Starting phenix.real_space_refine on Tue Dec 31 15:32:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwk_26834/12_2024/7uwk_26834.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwk_26834/12_2024/7uwk_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_26834/12_2024/7uwk_26834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwk_26834/12_2024/7uwk_26834.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwk_26834/12_2024/7uwk_26834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwk_26834/12_2024/7uwk_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-5532/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: 10.01, per 1000 atoms: 0.62 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: 3.87 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: 1.82 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: 4.33 Time building geometry restraints manager: 4.44 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 35.530 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- 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 16439 Z= 0.246 Angle : 0.801 10.932 22305 Z= 0.437 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 *********************** 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 : 1.645 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: 0.3430 time to fit residues: 218.7531 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 : 2.333 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 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 16439 Z= 0.179 Angle : 0.633 11.015 22305 Z= 0.323 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 *********************** 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 : 1.734 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 164 VAL cc_start: 0.6362 (p) cc_final: 0.5849 (t) REVERT: A 176 MET cc_start: 0.1721 (ppp) cc_final: 0.1493 (ppp) REVERT: C 67 ASN cc_start: 0.7309 (t0) cc_final: 0.7032 (t0) REVERT: C 84 THR cc_start: 0.7440 (m) cc_final: 0.7137 (m) REVERT: C 100 VAL cc_start: 0.5757 (m) cc_final: 0.5509 (p) REVERT: C 167 MET cc_start: 0.5527 (tpp) cc_final: 0.5232 (tpp) REVERT: C 262 ILE cc_start: 0.6607 (mt) cc_final: 0.6192 (mt) REVERT: B 96 ARG cc_start: 0.7387 (tpp-160) cc_final: 0.7054 (tpp80) REVERT: E 103 GLN cc_start: 0.8054 (mm110) cc_final: 0.7445 (mm-40) REVERT: E 124 MET cc_start: 0.5652 (tpt) cc_final: 0.4987 (tpt) REVERT: I 50 VAL cc_start: 0.8211 (t) cc_final: 0.7674 (p) REVERT: I 82 LYS cc_start: 0.7141 (pttm) cc_final: 0.6655 (mtmm) REVERT: I 148 GLU cc_start: 0.5937 (mp0) cc_final: 0.5735 (mp0) REVERT: I 206 ARG cc_start: 0.6891 (ttp80) cc_final: 0.6152 (ttp80) REVERT: G 96 ARG cc_start: 0.6936 (tpt90) cc_final: 0.6357 (tpt170) REVERT: G 176 MET cc_start: 0.5086 (mmm) cc_final: 0.4718 (tpt) REVERT: K 82 LYS cc_start: 0.6689 (pttt) cc_final: 0.6432 (pttp) REVERT: K 147 ASN cc_start: 0.8366 (m110) cc_final: 0.7943 (m-40) REVERT: F 141 TYR cc_start: 0.6182 (m-10) cc_final: 0.5956 (m-10) REVERT: J 35 MET cc_start: 0.6831 (ptp) cc_final: 0.5899 (tmm) REVERT: J 172 LYS cc_start: 0.8742 (tptp) cc_final: 0.7708 (tppt) REVERT: J 181 ASP cc_start: 0.7095 (t0) cc_final: 0.6626 (t0) REVERT: J 208 MET cc_start: 0.4311 (mpp) cc_final: 0.4029 (mpp) REVERT: H 99 ASN cc_start: 0.6395 (m-40) cc_final: 0.5716 (t0) REVERT: H 133 LEU cc_start: 0.7669 (mm) cc_final: 0.7342 (mm) REVERT: L 35 MET cc_start: 0.6380 (mtm) cc_final: 0.6055 (mtm) REVERT: L 197 ASN cc_start: 0.7117 (t0) cc_final: 0.6400 (t0) REVERT: L 229 LYS cc_start: 0.8739 (tptt) cc_final: 0.8496 (tptp) outliers start: 7 outliers final: 3 residues processed: 459 average time/residue: 0.3416 time to fit residues: 218.2647 Evaluate