle 7.70793 ( 744) SS BOND : bond 0.00446 ( 41) SS BOND : angle 1.75333 ( 82) covalent geometry : bond 0.00314 (16439) covalent geometry : angle 0.64499 (22305) *********************** 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 441 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 2.505 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: A 93 GLU cc_start: 0.7923 (mp0) cc_final: 0.6846 (mp0) REVERT: A 105 LEU cc_start: 0.7997 (mt) cc_final: 0.7681 (mt) REVERT: A 129 ASN cc_start: 0.6712 (p0) cc_final: 0.6470 (p0) REVERT: A 137 GLN cc_start: 0.7311 (pm20) cc_final: 0.6927 (pm20) REVERT: A 157 LEU cc_start: 0.8548 (tp) cc_final: 0.8308 (tp) REVERT: A 162 TYR cc_start: 0.6427 (t80) cc_final: 0.6050 (t80) REVERT: C 49 ARG cc_start: 0.6724 (tpt90) cc_final: 0.6351 (tpt90) REVERT: C 92 SER cc_start: 0.6948 (t) cc_final: 0.6428 (p) REVERT: C 100 VAL cc_start: 0.6827 (m) cc_final: 0.6391 (p) REVERT: C 167 MET cc_start: 0.6635 (tpp) cc_final: 0.5976 (tpp) REVERT: C 219 PHE cc_start: 0.6960 (p90) cc_final: 0.6648 (p90) REVERT: C 262 ILE cc_start: 0.6659 (mt) cc_final: 0.6213 (mt) REVERT: B 96 ARG cc_start: 0.7855 (tpp80) cc_final: 0.7474 (tpp-160) REVERT: B 105 LEU cc_start: 0.8078 (mt) cc_final: 0.7815 (mt) REVERT: B 123 HIS cc_start: 0.7704 (m90) cc_final: 0.7350 (m90) REVERT: B 141 TYR cc_start: 0.6925 (t80) cc_final: 0.5973 (t80) REVERT: B 176 MET cc_start: 0.4104 (ptm) cc_final: 0.3875 (ptm) REVERT: D 126 PHE cc_start: 0.6126 (m-80) cc_final: 0.5571 (m-80) REVERT: D 146 MET cc_start: -0.1063 (mmt) cc_final: -0.1280 (mmt) REVERT: E 103 GLN cc_start: 0.7929 (mm110) cc_final: 0.7359 (mm-40) REVERT: E 124 MET cc_start: 0.6376 (tpt) cc_final: 0.5528 (tpt) REVERT: I 35 MET cc_start: 0.8099 (mtm) cc_final: 0.7732 (mtm) REVERT: I 50 VAL cc_start: 0.8330 (m) cc_final: 0.7707 (p) REVERT: I 82 LYS cc_start: 0.7514 (pttm) cc_final: 0.6907 (mtmm) REVERT: I 139 HIS cc_start: 0.7409 (p90) cc_final: 0.7108 (p90) REVERT: G 96 ARG cc_start: 0.7424 (tpt90) cc_final: 0.7034 (tpt170) REVERT: G 114 HIS cc_start: 0.6525 (m-70) cc_final: 0.6066 (m-70) REVERT: G 124 MET cc_start: 0.5573 (tpt) cc_final: 0.5348 (tpt) REVERT: G 143 ARG cc_start: 0.7733 (mpt180) cc_final: 0.7482 (mmt-90) REVERT: K 82 LYS cc_start: 0.6234 (pttt) cc_final: 0.5973 (tppt) REVERT: K 91 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7908 (ptpp) REVERT: K 146 MET cc_start: 0.5863 (mpp) cc_final: 0.5562 (mpp) REVERT: K 147 ASN cc_start: 0.8466 (m110) cc_final: 0.7962 (m-40) REVERT: K 157 PHE cc_start: 0.7744 (t80) cc_final: 0.7523 (t80) REVERT: K 198 PHE cc_start: 0.7599 (p90) cc_final: 0.7258 (p90) REVERT: K 265 LYS cc_start: 0.8043 (mptt) cc_final: 0.7626 (mptt) REVERT: F 98 LEU cc_start: 0.8857 (mt) cc_final: 0.8420 (mt) REVERT: F 141 TYR cc_start: 0.6773 (m-10) cc_final: 0.6474 (m-10) REVERT: F 160 ARG cc_start: 0.8393 (mpt180) cc_final: 0.7982 (mmt180) REVERT: J 35 MET cc_start: 0.7537 (ptp) cc_final: 0.6856 (tmm) REVERT: J 172 LYS cc_start: 0.8750 (tptp) cc_final: 0.8211 (tppt) REVERT: J 175 LYS cc_start: 0.7567 (ptpp) cc_final: 0.7253 (pttm) REVERT: J 180 TRP cc_start: 0.5249 (t60) cc_final: 0.4866 (t60) REVERT: J 181 ASP cc_start: 0.7656 (t0) cc_final: 0.7067 (t0) REVERT: J 208 MET cc_start: 0.5815 (mpp) cc_final: 0.4820 (mpp) REVERT: H 91 ARG cc_start: 0.6905 (mpp-170) cc_final: 0.6577 (mtm-85) REVERT: H 95 ASP cc_start: 0.8251 (t0) cc_final: 0.7646 (t0) REVERT: H 105 LEU cc_start: 0.7792 (mt) cc_final: 0.7585 (mt) REVERT: H 131 GLU cc_start: 0.6538 (pm20) cc_final: 0.6006 (pm20) REVERT: H 162 TYR cc_start: 0.6686 (t80) cc_final: 0.6339 (t80) REVERT: L 35 MET cc_start: 0.6699 (mtm) cc_final: 0.6310 (mtm) REVERT: L 91 LYS cc_start: 0.7185 (mttm) cc_final: 0.6631 (mttt) REVERT: L 140 ASN cc_start: 0.7728 (p0) cc_final: 0.7322 (p0) REVERT: L 171 LYS cc_start: 0.8094 (mptt) cc_final: 0.7758 (mmtt) REVERT: L 197 ASN cc_start: 0.7463 (t0) cc_final: 0.6837 (t0) REVERT: L 213 HIS cc_start: 0.6400 (t70) cc_final: 0.5971 (t70) REVERT: L 228 LYS cc_start: 0.8540 (tptm) cc_final: 0.8110 (mmmm) REVERT: L 229 LYS cc_start: 0.8973 (tptt) cc_final: 0.8655 (tptp) REVERT: L 249 GLN cc_start: 0.5740 (pm20) cc_final: 0.5351 (pm20) outliers start: 1 outliers final: 0 residues processed: 441 average time/residue: 0.3825 time to fit residues: 238.6401 Evaluate side-chains 414 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 145 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN F 123 HIS F 152 HIS J 23 GLN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.209160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.182360 restraints weight = 37703.