Starting phenix.real_space_refine on Sat Jul 4 11:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21kr_67778/07_2026/21kr_67778.cif Found real_map, /net/cci-nas-00/data/ceres_data/21kr_67778/07_2026/21kr_67778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21kr_67778/07_2026/21kr_67778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21kr_67778/07_2026/21kr_67778.map" model { file = "/net/cci-nas-00/data/ceres_data/21kr_67778/07_2026/21kr_67778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21kr_67778/07_2026/21kr_67778.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 100 atoms to isotropic. 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 167 5.16 5 C 12478 2.51 5 N 3499 2.21 5 O 3756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19900 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2611 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 317} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4903 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 23, 'TRANS': 592} Chain: "C" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2611 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 317} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4903 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 23, 'TRANS': 592} Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'RAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.20 Number of scatterers: 19900 At special positions: 0 Unit cell: (128.128, 141.44, 187.2, 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 167 16.00 O 3756 8.00 N 3499 7.00 C 12478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 893 " - pdb=" SG CYS B 904 " distance=2.03 Simple disulfide: pdb=" SG CYS B 900 " - pdb=" SG CYS B 914 " distance=2.03 Simple disulfide: pdb=" SG CYS B 916 " - pdb=" SG CYS B 929 " distance=2.03 Simple disulfide: pdb=" SG CYS B1207 " - pdb=" SG CYS B1218 " distance=2.03 Simple disulfide: pdb=" SG CYS B1214 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1230 " - pdb=" SG CYS B1243 " distance=2.04 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 118 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 118 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 56 " distance=2.03 Simple disulfide: pdb=" SG CYS E 77 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 205 " - pdb=" SG CYS E 212 " distance=2.04 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 312 " distance=2.03 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 307 " distance=2.03 Simple disulfide: pdb=" SG CYS E 311 " - pdb=" SG CYS E 351 " distance=2.03 Simple disulfide: pdb=" SG CYS E 327 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 329 " - pdb=" SG CYS E 339 " distance=2.04 Simple disulfide: pdb=" SG CYS F 893 " - pdb=" SG CYS F 904 " distance=2.03 Simple disulfide: pdb=" SG CYS F 900 " - pdb=" SG CYS F 914 " distance=2.03 Simple disulfide: pdb=" SG CYS F 916 " - pdb=" SG CYS F 929 " distance=2.05 Simple disulfide: pdb=" SG CYS F1207 " - pdb=" SG CYS F1218 " distance=2.03 Simple disulfide: pdb=" SG CYS F1214 " - pdb=" SG CYS F1228 " distance=2.03 Simple disulfide: pdb=" SG CYS F1230 " - pdb=" SG CYS F1243 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 118 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 111 " - pdb=" SG CYS G 135 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 118 " distance=2.03 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 135 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 401 " - " ASN A 87 " " NAG B1401 " - " ASN B 692 " " NAG B1402 " - " ASN B1039 " " NAG B1403 " - " ASN B 859 " " NAG J 1 " - " ASN A 298 " " NAG K 1 " - " ASN E 87 " " NAG L 1 " - " ASN E 298 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 847.2 milliseconds 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 44 sheets defined 21.6% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 6.244A pdb=" N GLY A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Proline residue: A 30 - end of helix removed outlier: 3.912A pdb=" N SER A 34 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 62 through 81 Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.881A pdb=" N VAL A 101 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 104 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'A' and resid 178 through 197 removed outlier: 3.599A pdb=" N ILE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'B' and resid 892 through 897 removed outlier: 4.479A pdb=" N SER B 896 " --> pdb=" O GLU B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 900 No H-bonds generated for 'chain 'B' and resid 898 through 900' Processing helix chain 'B' and resid 1198 through 1204 Processing helix chain 'B' and resid 1209 through 1214 Processing helix chain 'C' and resid 40 through 44 removed outlier: 3.563A pdb=" N LYS C 44 " --> pdb=" O PRO C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.682A pdb=" N ILE C 78 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 removed outlier: 4.035A pdb=" N LYS C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE C 86 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 118 through 126 removed outlier: 4.132A pdb=" N ARG C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.713A pdb=" N LYS D 44 " --> pdb=" O PRO D 41 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY D 45 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 46 " --> pdb=" O CYS D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 70 removed outlier: 3.526A pdb=" N ALA D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 78 Processing helix chain 'D' and resid 82 through 93 removed outlier: 4.443A pdb=" N PHE D 86 " --> pdb=" O PRO D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 116 Processing helix chain 'D' and resid 118 through 123 removed outlier: 3.950A pdb=" N ARG D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'E' and resid 22 through 28 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 41 through 45 Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 62 through 81 Processing helix chain 'E' and