side-chains 411 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 408 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 146 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS C 23 GLN C 95 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5535 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16439 Z= 0.224 Angle : 0.649 10.782 22305 Z= 0.332 Chirality : 0.046 0.221 2482 Planarity : 0.006 0.060 2871 Dihedral : 5.269 26.021 2241 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.17 % Allowed : 3.46 % Favored : 96.38 % 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: -1.59 (0.18), residues: 2005 helix: -2.79 (0.54), residues: 66 sheet: -0.69 (0.19), residues: 746 loop : -1.18 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 34 HIS 0.005 0.001 HIS F 135 PHE 0.019 0.001 PHE K 94 TYR 0.016 0.002 TYR H 134 ARG 0.013 0.001 ARG H 159 *********************** 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 458 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 455 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.6062 (p) cc_final: 0.5753 (t) REVERT: C 84 THR cc_start: 0.7692 (m) cc_final: 0.7338 (m) REVERT: C 92 SER cc_start: 0.7484 (t) cc_final: 0.7246 (p) REVERT: C 95 GLN cc_start: 0.6743 (tp40) cc_final: 0.6359 (tm-30) REVERT: C 100 VAL cc_start: 0.6357 (m) cc_final: 0.5982 (p) REVERT: C 167 MET cc_start: 0.5702 (tpp) cc_final: 0.5304 (tpp) REVERT: C 214 SER cc_start: 0.7609 (p) cc_final: 0.7366 (p) REVERT: B 141 TYR cc_start: 0.5629 (t80) cc_final: 0.5018 (t80) REVERT: E 103 GLN cc_start: 0.7998 (mm110) cc_final: 0.7443 (mm-40) REVERT: E 124 MET cc_start: 0.5687 (tpt) cc_final: 0.5132 (tpt) REVERT: I 50 VAL cc_start: 0.8150 (t) cc_final: 0.7937 (m) REVERT: I 82 LYS cc_start: 0.7203 (pttm) cc_final: 0.6623 (mtmm) REVERT: I 206 ARG cc_start: 0.7011 (ttp80) cc_final: 0.6166 (ttp80) REVERT: G 96 ARG cc_start: 0.6991 (tpt90) cc_final: 0.6547 (tpt170) REVERT: G 140 PHE cc_start: 0.6582 (m-10) cc_final: 0.6372 (m-10) REVERT: K 147 ASN cc_start: 0.8407 (m110) cc_final: 0.7969 (m-40) REVERT: F 141 TYR cc_start: 0.6350 (m-10) cc_final: 0.5798 (m-10) REVERT: J 35 MET cc_start: 0.6539 (ptp) cc_final: 0.6220 (tmm) REVERT: J 51 GLU cc_start: 0.6397 (mp0) cc_final: 0.6185 (mp0) REVERT: J 172 LYS cc_start: 0.8479 (tptp) cc_final: 0.8013 (tppt) REVERT: J 175 LYS cc_start: 0.7195 (ptpp) cc_final: 0.6801 (pttm) REVERT: J 181 ASP cc_start: 0.7320 (t0) cc_final: 0.6758 (t0) REVERT: J 208 MET cc_start: 0.4515 (mpp) cc_final: 0.3722 (mpp) REVERT: J 215 THR cc_start: 0.4931 (p) cc_final: 0.3860 (p) REVERT: H 95 ASP cc_start: 0.7868 (t0) cc_final: 0.7631 (t0) REVERT: H 105 LEU cc_start: 0.7314 (mt) cc_final: 0.7041 (mm) REVERT: H 162 TYR cc_start: 0.6839 (t80) cc_final: 0.6052 (t80) REVERT: L 197 ASN cc_start: 0.7070 (t0) cc_final: 0.6248 (t0) REVERT: L 228 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7768 (tmmt) REVERT: L 229 LYS cc_start: 0.8760 (tptt) cc_final: 0.8517 (tptp) outliers start: 3 outliers final: 0 residues processed: 457 average time/residue: 0.3541 time to fit residues: 228.0716 Evaluate side-chains 417 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 123 HIS F 152 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** L 213 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 16439 Z= 0.293 Angle : 0.706 13.623 22305 Z= 0.362 Chirality : 0.047 0.216 2482 Planarity : 0.006 0.098 2871 Dihedral : 5.581 28.775 2241 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % 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: -1.96 (0.18), residues: 2005 helix: -2.80 (0.52), residues: 72 sheet: -1.01 (0.18), residues: 793 loop : -1.39 