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.182012 restraints weight = 44088.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.183669 restraints weight = 39884.432| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16480 Z= 0.181 Angle : 0.688 11.955 22387 Z= 0.352 Chirality : 0.047 0.230 2482 Planarity : 0.006 0.058 2871 Dihedral : 5.497 28.533 2241 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.11 % Allowed : 2.34 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 2005 helix: -2.61 (0.57), residues: 66 sheet: -1.09 (0.18), residues: 777 loop : -1.38 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 34 HIS 0.011 0.001 HIS F 135 PHE 0.019 0.001 PHE K 94 TYR 0.015 0.002 TYR K 97 ARG 0.009 0.001 ARG H 142 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 293) hydrogen bonds : angle 7.78959 ( 744) SS BOND : bond 0.00478 ( 41) SS BOND : angle 1.84594 ( 82) covalent geometry : bond 0.00383 (16439) covalent geometry : angle 0.68061 (22305) *********************** 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 444 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 442 time to evaluate : 1.764 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: A 105 LEU cc_start: 0.7933 (mt) cc_final: 0.7600 (mt) REVERT: A 129 ASN cc_start: 0.6745 (p0) cc_final: 0.6393 (p0) REVERT: A 157 LEU cc_start: 0.8583 (tp) cc_final: 0.8338 (tp) REVERT: A 162 TYR cc_start: 0.6531 (t80) cc_final: 0.6227 (t80) REVERT: C 49 ARG cc_start: 0.6951 (tpt90) cc_final: 0.6616 (tpt90) REVERT: C 84 THR cc_start: 0.8269 (m) cc_final: 0.7999 (m) REVERT: C 100 VAL cc_start: 0.6903 (m) cc_final: 0.6462 (p) REVERT: C 167 MET cc_start: 0.6695 (tpp) cc_final: 0.6021 (tpp) REVERT: C 219 PHE cc_start: 0.6861 (p90) cc_final: 0.6624 (p90) REVERT: C 262 ILE cc_start: 0.6616 (mt) cc_final: 0.6061 (mt) REVERT: B 93 GLU cc_start: 0.5743 (mp0) cc_final: 0.5439 (mp0) REVERT: B 96 ARG cc_start: 0.7901 (tpp80) cc_final: 0.7544 (tpp-160) REVERT: B 123 HIS cc_start: 0.7561 (m90) cc_final: 0.7262 (m90) REVERT: B 141 TYR cc_start: 0.6653 (t80) cc_final: 0.5751 (t80) REVERT: D 126 PHE cc_start: 0.6032 (m-80) cc_final: 0.5543 (m-80) REVERT: D 146 MET cc_start: -0.1019 (mmt) cc_final: -0.1271 (mmt) REVERT: E 103 GLN cc_start: 0.8048 (mm110) cc_final: 0.7447 (mm-40) REVERT: E 124 MET cc_start: 0.6336 (tpt) cc_final: 0.5524 (tpt) REVERT: I 50 VAL cc_start: 0.8444 (m) cc_final: 0.7796 (p) REVERT: I 82 LYS cc_start: 0.7489 (pttm) cc_final: 0.6817 (mtmm) REVERT: I 139 HIS cc_start: 0.7401 (p90) cc_final: 0.7127 (p90) REVERT: I 249 GLN cc_start: 0.7044 (tp-100) cc_final: 0.6395 (tp40) REVERT: G 96 ARG cc_start: 0.7442 (tpt90) cc_final: 0.6914 (tpt170) REVERT: G 114 HIS cc_start: 0.6574 (m-70) cc_final: 0.6118 (m-70) REVERT: G 124 MET cc_start: 0.5790 (tpt) cc_final: 0.5545 (tpt) REVERT: K 67 ASN cc_start: 0.6594 (m-40) cc_final: 0.6234 (m-40) REVERT: K 91 LYS cc_start: 0.8142 (ptpt) cc_final: 0.7864 (ptpp) REVERT: K 146 MET cc_start: 0.5700 (mpp) cc_final: 0.5485 (mpp) REVERT: K 147 ASN cc_start: 0.8467 (m110) cc_final: 0.7992 (m-40) REVERT: K 198 PHE cc_start: 0.7407 (p90) cc_final: 0.7086 (p90) REVERT: K 219 PHE cc_start: 0.6336 (t80) cc_final: 0.6034 (t80) REVERT: K 265 LYS cc_start: 0.7925 (mptt) cc_final: 0.7496 (mptt) REVERT: F 98 LEU cc_start: 0.8847 (mt) cc_final: 0.8579 (mt) REVERT: F 160 ARG cc_start: 0.8384 (mpt180) cc_final: 0.8056 (mmp80) REVERT: J 35 MET cc_start: 0.7477 (ptp) cc_final: 0.6752 (tmm) REVERT: J 172 LYS cc_start: 0.8706 (tptp) cc_final: 0.8125 (tppt) REVERT: J 175 LYS cc_start: 0.7606 (ptpp) cc_final: 0.7330 (pttm) REVERT: J 181 ASP cc_start: 0.7899 (t0) cc_final: 0.7340 (t0) REVERT: J 208 MET cc_start: 0.5637 (mpp) cc_final: 0.4869 (mpp) REVERT: H 91 ARG cc_start: 0.6886 (mpp-170) cc_final: 0.6557 (mtm-85) REVERT: H 95 ASP cc_start: 