resid 98 through 104 removed outlier: 4.053A pdb=" N VAL E 101 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU E 102 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS E 104 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 Processing helix chain 'E' and resid 158 through 171 removed outlier: 3.815A pdb=" N GLY E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 197 removed outlier: 3.524A pdb=" N ALA E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 195 " --> pdb=" O GLY E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'E' and resid 223 through 237 Processing helix chain 'E' and resid 306 through 311 removed outlier: 3.540A pdb=" N CYS E 311 " --> pdb=" O CYS E 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 895 Processing helix chain 'F' and resid 896 through 900 Processing helix chain 'F' and resid 1198 through 1203 Processing helix chain 'F' and resid 1209 through 1214 Processing helix chain 'G' and resid 61 through 70 Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'G' and resid 83 through 93 Processing helix chain 'G' and resid 107 through 116 Processing helix chain 'G' and resid 118 through 123 removed outlier: 3.685A pdb=" N ARG G 123 " --> pdb=" O ALA G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'H' and resid 61 through 70 removed outlier: 3.652A pdb=" N ALA H 65 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 78 removed outlier: 3.516A pdb=" N VAL H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 93 removed outlier: 4.318A pdb=" N LYS H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE H 86 " --> pdb=" O PRO H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 removed outlier: 5.411A pdb=" N GLY H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 124 through 126 No H-bonds generated for 'chain 'H' and resid 124 through 126' Processing helix chain 'I' and resid 56 through 63 Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 206 removed outlier: 3.749A pdb=" N VAL A 214 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 258 Processing sheet with id=AA3, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297 removed outlier: 4.453A pdb=" N HIS A 349 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS A 342 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS A 326 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG A 344 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG A 324 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR A 346 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG A 322 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 348 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR A 320 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR A 350 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA A 318 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.987A pdb=" N ASP B 878 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 664 through 670 removed outlier: 6.265A pdb=" N THR B 679 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU B 667 " --> pdb=" O TYR B 677 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR B 677 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 669 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG B 675 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG B 688 " --> pdb=" O HIS B 698 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N HIS B 698 " --> pdb=" O ARG B 688 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 707 through 713 removed outlier: 6.683A pdb=" N ILE B 729 " --> pdb=" O LEU B 742 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 750 through 756 removed outlier: 6.214A pdb=" N THR B 765 " --> pdb=" O ARG B 751 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 753 " --> pdb=" O TYR B 763 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR B 763 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU B 755 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE B 761 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 773 " --> pdb=" O LEU B 786 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 793 through 799 removed outlier: 5.482A pdb=" N GLY B 795 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR B 808 " --> pdb=" O GLY B 795 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 835 through 841 removed outlier: 6.357A pdb=" N THR B 848 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 838 " --> pdb=" O TYR B 846 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 846 " --> pdb=" O LEU B 838 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN B 840 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR B 844 " --> pdb=" O GLN B 840 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 855 " --> pdb=" O ILE B 869 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 903 through 907 Processing sheet with id=AB3, first strand: chain 'B' and resid 921 through 922 Processing sheet with id=AB4, first strand: chain 'B' and resid 957 through 958 removed outlier: 6.713A pdb=" N PHE B 935 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA B1193 " --> pdb=" O PHE B 935 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 937 " --> pdb=" O ILE B1191 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B1191 " --> pdb=" O LEU B 937 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER B 939 " --> pdb=" O SER B1189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 967 through 973 removed outlier: 3.943A pdb=" N ALA B 969 " --> pdb=" O ILE B 982 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 989 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1016 through 1022 removed outlier: 3.804A pdb=" N ASP B1018 " --> pdb=" O THR B1031 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B1037 " --> pdb=" O CYS B1032 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 3.873A pdb=" N GLN B1077 " --> pdb=" O SER B1080 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B1083 " --> pdb=" O LEU B1096 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1104 through 1110 removed outlier: 3.600A pdb=" N ALA B1106 " --> pdb=" O