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 34 HIS 0.007 0.001 HIS E 135 PHE 0.022 0.002 PHE K 135 TYR 0.023 0.002 TYR K 97 ARG 0.010 0.001 ARG B 109 *********************** 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 456 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 454 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7303 (tp) cc_final: 0.6879 (tp) REVERT: A 94 LEU cc_start: 0.7144 (tp) cc_final: 0.6847 (tp) REVERT: C 84 THR cc_start: 0.7718 (m) cc_final: 0.7310 (m) REVERT: C 92 SER cc_start: 0.7329 (t) cc_final: 0.7001 (p) REVERT: C 100 VAL cc_start: 0.6153 (m) cc_final: 0.5855 (p) REVERT: C 167 MET cc_start: 0.5341 (tpp) cc_final: 0.4849 (tpp) REVERT: C 214 SER cc_start: 0.7655 (p) cc_final: 0.7411 (p) REVERT: C 262 ILE cc_start: 0.6646 (mt) cc_final: 0.6115 (mt) REVERT: B 141 TYR cc_start: 0.5926 (t80) cc_final: 0.5270 (t80) REVERT: D 146 MET cc_start: -0.0371 (mmt) cc_final: -0.0755 (mmt) REVERT: E 103 GLN cc_start: 0.8031 (mm110) cc_final: 0.7619 (mm-40) REVERT: E 124 MET cc_start: 0.5870 (tpt) cc_final: 0.5425 (tpt) REVERT: I 82 LYS cc_start: 0.7226 (pttm) cc_final: 0.6535 (mtmm) REVERT: I 206 ARG cc_start: 0.7004 (ttp80) cc_final: 0.6180 (ttp80) REVERT: G 96 ARG cc_start: 0.7188 (tpt90) cc_final: 0.6734 (tpt170) REVERT: K 91 LYS cc_start: 0.7763 (ptpp) cc_final: 0.7254 (mtmm) REVERT: K 147 ASN cc_start: 0.8361 (m110) cc_final: 0.7806 (m-40) REVERT: K 219 PHE cc_start: 0.5610 (t80) cc_final: 0.5378 (t80) REVERT: K 265 LYS cc_start: 0.7931 (mptt) cc_final: 0.7608 (mptt) REVERT: J 35 MET cc_start: 0.6937 (ptp) cc_final: 0.6469 (tmm) REVERT: J 171 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8189 (mmtm) REVERT: J 172 LYS cc_start: 0.8576 (tptp) cc_final: 0.8083 (tppt) REVERT: J 175 LYS cc_start: 0.7370 (ptpp) cc_final: 0.6944 (pttm) REVERT: J 181 ASP cc_start: 0.7644 (t0) cc_final: 0.7032 (t0) REVERT: J 208 MET cc_start: 0.4211 (mpp) cc_final: 0.3781 (mpp) REVERT: L 35 MET cc_start: 0.6525 (mtm) cc_final: 0.6259 (mtm) REVERT: L 197 ASN cc_start: 0.7364 (t0) cc_final: 0.6530 (t0) REVERT: L 228 LYS cc_start: 0.8104 (tmtt) cc_final: 0.7785 (mmmm) outliers start: 2 outliers final: 0 residues processed: 456 average time/residue: 0.3312 time to fit residues: 211.0183 Evaluate side-chains 417 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 0.0040 chunk 174 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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** D 249 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 GLN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16439 Z= 0.211 Angle : 0.657 10.078 22305 Z= 0.334 Chirality : 0.046 0.216 2482 Planarity : 0.005 0.064 2871 Dihedral : 5.369 28.406 2241 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.10 % 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: -1.85 (0.18), residues: 2005 helix: -2.50 (0.60), residues: 60 sheet: -0.98 (0.18), residues: 801 loop : -1.31 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 34 HIS 0.007 0.001 HIS G 107 PHE 0.016 0.001 PHE K 94 TYR 0.020 0.001 TYR F 141 ARG 0.006 0.001 ARG A 142 *********************** 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 447 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 445 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.5752 (p) cc_final: 0.5217 (t) REVERT: C 84 THR cc_start: 0.7686 (m) cc_final: 0.7297 (m) REVERT: C 92 SER cc_start: 0.6960 (t) cc_final: 0.6543 (p) REVERT: C 100 VAL cc_start: 0.6123 (m) cc_final: 0.5694 (p) REVERT: C 167 MET cc_start: 0.5478 (tpp) cc_final: 0.4943 (tpp) REVERT: C 214 SER cc_start: 0.7652 (p) cc_final: 0.7396 (p) REVERT: C 262 ILE cc_start: 0.6551 (mt) cc_final: 0.6047 (mt) REVERT: B 