0.8303 (t0) cc_final: 0.7866 (t70) REVERT: H 103 GLN cc_start: 0.7351 (pt0) cc_final: 0.6877 (mt0) REVERT: H 109 ARG cc_start: 0.7236 (mmt-90) cc_final: 0.7006 (mmt-90) REVERT: H 131 GLU cc_start: 0.6628 (pm20) cc_final: 0.6070 (pm20) REVERT: H 157 LEU cc_start: 0.8413 (tp) cc_final: 0.8136 (tp) REVERT: H 162 TYR cc_start: 0.6777 (t80) cc_final: 0.6435 (t80) REVERT: L 35 MET cc_start: 0.6518 (mtm) cc_final: 0.6178 (mtm) REVERT: L 140 ASN cc_start: 0.7965 (p0) cc_final: 0.7469 (p0) REVERT: L 172 LYS cc_start: 0.8812 (mppt) cc_final: 0.8505 (mppt) REVERT: L 197 ASN cc_start: 0.7281 (t0) cc_final: 0.6720 (t0) REVERT: L 210 LEU cc_start: 0.7063 (mm) cc_final: 0.6858 (mm) REVERT: L 213 HIS cc_start: 0.6441 (t70) cc_final: 0.6010 (t70) REVERT: L 228 LYS cc_start: 0.8547 (tptm) cc_final: 0.7968 (tptp) REVERT: L 229 LYS cc_start: 0.8859 (tptt) cc_final: 0.8551 (tptp) outliers start: 2 outliers final: 0 residues processed: 444 average time/residue: 0.3495 time to fit residues: 217.9405 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 : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 148 optimal weight: 0.2980 chunk 163 optimal weight: 0.0070 chunk 174 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 191 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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** G 119 GLN F 123 HIS J 23 GLN ** J 249 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 = 0.4840 r_free = 0.4840 target = 0.215557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.188639 restraints weight = 48207.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.189591 restraints weight = 54734.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.190706 restraints weight = 47295.406| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16480 Z= 0.121 Angle : 0.650 9.682 22387 Z= 0.327 Chirality : 0.045 0.251 2482 Planarity : 0.005 0.056 2871 Dihedral : 5.170 25.685 2241 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.11 % Allowed : 1.00 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2005 helix: -2.49 (0.59), residues: 66 sheet: -0.92 (0.18), residues: 786 loop : -1.25 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 180 HIS 0.006 0.001 HIS F 135 PHE 0.013 0.001 PHE K 94 TYR 0.011 0.001 TYR J 253 ARG 0.013 0.001 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 293) hydrogen bonds : angle 7.38794 ( 744) SS BOND : bond 0.00435 ( 41) SS BOND : angle 1.65099 ( 82) covalent geometry : bond 0.00278 (16439) covalent geometry : angle 0.64341 (22305) *********************** 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 444 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 442 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8006 (mt) cc_final: 0.7692 (mt) REVERT: A 129 ASN cc_start: 0.6852 (p0) cc_final: 0.6523 (p0) REVERT: A 159 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7522 (ttp80) REVERT: A 162 TYR cc_start: 0.6489 (t80) cc_final: 0.6123 (t80) REVERT: C 49 ARG cc_start: 0.6858 (tpt90) cc_final: 0.6460 (tpt90) REVERT: C 92 SER cc_start: 0.6962 (t) cc_final: 0.6474 (p) REVERT: C 98 SER cc_start: 0.6457 (t) cc_final: 0.6246 (p) REVERT: C 100 VAL cc_start: 0.6498 (m) cc_final: 0.6228 (p) REVERT: C 146 MET cc_start: 0.7855 (ppp) cc_final: 0.7373 (ppp) REVERT: C 167 MET cc_start: 0.6465 (tpp) cc_final: 0.5927 (tpp) REVERT: C 219 PHE cc_start: 0.6957 (p90) cc_final: 0.6656 (p90) REVERT: C 262 ILE cc_start: 0.6609 (mt) cc_final: 0.6142 (mt) REVERT: B 96 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7476 (tpp-160) REVERT: B 107 HIS cc_start: 0.5376 (m-70) cc_final: 0.5123 (m90) REVERT: B 162 TYR cc_start: 0.7249 (t80) cc_final: 0.6798 (t80) REVERT: B 176 MET cc_start: 0.4487 (ptm) cc_final: 0.4119 (ptm) REVERT: D 126 PHE cc_start: 0.6028 (m-80) cc_final: 0.5450 (m-80) REVERT: D 146 MET cc_start: -0.1176 (mmt) cc_final: -0.1379 (mmt) REVERT: E 103 GLN cc_start: 0.7946 (mm110) cc_final: 0.7451 (mm-40) REVERT: E 124 MET cc_start: 0.6422 (tpt) cc_final: 0.5543 (tpt) REVERT: I 35 MET cc_start: 0.8074 (mtm) cc_final: 0.7704 (mtm) REVERT: I 50 VAL cc_start: 0.8331 (m) cc_final: 0.7641 (p) REVERT: I 82 LYS cc_start: 0.7634 (pttm) cc_final: 0.6945 (mtmm) REVERT: I 