ALA B1119 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B1126 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1147 through 1153 removed outlier: 3.736A pdb=" N GLY B1149 " --> pdb=" O ILE B1160 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS B1169 " --> pdb=" O LYS B1180 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS B1180 " --> pdb=" O LYS B1169 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1217 through 1220 Processing sheet with id=AC2, first strand: chain 'B' and resid 1235 through 1236 Processing sheet with id=AC3, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'E' and resid 200 through 206 removed outlier: 3.895A pdb=" N VAL E 214 " --> pdb=" O HIS E 206 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 251 through 258 Processing sheet with id=AC7, first strand: chain 'E' and resid 296 through 297 removed outlier: 4.341A pdb=" N HIS E 349 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 17.571A pdb=" N CYS E 339 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 13.716A pdb=" N SER I 8 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU E 341 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR I 6 " --> pdb=" O GLU E 341 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG I 71 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP I 37 " --> pdb=" O GLY I 28 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU I 30 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LYS I 35 " --> pdb=" O LEU I 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 316 through 332 removed outlier: 5.569A pdb=" N ALA E 318 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR E 350 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR E 320 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL E 348 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG E 322 " --> pdb=" O TYR E 346 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR E 346 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG E 324 " --> pdb=" O ARG E 344 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG E 344 " --> pdb=" O ARG E 324 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS E 326 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS E 342 " --> pdb=" O LYS E 326 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS E 328 " --> pdb=" O GLN E 340 " (cutoff:3.500A) removed outlier: 17.571A pdb=" N CYS E 339 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 13.716A pdb=" N SER I 8 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU E 341 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR I 6 " --> pdb=" O GLU E 341 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG I 71 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL I 23 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU I 106 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR I 21 " --> pdb=" O LEU I 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL I 24 " --> pdb=" O PHE I 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 653 through 655 removed outlier: 3.631A pdb=" N VAL F 654 " --> pdb=" O ARG F 644 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE F 633 " --> pdb=" O PHE F 882 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP F 878 " --> pdb=" O SER F 637 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 664 through 670 removed outlier: 6.397A pdb=" N THR F 679 " --> pdb=" O SER F 665 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU F 667 " --> pdb=" O TYR F 677 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR F 677 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE F 669 " --> pdb=" O ARG F 675 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG F 675 " --> pdb=" O PHE F 669 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG F 688 " --> pdb=" O HIS F 698 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS F 698 " --> pdb=" O ARG F 688 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 707 through 713 removed outlier: 6.716A pdb=" N ILE F 729 " --> pdb=" O LEU F 742 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 750 through 756 removed outlier: 6.454A pdb=" N THR F 765 " --> pdb=" O ARG F 751 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU F 753 " --> pdb=" O TYR F 763 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR F 763 " --> pdb=" O LEU F 753 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU F 755 " --> pdb=" O PHE F 761 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE F 761 " --> pdb=" O LEU F 755 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE F 773 " --> pdb=" O LEU F 786 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 793 through 799 removed outlier: 5.349A pdb=" N GLY F 795 " --> pdb=" O THR F 808 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR F 808 " --> pdb=" O GLY F 795 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER F 817 " --> pdb=" O VAL F 827 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL F 827 " --> pdb=" O SER F 817 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 835 through 841 removed outlier: 3.853A pdb=" N GLY F 837 " --> pdb=" O THR F 848 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE F 855 " --> pdb=" O ILE F 869 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR F 867 " --> pdb=" O ARG F 857 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 903 through 907 Processing sheet with id=AD7, first strand: chain 'F' and resid 921 through 922 Processing sheet with id=AD8, first strand: chain 'F' and resid 957 through 958 removed outlier: 3.740A pdb=" N ALA F 943 " --> pdb=" O GLN F 940 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE F 935 " --> pdb=" O ALA F1193 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA F1193 " --> pdb=" O PHE F 935 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU F 937 " --> pdb=" O ILE F1191 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE F1191 " --> pdb=" O LEU F 937 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER F 939 " --> pdb=" O SER F1189 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 967 through 