141 TYR cc_start: 0.5937 (t80) cc_final: 0.5268 (t80) REVERT: D 146 MET cc_start: -0.0436 (mmt) cc_final: -0.0762 (mmt) REVERT: E 103 GLN cc_start: 0.7951 (mm110) cc_final: 0.7502 (mm-40) REVERT: E 124 MET cc_start: 0.5844 (tpt) cc_final: 0.5627 (tpt) REVERT: I 50 VAL cc_start: 0.7903 (t) cc_final: 0.7666 (m) REVERT: I 82 LYS cc_start: 0.7121 (pttm) cc_final: 0.6573 (mtmm) REVERT: G 96 ARG cc_start: 0.7026 (tpt90) cc_final: 0.6555 (tpt170) REVERT: G 124 MET cc_start: 0.5285 (tpt) cc_final: 0.4872 (tpt) REVERT: K 51 GLU cc_start: 0.5023 (tm-30) cc_final: 0.4669 (tm-30) REVERT: K 91 LYS cc_start: 0.7662 (ptpp) cc_final: 0.7363 (mtpt) REVERT: K 124 ILE cc_start: 0.8528 (mp) cc_final: 0.8325 (mm) REVERT: K 147 ASN cc_start: 0.8308 (m110) cc_final: 0.7801 (m-40) REVERT: K 265 LYS cc_start: 0.7669 (mptt) cc_final: 0.7331 (mptt) REVERT: F 98 LEU cc_start: 0.8344 (mt) cc_final: 0.8027 (mt) REVERT: J 35 MET cc_start: 0.6976 (ptp) cc_final: 0.6613 (tmm) REVERT: J 171 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8187 (mmtm) REVERT: J 172 LYS cc_start: 0.8576 (tptp) cc_final: 0.8084 (tppt) REVERT: J 175 LYS cc_start: 0.7288 (ptpp) cc_final: 0.6947 (pttm) REVERT: J 181 ASP cc_start: 0.7325 (t0) cc_final: 0.7086 (t0) REVERT: J 208 MET cc_start: 0.3611 (mpp) cc_final: 0.3258 (mpp) REVERT: H 103 GLN cc_start: 0.7034 (pt0) cc_final: 0.6594 (mt0) REVERT: H 109 ARG cc_start: 0.6797 (mmt-90) cc_final: 0.6576 (mmt-90) REVERT: L 35 MET cc_start: 0.6426 (mtm) cc_final: 0.5995 (mtm) REVERT: L 91 LYS cc_start: 0.7729 (mttm) cc_final: 0.7458 (mttt) REVERT: L 197 ASN cc_start: 0.7013 (t0) cc_final: 0.6214 (t0) REVERT: L 228 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7698 (mmmm) outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.3371 time to fit residues: 211.0010 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 : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 GLN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16439 Z= 0.241 Angle : 0.669 11.360 22305 Z= 0.341 Chirality : 0.046 0.234 2482 Planarity : 0.005 0.058 2871 Dihedral : 5.410 28.039 2241 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.94 % 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: -1.93 (0.18), residues: 2005 helix: -2.58 (0.57), residues: 66 sheet: -1.05 (0.18), residues: 802 loop : -1.34 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 180 HIS 0.007 0.001 HIS F 135 PHE 0.018 0.001 PHE K 94 TYR 0.014 0.002 TYR K 97 ARG 0.008 0.001 ARG E 142 *********************** 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 441 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 439 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.5730 (p) cc_final: 0.5178 (t) REVERT: C 92 SER cc_start: 0.6964 (t) cc_final: 0.6657 (p) REVERT: C 167 MET cc_start: 0.6453 (tpp) cc_final: 0.5742 (tpp) REVERT: C 214 SER cc_start: 0.7685 (p) cc_final: 0.7414 (p) REVERT: C 230 GLN cc_start: 0.6628 (pp30) cc_final: 0.6422 (pp30) REVERT: C 262 ILE cc_start: 0.6583 (mt) cc_final: 0.6063 (mt) REVERT: B 141 TYR cc_start: 0.6008 (t80) cc_final: 0.5326 (t80) REVERT: B 164 VAL cc_start: 0.7197 (p) cc_final: 0.6944 (t) REVERT: D 146 MET cc_start: -0.0386 (mmt) cc_final: -0.0736 (mmt) REVERT: E 103 GLN cc_start: 0.7990 (mm110) cc_final: 0.7532 (mm-40) REVERT: E 124 MET cc_start: 0.5890 (tpt) cc_final: 0.5468 (tpt) REVERT: I 50 VAL cc_start: 0.7641 (t) cc_final: 0.7359 (m) REVERT: I 82 LYS cc_start: 0.7271 (pttm) cc_final: 0.6614 (mtmm) REVERT: I 128 VAL cc_start: 0.8318 (t) cc_final: 0.8016 (m) REVERT: G 96 ARG cc_start: 0.7144 (tpt90) cc_final: 0.6599 (tpt170) REVERT: G 124 MET cc_start: 0.5435 (tpt) cc_final: 0.5109 (tpt) REVERT: K 147 ASN