89 THR cc_start: 0.8486 (m) cc_final: 0.8073 (p) REVERT: I 91 LYS cc_start: 0.8223 (ttmt) cc_final: 0.8016 (tttm) REVERT: I 139 HIS cc_start: 0.7365 (p90) cc_final: 0.7127 (p90) REVERT: G 96 ARG cc_start: 0.7385 (tpt90) cc_final: 0.6982 (tpt170) REVERT: G 114 HIS cc_start: 0.6526 (m-70) cc_final: 0.6088 (m-70) REVERT: G 124 MET cc_start: 0.5604 (tpt) cc_final: 0.5376 (tpt) REVERT: K 91 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7511 (mtpt) REVERT: K 147 ASN cc_start: 0.8469 (m110) cc_final: 0.8065 (m-40) REVERT: K 157 PHE cc_start: 0.7763 (t80) cc_final: 0.7487 (t80) REVERT: K 198 PHE cc_start: 0.7572 (p90) cc_final: 0.7214 (p90) REVERT: K 265 LYS cc_start: 0.7880 (mptt) cc_final: 0.7440 (mptt) REVERT: F 109 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7832 (mmt90) REVERT: F 160 ARG cc_start: 0.8444 (mpt180) cc_final: 0.7910 (mmt-90) REVERT: J 23 GLN cc_start: 0.1691 (OUTLIER) cc_final: 0.1466 (pp30) REVERT: J 34 TRP cc_start: 0.7779 (t-100) cc_final: 0.7243 (t-100) REVERT: J 35 MET cc_start: 0.7578 (ptp) cc_final: 0.6883 (tmm) REVERT: J 172 LYS cc_start: 0.8736 (tptp) cc_final: 0.8236 (tppt) REVERT: J 175 LYS cc_start: 0.7307 (ptpp) cc_final: 0.7060 (pttm) REVERT: J 181 ASP cc_start: 0.7804 (t0) cc_final: 0.7564 (t0) REVERT: J 208 MET cc_start: 0.5547 (mpp) cc_final: 0.4669 (mpp) REVERT: J 250 LEU cc_start: 0.7305 (tp) cc_final: 0.6767 (tp) REVERT: H 91 ARG cc_start: 0.6804 (mpp-170) cc_final: 0.6464 (mtm-85) REVERT: H 95 ASP cc_start: 0.8369 (t0) cc_final: 0.7795 (t70) REVERT: H 103 GLN cc_start: 0.7234 (pt0) cc_final: 0.6743 (mt0) REVERT: H 105 LEU cc_start: 0.7718 (mt) cc_final: 0.7436 (mp) REVERT: H 131 GLU cc_start: 0.6505 (pm20) cc_final: 0.5971 (pm20) REVERT: H 157 LEU cc_start: 0.8234 (tp) cc_final: 0.8028 (tp) REVERT: L 85 LYS cc_start: 0.8647 (tptt) cc_final: 0.8203 (tptt) REVERT: L 140 ASN cc_start: 0.7609 (p0) cc_final: 0.7144 (p0) REVERT: L 171 LYS cc_start: 0.7933 (mptt) cc_final: 0.7640 (mmtt) REVERT: L 172 LYS cc_start: 0.8864 (mppt) cc_final: 0.8565 (mppt) REVERT: L 197 ASN cc_start: 0.7554 (t0) cc_final: 0.7010 (t0) REVERT: L 213 HIS cc_start: 0.6499 (t70) cc_final: 0.6043 (t-170) REVERT: L 228 LYS cc_start: 0.8554 (tptm) cc_final: 0.8128 (mmmm) REVERT: L 229 LYS cc_start: 0.8964 (tptt) cc_final: 0.8590 (tptp) REVERT: L 249 GLN cc_start: 0.6119 (pm20) cc_final: 0.5383 (pm20) outliers start: 2 outliers final: 0 residues processed: 444 average time/residue: 0.3759 time to fit residues: 235.4717 Evaluate side-chains 413 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 108 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 16 optimal weight: 0.0570 chunk 160 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN I 249 GLN G 119 GLN K 249 GLN F 123 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.212155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.185055 restraints weight = 41357.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.183624 restraints weight = 46138.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.185934 restraints weight = 38422.889| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16480 Z= 0.141 Angle : 0.664 10.593 22387 Z= 0.334 Chirality : 0.046 0.248 2482 Planarity : 0.005 0.054 2871 Dihedral : 5.202 26.180 2241 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.11 % Allowed : 1.06 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.18), residues: 2005 helix: -2.78 (0.55), residues: 66 sheet: -0.96 (0.19), residues: 752 loop : -1.18 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 180 HIS 0.006 0.001 HIS F 135 PHE 0.027 0.001 PHE C 157 TYR 0.015 0.001 TYR J 253 ARG 0.011 0.001 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 293) hydrogen bonds : angle 7.44548 ( 744) SS BOND : bond 0.00458 ( 41) SS BOND : angle 1.66471 ( 82) covalent geometry : bond 0.00315 (16439) covalent geometry : angle 0.65768 (22305) *********************** 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 434 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 432 time to evaluate : 1.658 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: 0.8022 (mt) cc_final: 0.7660 (mt) REVERT: A 129 ASN cc_start: 0.6775 (p0) cc_final: 0.6410 (p0) REVERT: A 162 TYR cc_start: 0.6594 (t80) cc_final: 0.6268 (t80) REVERT: C 100 VAL cc_start: 0.6679 (m) cc_final: 0.6377 (p) REVERT: C 146 MET cc_start: 0.7606 (ppp) cc_final: 0.7041 (ppp) REVERT: C 167 MET cc_start: 0.6534 (tpp) cc_final: 0.5940 (tpp) REVERT: C 219 PHE cc_start: 0.6964 (p90) cc_final: 0.6648 (p90) REVERT: C 262 ILE cc_start: 0.6599 (mt) cc_final: 0.6145 (mt) REVERT: B 96 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7441 (tpp-160) REVERT: B 123 HIS cc_start: 0.7726 (m90) cc_final: 0.7463 (m90) REVERT: B 141 TYR cc_start: 0.7130 (t80) cc_final: 0.6097 (t80) REVERT: B 176 MET cc_start: 0.4727 (ptm) cc_final: 0.4308 (ptm) REVERT: D 126 PHE cc_start: 0.6217 (m-80) cc_final: 0.5558 (m-80) REVERT: E 103 GLN cc_start: 0.8104 (mm110) cc_final: 0.7580 (mm-40) REVERT: E 124 MET cc_start: 0.6490 (tpt) cc_final: 0.5616 (tpt) REVERT: I 35 MET cc_start: 0.7956 (mtm) cc_final: 0.7634 (mtm) REVERT: I 50 VAL cc_start: 0.8347 (m) cc_final: 0.7686 (p) REVERT: I 82 LYS cc_start: 0.7508 (pttm) cc_final: 0.6790 (mtmm) REVERT: I 89 THR cc_start: 0.8556 (m) cc_final: 0.8184 (p) REVERT: G 96 ARG cc_start: 0.7392 (tpt90) cc_final: 0.7086 (tpt170) REVERT: G 97 ASP cc_start: 0.7057 (t70) cc_final: 0.6698 (t0) REVERT: G 114 HIS cc_start: 0.6685 (m-70) cc_final: 0.6260 (m-70) REVERT: G 124 MET cc_start: 0.5901 (tpt) cc_final: 0.5645 (tpt) REVERT: G 143 ARG cc_start: 0.7414 (mpt180) cc_final: 0.7111 (mmt180) REVERT: K 51 GLU cc_start: 0.5645 (tm-30) cc_final: 0.5210 (tm-30) REVERT: K 67 ASN cc_start: 0.6562 (m-40) cc_final: 0.5418 (m-40) REVERT: K 147 ASN cc_start: 0.8495 (m110) cc_final: 0.8056 (m-40) REVERT: K 172 LYS cc_start: 0.8330 (mmtp) cc_final: 0.7764 (mmtm) REVERT: K 198 PHE cc_start: 0.7656 (p90) cc_final: 0.7305 (p90) REVERT: K 219 PHE cc_start: 0.6325 (t80) cc_final: 0.6006 (t80) REVERT: K 265 LYS cc_start: 0.7999 (mptt) cc_final: 0.7610 (mptt) REVERT: F 109 ARG cc_start: 0.8164 (mmt90) cc_final: 0.7960 (mmt90) REVERT: F 123 HIS cc_start: 0.5587 (m90) cc_final: 0.5362 (m-70) REVERT: F 160 ARG cc_start: 0.8287 (mpt180) cc_final: 0.7808 (mmt-90) REVERT: J 34 TRP cc_start: 0.7768 (t-100) cc_final: 0.7239 (t-100) REVERT: J 35 MET cc_start: 0.7449 (ptp) cc_final: 0.6740 (tmm) REVERT: J 172 LYS cc_start: 0.8722 (tptp) cc_final: 0.8117 (tppt) REVERT: J 175 LYS cc_start: 0.7305 (ptpp) cc_final: 0.7077 (pttm) REVERT: J 181 ASP cc_start: 0.8540 (t0) cc_final: 0.8005 (t0) REVERT: J 208 MET cc_start: 0.5977 (mpp) cc_final: 0.5364 (mpp) REVERT: J 248 VAL cc_start: 0.7448 (m) cc_final: 0.6967 (p) REVERT: H 91 ARG cc_start: 0.6998 (mpp-170) cc_final: 0.6539 (mtm-85) REVERT: H 95 ASP cc_start: 0.8154 (t0) cc_final: 0.7740 (t70) REVERT: H 103 GLN cc_start: 0.7250 (pt0) cc_final: 0.6783 (mt0) REVERT: H 105 LEU cc_start: 0.7654 (mt) cc_final: 0.7056 (mt) REVERT: H 131 GLU cc_start: 0.6616 (pm20) cc_final: 0.6226 (pm20) REVERT: H 157 LEU cc_start: 0.8387 (tp) cc_final: 0.8164 (tp) REVERT: L 140 ASN cc_start: 0.7835 (p0) cc_final: 0.7335 (p0) REVERT: L 171 LYS cc_start: 0.7958 (mptt) cc_final: 0.7284 (mmtt) REVERT: L 172 LYS cc_start: 0.8746 (mppt) cc_final: 0.8277 (mppt) REVERT: L 197 ASN cc_start: 0.7618 (t0) cc_final: 0.7370 (t0) REVERT: L 210 LEU cc_start: 0.7253 (mm) cc_final: 0.7019 (mm) REVERT: L 213 HIS cc_start: 0.6567 (t70) cc_final: 0.6112 (t-170) REVERT: L 228 LYS cc_start: 0.8541 (tptm) cc_final: 0.7959 (tptp) REVERT: L 229 LYS cc_start: 0.8884 (tptt) cc_final: 0.8569 (tptp) outliers start: 2 outliers final: 1 residues processed: 434 average time/residue: 0.3234 time to fit residues: 200.6087 Evaluate side-chains 411 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 60 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 115 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.214754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.187381 restraints weight = 48004.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.187884 restraints weight = 56540.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.189476 restraints weight = 48825.936| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5790 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16480 Z= 0.137 Angle : 0.661 10.555 22387 Z= 0.332 Chirality : 0.046 0.226 2482 Planarity : 0.005 0.056 2871 Dihedral : 5.176 26.030 2241 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.06 % Allowed : 0.95 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 2005 helix: -2.68 (0.55), residues: 66 sheet: -0.87 (0.19), residues: 753 loop : -1.19 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 180 HIS 0.008 0.001 HIS H 135 PHE 0.014 0.001 PHE K 94 TYR 0.014 0.001 TYR J 253 ARG 0.010 0.001 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 293) hydrogen bonds : angle 7.30593 ( 744) SS BOND : bond 0.00500 ( 41) SS BOND : angle 1.66779 ( 82) covalent geometry : bond 0.00309 (16439) covalent geometry : angle 0.65444 (22305) *********************** 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 444 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 2.020 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: 0.8091 (mt) cc_final: 0.7712 (mt) REVERT: A 129 ASN cc_start: 0.6843 (p0) cc_final: 0.6486 (p0) REVERT: A 143 ARG cc_start: 0.6220 (tmm160) cc_final: 0.5792 (tmt170) REVERT: A 156 CYS cc_start: 0.5594 (m) cc_final: 0.2233 (m) REVERT: A 157 LEU cc_start: 0.8651 (tp) cc_final: 0.8310 (tp) REVERT: A 162 TYR cc_start: 0.6662 (t80) cc_final: 0.6174 (t80) REVERT: C 49 ARG cc_start: 0.6854 (tpt90) cc_final: 0.6513 (tpt90) REVERT: C 100 VAL cc_start: 0.6732 (m) cc_final: 0.6458 (p) REVERT: C 146 MET cc_start: 0.7674 (ppp) cc_final: 0.7121 (ppp) REVERT: C 167 MET cc_start: 0.6558 (tpp) cc_final: 0.6000 (tpp) REVERT: C 219 PHE cc_start: 0.6950 (p90) cc_final: 0.6643 (p90) REVERT: C 262 ILE cc_start: 0.6770 (mt) cc_final: 0.6361 (mt) REVERT: B 96 ARG cc_start: 0.7670 (tpp80) cc_final: 0.7424 (tpp-160) REVERT: B 105 LEU cc_start: 0.8232 (mt) cc_final: 0.8009 (mt) REVERT: B 107 HIS cc_start: 0.5918 (m-70) cc_final: 0.5237 (m-70) REVERT: B 123 HIS cc_start: 0.7627 (m90) cc_final: 0.7322 (m90) REVERT: B 162 TYR cc_start: 0.7359 (t80) cc_final: 0.6863 (t80) REVERT: B 164 VAL cc_start: 0.7435 (t) cc_final: 0.6933 (t) REVERT: B 176 MET cc_start: 0.4743 (ptm) cc_final: 0.4266 (ptm) REVERT: D 126 PHE cc_start: 0.6127 (m-80) cc_final: 0.5521 (m-80) REVERT: D 146 MET cc_start: -0.0152 (mmt) cc_final: -0.0674 (mmm) REVERT: E 96 ARG cc_start: 0.6511 (tmm160) cc_final: 0.6056 (tmm160) REVERT: E 103 GLN cc_start: 0.7974 (mm110) cc_final: 0.7450 (mm-40) REVERT: E 124 MET cc_start: 0.6459 (tpt) cc_final: 0.5570 (tpt) REVERT: I 35 MET cc_start: 0.8131 (mtm) cc_final: 0.7726 (mtm) REVERT: I 50 VAL cc_start: 0.8463 (m) cc_final: 0.7775 (p) REVERT: I 82 LYS cc_start: 0.7643 (pttm) cc_final: 0.7040 (mtmm) REVERT: I 89 THR cc_start: 0.8372 (m) cc_final: 0.7938 (p) REVERT: I 128 VAL cc_start: 0.8423 (t) cc_final: 0.8049 (m) REVERT: I 146 MET cc_start: 0.7233 (pmm) cc_final: 0.6754 (mmt) REVERT: I 249 GLN cc_start: 0.6895 (mm110) cc_final: 0.5878 (tp40) REVERT: G 96 ARG cc_start: 0.7558 (tpt90) cc_final: 0.7313 (tpt90) REVERT: G 97 ASP cc_start: 0.7331 (t70) cc_final: 0.7085 (t0) REVERT: G 114 HIS cc_start: 0.6593 (m-70) cc_final: 0.6176 (m-70) REVERT: G 124 MET cc_start: 0.5597 (tpt) cc_final: 0.5322 (tpt) REVERT: K 51 GLU cc_start: 0.5721 (tm-30) cc_final: 0.5255 (tm-30) REVERT: K 67 ASN cc_start: 0.6621 (m-40) cc_final: 0.5510 (m-40) REVERT: K 72 LEU cc_start: 0.8446 (pp) cc_final: 0.8072 (pp) REVERT: K 73 ARG cc_start: 0.7222 (tpp-160) cc_final: 0.6701 (tpm170) REVERT: K 91 LYS cc_start: 0.7991 (ptpt) cc_final: 0.7715 (ptpp) REVERT: K 147 ASN cc_start: 0.8503 (m110) cc_final: 0.8063 (m-40) REVERT: K 157 PHE cc_start: 0.7771 (t80) cc_final: 0.7515 (t80) REVERT: K 172 LYS cc_start: 0.8317 (mmtp) cc_final: 0.7742 (mmtm) REVERT: K 198 PHE cc_start: 0.7594 (p90) cc_final: 0.7156 (p90) REVERT: K 219 PHE cc_start: 0.6395 (t80) cc_final: 0.6107 (t80) REVERT: F 123 HIS cc_start: 0.5834 (m90) cc_final: 0.5594 (m-70) REVERT: F 160 ARG cc_start: 0.8423 (mpt180) cc_final: 0.8021 (mmp80) REVERT: J 35 MET cc_start: 0.7495 (ptp) cc_final: 0.6837 (tmm) REVERT: J 89 THR cc_start: 0.4008 (m) cc_final: 0.3779 (p) REVERT: J 172 LYS cc_start: 0.8756 (tptp) cc_final: 0.8107 (tppt) REVERT: J 175 LYS cc_start: 0.7279 (ptpp) cc_final: 0.7051 (pttm) REVERT: J 181 ASP cc_start: 0.8576 (t0) cc_final: 0.8087 (t0) REVERT: J 208 