cc_start: 0.8304 (m110) cc_final: 0.7859 (m-40) REVERT: K 265 LYS cc_start: 0.7485 (mppt) cc_final: 0.7201 (mptt) REVERT: F 141 TYR cc_start: 0.6432 (m-10) cc_final: 0.6140 (m-10) REVERT: J 35 MET cc_start: 0.6903 (ptp) cc_final: 0.6552 (tmm) REVERT: J 172 LYS cc_start: 0.8529 (tptp) cc_final: 0.8050 (tppt) REVERT: J 175 LYS cc_start: 0.7295 (ptpp) cc_final: 0.6998 (pttm) REVERT: J 181 ASP cc_start: 0.8220 (t0) cc_final: 0.7730 (t0) REVERT: J 208 MET cc_start: 0.3633 (mpp) cc_final: 0.3279 (mpp) REVERT: H 103 GLN cc_start: 0.6985 (pt0) cc_final: 0.6617 (mt0) REVERT: H 164 VAL cc_start: 0.6928 (t) cc_final: 0.6591 (t) REVERT: L 35 MET cc_start: 0.6241 (mtm) cc_final: 0.6004 (mtm) REVERT: L 197 ASN cc_start: 0.6948 (t0) cc_final: 0.6425 (t0) REVERT: L 210 LEU cc_start: 0.7331 (mm) cc_final: 0.7095 (mm) outliers start: 2 outliers final: 0 residues processed: 441 average time/residue: 0.3349 time to fit residues: 208.4451 Evaluate side-chains 415 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16439 Z= 0.233 Angle : 0.670 11.198 22305 Z= 0.340 Chirality : 0.046 0.223 2482 Planarity : 0.005 0.052 2871 Dihedral : 5.416 27.575 2241 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.06 % Allowed : 1.51 % Favored : 98.44 % 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: -1.92 (0.18), residues: 2005 helix: -2.49 (0.59), residues: 66 sheet: -1.07 (0.18), residues: 790 loop : -1.31 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 34 HIS 0.010 0.001 HIS F 135 PHE 0.017 0.001 PHE K 94 TYR 0.013 0.001 TYR K 97 ARG 0.007 0.001 ARG C 49 *********************** 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 441 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 1.686 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: C 84 THR cc_start: 0.7711 (m) cc_final: 0.7383 (m) REVERT: C 92 SER cc_start: 0.6880 (t) cc_final: 0.6428 (p) REVERT: C 146 MET cc_start: 0.7375 (ppp) cc_final: 0.6939 (ppp) REVERT: C 153 MET cc_start: 0.5109 (mpp) cc_final: 0.4535 (mpp) REVERT: C 167 MET cc_start: 0.6222 (tpp) cc_final: 0.5635 (tpp) REVERT: C 214 SER cc_start: 0.7686 (p) cc_final: 0.7438 (p) REVERT: C 262 ILE cc_start: 0.6547 (mt) cc_final: 0.6082 (mt) REVERT: B 141 TYR cc_start: 0.5985 (t80) cc_final: 0.5397 (t80) REVERT: B 164 VAL cc_start: 0.7235 (p) cc_final: 0.6951 (t) REVERT: D 146 MET cc_start: -0.0379 (mmt) cc_final: -0.0697 (mmt) REVERT: E 103 GLN cc_start: 0.7989 (mm110) cc_final: 0.7506 (mm-40) REVERT: E 124 MET cc_start: 0.5904 (tpt) cc_final: 0.5495 (tpt) REVERT: I 82 LYS cc_start: 0.7321 (pttm) cc_final: 0.6730 (mtmm) REVERT: I 89 THR cc_start: 0.8124 (m) cc_final: 0.7566 (p) REVERT: I 249 GLN cc_start: 0.6727 (tp-100) cc_final: 0.6267 (tp40) REVERT: G 96 ARG cc_start: 0.7190 (tpt90) cc_final: 0.6586 (tpt170) REVERT: G 124 MET cc_start: 0.5816 (tpt) cc_final: 0.5546 (tpt) REVERT: K 67 ASN cc_start: 0.5788 (m-40) cc_final: 0.5499 (m-40) REVERT: K 147 ASN cc_start: 0.8301 (m110) cc_final: 0.7769 (m-40) REVERT: J 35 MET cc_start: 0.6931 (ptp) cc_final: 0.6619 (tmm) REVERT: J 172 LYS cc_start: 0.8602 (tptp) cc_final: 0.8094 (tppt) REVERT: J 175 LYS cc_start: 0.7012 (ptpp) cc_final: 0.6733 (pttm) REVERT: J 181 ASP cc_start: 0.8635 (t0) cc_final: 0.8017 (t0) REVERT: J 208 MET cc_start: 0.3849 (mpp) cc_final: 0.3616 (mpp) REVERT: H 103 GLN cc_start: 0.6934 (pt0) cc_final: 0.6564 (mt0) REVERT: H 142 ARG cc_start: 0.8143 (ptp-110) cc_final: 0.7709 (ptp-170) REVERT: L 213 HIS cc_start: 0.6165 (t70) cc_final: 0.5910 (t-170) REVERT: L 228 LYS cc_start: 0.8340 (tptp) cc_final: 0.7850 (mmmm) outliers start: 1 outliers final: 0 residues processed: 441 average time/residue: 0.3298 time to fit residues: 