MET cc_start: 0.5979 (mpp) cc_final: 0.5642 (mpp) REVERT: H 91 ARG cc_start: 0.6997 (mpp-170) cc_final: 0.6521 (mtm-85) REVERT: H 95 ASP cc_start: 0.8337 (t0) cc_final: 0.7806 (t70) REVERT: H 103 GLN cc_start: 0.7291 (pt0) cc_final: 0.6726 (mt0) REVERT: H 105 LEU cc_start: 0.7410 (mt) cc_final: 0.6919 (mt) REVERT: H 131 GLU cc_start: 0.6440 (pm20) cc_final: 0.5914 (pm20) REVERT: H 157 LEU cc_start: 0.8412 (tp) cc_final: 0.8083 (tp) REVERT: H 158 GLU cc_start: 0.7598 (tt0) cc_final: 0.6861 (tm-30) REVERT: L 85 LYS cc_start: 0.8588 (tptt) cc_final: 0.8164 (tptt) REVERT: L 140 ASN cc_start: 0.7847 (p0) cc_final: 0.7338 (p0) REVERT: L 171 LYS cc_start: 0.7901 (mptt) cc_final: 0.7582 (mmtt) REVERT: L 172 LYS cc_start: 0.8792 (mppt) cc_final: 0.8509 (mppt) REVERT: L 197 ASN cc_start: 0.7635 (t0) cc_final: 0.7360 (t0) REVERT: L 210 LEU cc_start: 0.7289 (mm) cc_final: 0.7045 (mm) REVERT: L 213 HIS cc_start: 0.6540 (t70) cc_final: 0.5915 (t-170) REVERT: L 228 LYS cc_start: 0.8578 (tptm) cc_final: 0.8038 (mmmm) REVERT: L 229 LYS cc_start: 0.8869 (tptt) cc_final: 0.8509 (tptp) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.3514 time to fit residues: 218.6024 Evaluate side-chains 409 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 179 optimal weight: 0.0170 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 192 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 0.1980 chunk 100 optimal weight: 0.8980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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** C 139 HIS ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.213667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.187934 restraints weight = 41659.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.188930 restraints weight = 43217.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.190049 restraints weight = 39092.310| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.4215 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= 0.115 Angle : 0.656 10.670 22387 Z= 0.326 Chirality : 0.046 0.233 2482 Planarity : 0.005 0.055 2871 Dihedral : 5.023 24.487 2241 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.18), residues: 2005 helix: -2.66 (0.55), residues: 66 sheet: -0.85 (0.19), residues: 757 loop : -1.15 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 180 HIS 0.008 0.001 HIS A 135 PHE 0.012 0.001 PHE K 94 TYR 0.013 0.001 TYR J 253 ARG 0.015 0.001 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 293) hydrogen bonds : angle 7.23538 ( 744) SS BOND : bond 0.00438 ( 41) SS BOND : angle 1.60545 ( 82) covalent geometry : bond 0.00268 (16439) covalent geometry : angle 0.64987 (22305) ********************** 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 446 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 445 time to evaluate : 3.862 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: 0.8051 (mt) cc_final: 0.7582 (mt) REVERT: A 129 ASN cc_start: 0.6363 (p0) cc_final: 0.6038 (p0) REVERT: A 162 TYR cc_start: 0.6339 (t80) cc_final: 0.6043 (t80) REVERT: C 49 ARG cc_start: 0.6867 (tpt90) cc_final: 0.6516 (tpt90) REVERT: C 100 VAL cc_start: 0.6754 (m) cc_final: 0.6332 (t) REVERT: C 146 MET cc_start: 0.7512 (ppp) cc_final: 0.6889 (ppp) REVERT: C 167 MET cc_start: 0.6417 (tpp) cc_final: 0.5742 (tpp) REVERT: C 219 PHE cc_start: 0.6774 (p90) cc_final: 0.6524 (p90) REVERT: C 262 ILE cc_start: 0.6687 (mt) cc_final: 0.6261 (mt) REVERT: B 96 ARG cc_start: 0.7642 (tpp80) cc_final: 0.7422 (tpp-160) REVERT: B 123 HIS cc_start: 0.7449 (m90) cc_final: 0.7194 (m90) REVERT: B 162 TYR cc_start: 0.7045 (t80) cc_final: 0.6559 (t80) REVERT: B 164 VAL cc_start: 0.7607 (t) cc_final: 0.6973 (t) REVERT: B 176 MET cc_start: 0.4639 (ptm) cc_final: 0.4200 (ptm) REVERT: D 126 PHE cc_start: 0.5907 (m-80) cc_final: 0.5397 (m-80) REVERT: D 146 MET cc_start: -0.0429 (mmt) cc_final: -0.0631 (mmm) REVERT: E 96 ARG cc_start: 0.6416 (tmm160) cc_final: 0.5979 (tmm160) REVERT: E 103 GLN cc_start: 0.8009 (mm110) cc_final: 0.7483 (mm-40) REVERT: E 124 MET cc_start: 0.6407 (tpt) cc_final: 0.5598 (tpt) REVERT: I 35 MET cc_start: 0.8073 (mtm) cc_final: 0.7705 (mtm) REVERT: I 50 VAL cc_start: 0.8524 (m) cc_final: 0.7927 (p) REVERT: I 82 LYS cc_start: 0.7493 (pttm) cc_final: 0.6885 (mtmm) REVERT: I 89 THR cc_start: 0.8488 (m) cc_final: 0.8086 (p) REVERT: I 91 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7972 (tttm) REVERT: I 146 MET cc_start: 0.7014 (pmm) cc_final: 0.6636 (mmt) REVERT: I 195 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6637 (mm-30) REVERT: I 249 GLN cc_start: 0.6506 (mm110) cc_final: 0.5632 (tp40) REVERT: G 91 ARG cc_start: 0.8637 (ptt-90) cc_final: 0.8052 (ppt-90) REVERT: G 96 ARG cc_start: 0.7360 (tpt90) cc_final: 0.6944 (tpt170) REVERT: G 114 HIS cc_start: 0.6616 (m-70) cc_final: 0.6146 (m-70) REVERT: G 124 MET cc_start: 0.5734 (tpt) cc_final: 0.5460 (tpt) REVERT: K 51 GLU cc_start: 0.5684 (tm-30) cc_final: 0.5267 (tm-30) REVERT: K 67 ASN cc_start: 0.6363 (m-40) cc_final: 0.5206 (m-40) REVERT: K 73 ARG cc_start: 0.7457 (tpp-160) cc_final: 0.6696 (tpp-160) REVERT: K 147 ASN cc_start: 0.8506 (m110) cc_final: 0.7941 (m-40) REVERT: K 157 PHE cc_start: 0.7752 (t80) cc_final: 0.7470 (t80) REVERT: K 172 LYS cc_start: 0.8357 (mmtp) cc_final: 0.7778 (mmtm) REVERT: K 198 PHE cc_start: 0.7348 (p90) cc_final: 0.7047 (p90) REVERT: K 219 PHE cc_start: 0.6157 (t80) cc_final: 0.5896 (t80) REVERT: F 160 ARG cc_start: 0.8391 (mpt180) cc_final: 0.8018 (mmt-90) REVERT: J 34 TRP cc_start: 0.7727 (t-100) cc_final: 0.7206 (t-100) REVERT: J 35 MET cc_start: 0.7457 (ptp) cc_final: 0.6915 (tmm) REVERT: J 49 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8040 (mmm-85) REVERT: J 89 THR cc_start: 0.3949 (m) cc_final: 0.3724 (p) REVERT: J 172 LYS cc_start: 0.8785 (tptp) cc_final: 0.8234 (tppt) REVERT: J 181 ASP cc_start: 0.8661 (t0) cc_final: 0.8186 (t0) REVERT: J 251 THR cc_start: 0.7309 (m) cc_final: 0.6895 (m) REVERT: H 95 ASP cc_start: 0.8113 (t0) cc_final: 0.7713 (t70) REVERT: H 103 GLN cc_start: 0.7095 (pt0) cc_final: 0.6564 (mt0) REVERT: H 105 LEU cc_start: 0.7209 (mt) cc_final: 0.6719 (mt) REVERT: H 131 GLU cc_start: 0.6550 (pm20) cc_final: 0.6171 (pm20) REVERT: H 157 LEU cc_start: 0.8433 (tp) cc_final: 0.8112 (tp) REVERT: H 158 GLU cc_start: 0.7778 (tt0) cc_final: 0.7039 (tm-30) REVERT: L 85 LYS cc_start: 0.8673 (tptt) cc_final: 0.8191 (tptt) REVERT: L 140 ASN cc_start: 0.7633 (p0) cc_final: 0.7160 (p0) REVERT: L 171 LYS cc_start: 0.7841 (mptt) cc_final: 0.7198 (mmtt) REVERT: L 172 LYS cc_start: 0.8494 (mppt) cc_final: 0.8120 (mppt) REVERT: L 213 HIS cc_start: 0.6413 (t70) cc_final: 0.5819 (t-170) REVERT: L 228 LYS cc_start: 0.8515 (tptm) cc_final: 0.7975 (mmmm) REVERT: L 229 LYS cc_start: 0.8874 (tptt) cc_final: 0.8529 (tptp) REVERT: L 249 GLN cc_start: 0.6115 (pm20) cc_final: 0.5318 (mp10) outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.3384 time to fit residues: 214.3670 Evaluate side-chains 406 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 139 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 174 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 95 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.211133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.185166 restraints weight = 41434.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.185984 restraints weight = 44949.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.187514 restraints weight = 38555.034| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 moved from start: 0.4388 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= 0.158 Angle : 0.686 10.645 22387 Z= 0.345 Chirality : 0.046 0.207 2482 Planarity : 0.005 0.054 2871 Dihedral : 5.234 26.000 2241 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.18), residues: 2005 helix: -2.62 (0.60), residues: 60 sheet: -0.96 (0.18), residues: 781 loop : -1.15 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 34 HIS 0.007 0.001 HIS D 264 PHE 0.017 0.001 PHE K 94 TYR 0.015 0.001 TYR J 253 ARG 0.011 0.001 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 293) hydrogen bonds : angle 7.45506 ( 744) SS BOND : bond 0.00485 ( 41) SS BOND : angle 1.76749 ( 82) covalent geometry : bond 0.00346 (16439) covalent geometry : angle 0.67879 (22305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6793.03 seconds wall clock time: 123 minutes 27.18 seconds (7407.18 seconds total)