202.9779 Evaluate side-chains 415 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 152 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 GLN F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16439 Z= 0.271 Angle : 0.707 12.250 22305 Z= 0.360 Chirality : 0.047 0.282 2482 Planarity : 0.006 0.075 2871 Dihedral : 5.550 26.927 2241 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.06 % Allowed : 1.23 % Favored : 98.72 % 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: -2.09 (0.18), residues: 2005 helix: -2.82 (0.54), residues: 66 sheet: -1.23 (0.19), residues: 766 loop : -1.38 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 34 HIS 0.009 0.001 HIS H 135 PHE 0.027 0.001 PHE C 157 TYR 0.020 0.002 TYR I 253 ARG 0.010 0.001 ARG C 73 *********************** 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 442 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.5990 (tmm160) cc_final: 0.5645 (tmt170) REVERT: A 156 CYS cc_start: 0.4894 (m) cc_final: 0.1675 (m) REVERT: C 84 THR cc_start: 0.7712 (m) cc_final: 0.7439 (m) REVERT: C 146 MET cc_start: 0.7552 (ppp) cc_final: 0.6931 (ppp) REVERT: C 153 MET cc_start: 0.5438 (mpp) cc_final: 0.4853 (mpp) REVERT: C 167 MET cc_start: 0.6465 (tpp) cc_final: 0.5711 (tpp) REVERT: C 214 SER cc_start: 0.7718 (p) cc_final: 0.7439 (p) REVERT: C 262 ILE cc_start: 0.6747 (mt) cc_final: 0.6342 (mt) REVERT: B 176 MET cc_start: 0.4243 (ptm) cc_final: 0.3889 (ptm) REVERT: D 146 MET cc_start: -0.0371 (mmt) cc_final: -0.0741 (mmt) REVERT: E 98 LEU cc_start: 0.8046 (mt) cc_final: 0.7680 (mt) REVERT: E 103 GLN cc_start: 0.7983 (mm110) cc_final: 0.7581 (mm-40) REVERT: E 124 MET cc_start: 0.5855 (tpt) cc_final: 0.5490 (tpt) REVERT: I 82 LYS cc_start: 0.7327 (pttm) cc_final: 0.6658 (mtmm) REVERT: I 89 THR cc_start: 0.8172 (m) cc_final: 0.7642 (p) REVERT: G 96 ARG cc_start: 0.7380 (tpt90) cc_final: 0.6633 (tpt170) REVERT: G 124 MET cc_start: 0.5844 (tpt) cc_final: 0.5640 (tpt) REVERT: K 147 ASN cc_start: 0.8304 (m110) cc_final: 0.7829 (m110) REVERT: J 34 TRP cc_start: 0.7149 (t-100) cc_final: 0.6773 (t-100) REVERT: J 35 MET cc_start: 0.7032 (ptp) cc_final: 0.6671 (tmm) REVERT: J 172 LYS cc_start: 0.8634 (tptp) cc_final: 0.8105 (tppt) REVERT: J 175 LYS cc_start: 0.7075 (ptpp) cc_final: 0.6851 (pttm) REVERT: J 248 VAL cc_start: 0.7222 (m) cc_final: 0.6951 (p) REVERT: H 103 GLN cc_start: 0.6948 (pt0) cc_final: 0.6501 (mt0) REVERT: H 142 ARG cc_start: 0.8293 (ptp-110) cc_final: 0.8049 (ptp-170) REVERT: L 82 LYS cc_start: 0.6787 (pttm) cc_final: 0.6541 (pttm) REVERT: L 171 LYS cc_start: 0.7689 (mppt) cc_final: 0.7358 (mmtm) REVERT: L 172 LYS cc_start: 0.8422 (mppt) cc_final: 0.8185 (mppt) REVERT: L 213 HIS cc_start: 0.6325 (t70) cc_final: 0.6073 (t-170) REVERT: L 228 LYS cc_start: 0.8401 (tptp) cc_final: 0.7901 (mmmm) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.3456 time to fit residues: 214.3768 Evaluate side-chains 416 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 108 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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** I 249 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16439 Z= 0.211 Angle : 0.683 10.656 22305 Z= 0.343 Chirality : 0.046 0.245 2482 Planarity : 0.005 0.061 2871 Dihedral : 5.363 26.371 2241 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.06 % Allowed : 0.67 % Favored : 99.28 % 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: -1.93 (0.18), residues: 2005 helix: -2.82 (0.54), residues: 66 sheet: -1.04 (0.19), residues: 724 loop : -1.34 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 180 HIS 0.008 0.001 HIS A 135 PHE 0.016 0.001 PHE K 94 TYR 0.012 0.001 TYR F 106 ARG 0.010 0.001 ARG C 73 *********************** 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 440 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 439 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.5986 (tmm160) cc_final: 0.5627 (tmt170) REVERT: A 156 CYS cc_start: 0.4843 (m) cc_final: 0.1650 (m) REVERT: C 67 ASN cc_start: 0.7348 (t0) cc_final: 0.6945 (t0) REVERT: C 84 THR cc_start: 0.7688 (m) cc_final: 0.7455 (m) REVERT: C 146 MET cc_start: 0.7218 (ppp) cc_final: 0.6724 (ppp) REVERT: C 153 MET cc_start: 0.5710 (mpp) cc_final: 0.5119 (mpp) REVERT: C 167 MET cc_start: 0.6088 (tpp) cc_final: 0.5547 (tpp) REVERT: C 214 SER cc_start: 0.7693 (p) cc_final: 0.7434 (p) REVERT: C 262 ILE cc_start: 0.6747 (mt) cc_final: 0.6258 (mt) REVERT: B 176 MET cc_start: 0.4288 (ptm) cc_final: 0.3914 (ptm) REVERT: D 146 MET cc_start: -0.0793 (mmt) cc_final: -0.1115 (mmt) REVERT: D 265 LYS cc_start: 0.6336 (mppt) cc_final: 0.6109 (pttm) REVERT: E 98 LEU cc_start: 0.7885 (mt) cc_final: 0.7665 (mt) REVERT: E 103 GLN cc_start: 0.7944 (mm110) cc_final: 0.7426 (mm-40) REVERT: E 124 MET cc_start: 0.5850 (tpt) cc_final: 0.5497 (tpt) REVERT: I 50 VAL cc_start: 0.7505 (m) cc_final: 0.7223 (p) REVERT: I 82 LYS cc_start: 0.7311 (pttm) cc_final: 0.6634 (mtmm) REVERT: I 89 THR cc_start: 0.8093 (m) cc_final: 0.7551 (p) REVERT: G 96 ARG cc_start: 0.7331 (tpt90) cc_final: 0.6668 (tpt170) REVERT: K 72 LEU cc_start: 0.8227 (pp) cc_final: 0.7890 (pp) REVERT: K 147 ASN cc_start: 0.8313 (m110) cc_final: 0.7943 (m-40) REVERT: K 219 PHE cc_start: 0.6073 (t80) cc_final: 0.5665 (t80) REVERT: J 32 PRO cc_start: 0.4390 (Cg_exo) cc_final: 0.2340 (Cg_endo) REVERT: J 126 PHE cc_start: 0.6563 (m-80) cc_final: 0.6258 (m-80) REVERT: J 172 LYS cc_start: 0.8664 (tptp) cc_final: 0.8056 (tppt) REVERT: J 175 LYS cc_start: 0.7084 (ptpp) cc_final: 0.6812 (pttm) REVERT: J 181 ASP cc_start: 0.8606 (t0) cc_final: 0.8281 (t0) REVERT: J 208 MET cc_start: 0.4180 (mpp) cc_final: 0.3890 (mpp) REVERT: H 103 GLN cc_start: 0.6602 (pt0) cc_final: 0.6321 (mt0) REVERT: L 82 LYS cc_start: 0.6733 (pttm) cc_final: 0.6430 (pttm) REVERT: L 213 HIS cc_start: 0.6279 (t70) cc_final: 0.6028 (t-170) REVERT: L 222 VAL cc_start: 0.5954 (t) cc_final: 0.5749 (t) REVERT: L 228 LYS cc_start: 0.8395 (tptp) cc_final: 0.7896 (mmmm) outliers start: 1 outliers final: 0 residues processed: 440 average time/residue: 0.3515 time to fit residues: 215.8338 Evaluate side-chains 403 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 0.0170 chunk 200 optimal weight: 1.9990 chunk 184 optimal weight: 0.1980 chunk 159 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 123 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- 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** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS J 23 GLN ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 HIS L 103 ASN ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16439 Z= 0.182 Angle : 0.679 10.989 22305 Z= 0.337 Chirality : 0.046 0.227 2482 Planarity : 0.005 0.074 2871 Dihedral : 5.210 24.654 2241 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.11 % Allowed : 0.28 % Favored : 99.61 % 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: -1.81 (0.18), residues: 2005 helix: -2.76 (0.56), residues: 66 sheet: -0.96 (0.19), residues: 736 loop : -1.24 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 180 HIS 0.006 0.001 HIS K 264 PHE 0.013 0.001 PHE K 94 TYR 0.016 0.001 TYR E 92 ARG 0.008 0.001 ARG E 160 ********************** 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 436 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 434 time to evaluate : 1.947 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 162 TYR cc_start: 0.4386 (t80) cc_final: 0.3940 (t80) REVERT: C 67 ASN cc_start: 0.7269 (t0) cc_final: 0.6894 (t0) REVERT: C 84 THR cc_start: 0.7642 (m) cc_final: 0.7436 (m) REVERT: C 92 SER cc_start: 0.7735 (t) cc_final: 0.7123 (p) REVERT: C 146 MET cc_start: 0.7264 (ppp) cc_final: 0.6633 (ppp) REVERT: C 153 MET cc_start: 0.5699 (mpp) cc_final: 0.5110 (mpp) REVERT: C 167 MET cc_start: 0.6055 (tpp) cc_final: 0.5485 (tpp) REVERT: C 214 SER cc_start: 0.7672 (p) cc_final: 0.7406 (p) REVERT: C 262 ILE cc_start: 0.6708 (mt) cc_final: 0.6213 (mt) REVERT: B 176 MET cc_start: 0.4215 (ptm) cc_final: 0.3897 (ptm) REVERT: D 35 MET cc_start: 0.6777 (mmm) cc_final: 0.6224 (mpp) REVERT: D 146 MET cc_start: -0.0845 (mmt) cc_final: -0.1071 (mmt) REVERT: E 98 LEU cc_start: 0.7861 (mt) cc_final: 0.7656 (mt) REVERT: E 103 GLN cc_start: 0.7992 (mm110) cc_final: 0.7496 (mm-40) REVERT: E 124 MET cc_start: 0.5865 (tpt) cc_final: 0.5483 (tpt) REVERT: I 50 VAL cc_start: 0.7420 (m) cc_final: 0.7137 (p) REVERT: I 82 LYS cc_start: 0.7071 (pttm) cc_final: 0.6671 (mtmm) REVERT: I 89 THR cc_start: 0.8058 (m) cc_final: 0.7456 (p) REVERT: I 249 GLN cc_start: 0.5256 (mm110) cc_final: 0.4833 (tp40) REVERT: I 265 LYS cc_start: 0.7875 (tptt) cc_final: 0.7540 (tptp) REVERT: G 96 ARG cc_start: 0.7302 (tpt90) cc_final: 0.6792 (tpt170) REVERT: G 124 MET cc_start: 0.5538 (tpt) cc_final: 0.5204 (tpt) REVERT: K 147 ASN cc_start: 0.8329 (m110) cc_final: 0.8025 (m-40) REVERT: K 167 MET cc_start: 0.6035 (mmp) cc_final: 0.5662 (mmp) REVERT: K 172 LYS cc_start: 0.8328 (mmtp) cc_final: 0.7726 (mmtm) REVERT: K 219 PHE cc_start: 0.5934 (t80) cc_final: 0.5541 (t80) REVERT: J 172 LYS cc_start: 0.8680 (tptp) cc_final: 0.8043 (tppt) REVERT: J 250 LEU cc_start: 0.6672 (tp) cc_final: 0.6320 (tp) REVERT: H 103 GLN cc_start: 0.6500 (pt0) cc_final: 0.6135 (mt0) REVERT: H 132 LEU cc_start: 0.8534 (mt) cc_final: 0.8290 (mt) REVERT: L 82 LYS cc_start: 0.7363 (pttm) cc_final: 0.6896 (pttm) REVERT: L 85 LYS cc_start: 0.7948 (tptt) cc_final: 0.6813 (tptt) REVERT: L 171 LYS cc_start: 0.7473 (mptt) cc_final: 0.6953 (mmtt) REVERT: L 172 LYS cc_start: 0.8441 (mppt) cc_final: 0.8092 (mppt) REVERT: L 228 LYS cc_start: 0.8413 (tptp) cc_final: 0.7907 (mmmm) outliers start: 2 outliers final: 0 residues processed: 436 average time/residue: 0.3365 time to fit residues: 206.2909 Evaluate side-chains 407 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 147 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 159 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN 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 ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** 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 = 0.4819 r_free = 0.4819 target = 0.213659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.186958 restraints weight = 47833.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.189091 restraints weight = 50441.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.189332 restraints weight = 48285.492| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16439 Z= 0.212 Angle : 0.695 11.137 22305 Z= 0.347 Chirality : 0.046 0.219 2482 Planarity : 0.005 0.054 2871 Dihedral : 5.288 26.211 2241 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.85 (0.57), residues: 60 sheet: -0.97 (0.19), residues: 735 loop : -1.19 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 180 HIS 0.007 0.001 HIS H 135 PHE 0.020 0.001 PHE L 219 TYR 0.013 0.001 TYR J 253 ARG 0.008 0.001 ARG G 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.21 seconds wall clock time: 79 minutes 32.29 seconds (4772.29 seconds total)