973 removed outlier: 6.400A pdb=" N ILE F 982 " --> pdb=" O ARG F 968 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE F 970 " --> pdb=" O TYR F 980 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR F 980 " --> pdb=" O ILE F 970 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR F 972 " --> pdb=" O GLN F 978 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN F 978 " --> pdb=" O TYR F 972 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE F 989 " --> pdb=" O VAL F1002 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 1016 through 1022 removed outlier: 4.226A pdb=" N ASP F1018 " --> pdb=" O THR F1031 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL F1037 " --> pdb=" O CYS F1032 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 1063 through 1065 removed outlier: 3.809A pdb=" N GLN F1077 " --> pdb=" O SER F1080 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE F1083 " --> pdb=" O LEU F1096 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 1104 through 1110 removed outlier: 3.837A pdb=" N ALA F1106 " --> pdb=" O ALA F1119 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER F1128 " --> pdb=" O VAL F1138 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL F1138 " --> pdb=" O SER F1128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 1147 through 1153 removed outlier: 3.871A pdb=" N GLY F1149 " --> pdb=" O ILE F1160 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE F1167 " --> pdb=" O VAL F1181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 1217 through 1220 Processing sheet with id=AE6, first strand: chain 'F' and resid 1235 through 1236 Processing sheet with id=AE7, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 696 hydrogen bonds defined for protein. 1758 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: 4.10 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4081 1.33 - 1.46: 6611 1.46 - 1.59: 9464 1.59 - 1.72: 0 1.72 - 1.85: 224 Bond restraints: 20380 Sorted by residual: bond pdb=" C1 RAP I 201 " pdb=" O1 RAP I 201 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C8 RAP I 201 " pdb=" C9 RAP I 201 " ideal model delta sigma weight residual 1.533 1.462 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C GLY F 915 " pdb=" O GLY F 915 " ideal model delta sigma weight residual 1.233 1.273 -0.040 1.18e-02 7.18e+03 1.17e+01 bond pdb=" C THR H 93 " pdb=" O THR H 93 " ideal model delta sigma weight residual 1.241 1.207 0.034 1.14e-02 7.69e+03 8.95e+00 bond pdb=" CA THR B 797 " pdb=" C THR B 797 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.23e-02 6.61e+03 8.70e+00 ... (remaining 20375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 27146 2.38 - 4.75: 419 4.75 - 7.13: 60 7.13 - 9.50: 12 9.50 - 11.88: 3 Bond angle restraints: 27640 Sorted by residual: angle pdb=" N TYR C 92 " pdb=" CA TYR C 92 " pdb=" C TYR C 92 " ideal model delta sigma weight residual 111.14 104.21 6.93 1.08e+00 8.57e-01 4.11e+01 angle pdb=" N SER B 939 " pdb=" CA SER B 939 " pdb=" C SER B 939 " ideal model delta sigma weight residual 109.07 117.61 -8.54 1.61e+00 3.86e-01 2.81e+01 angle pdb=" N CYS E 339 " pdb=" CA CYS E 339 " pdb=" C CYS E 339 " ideal model delta sigma weight residual 109.95 117.03 -7.08 1.44e+00 4.82e-01 2.42e+01 angle pdb=" N CYS A 339 " pdb=" CA CYS A 339 " pdb=" C CYS A 339 " ideal model delta sigma weight residual 109.95 116.63 -6.68 1.44e+00 4.82e-01 2.15e+01 angle pdb=" N ILE A 40 " pdb=" CA ILE A 40 " pdb=" C ILE A 40 " ideal model delta sigma weight residual 108.23 114.70 -6.47 1.53e+00 4.27e-01 1.79e+01 ... (remaining 27635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.49: 11275 25.49 - 50.98: 1090 50.98 - 76.47: 180 76.47 - 101.96: 31 101.96 - 127.44: 13 Dihedral angle restraints: 12589 sinusoidal: 5398 harmonic: 7191 Sorted by residual: dihedral pdb=" CA TRP A 333 " pdb=" C TRP A 333 " pdb=" N CYS A 334 " pdb=" CA CYS A 334 " ideal model delta harmonic sigma weight residual -180.00 -52.56 -127.44 0 5.00e+00 4.00e-02 6.50e+02 dihedral pdb=" CA TRP E 333 " pdb=" C TRP E 333 " pdb=" N CYS E 334 " pdb=" CA CYS E 334 " ideal model delta harmonic sigma weight residual -180.00 -54.91 -125.09 0 5.00e+00 4.00e-02 6.26e+02 dihedral pdb=" CB CYS B1230 " pdb=" SG CYS B1230 " pdb=" SG CYS B1243 " pdb=" CB CYS B1243 " ideal model delta sinusoidal sigma weight residual -86.00 -174.57 88.57 1 1.00e+01 1.00e-02 9.36e+01 ... (remaining 12586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2671 0.077 - 0.154: 291 0.154 - 0.232: 7 0.232 - 0.309: 2 0.309 - 0.386: 2 Chirality restraints: 2973 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.87e+00 chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B 692 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN E 87 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 2970 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 RAP I 201 " 0.056 2.00e-02 2.50e+03 3.99e-02 2.38e+01 pdb=" C6 RAP I 201 " -0.035 2.00e-02 2.50e+03 pdb=" C8 RAP I 201 " -0.003 2.00e-02 2.50e+03 pdb=" C9 RAP I 201 " 0.051 2.00e-02 2.50e+03 pdb=" N7 RAP I 201 " -0.022 2.00e-02 2.50e+03 pdb=" O3 RAP I 201 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1402 " 0.052 2.00e-02 2.50e+03 4.24e-02 2.25e+01 pdb=" C7 NAG B1402 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG B1402 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG B1402 " -0.067 2.00e-02 2.50e+03 pdb=" O7 NAG B1402 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO I 92 " -0.067 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO I 93 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO I 93 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO I 93 " -0.053 5.00e-02 4.00e+02 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1538 2.74 - 3.28: 19153 3.28 - 3.82: 33789 3.82 - 4.36: 40631 4.36 - 4.90: 69760 Nonbonded interactions: 164871 Sorted by model distance: nonbonded pdb=" OH TYR C 48 " pdb=" O CYS C 89 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASN F 923 " pdb=" OG SER F 930 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR H 48 " pdb=" O THR H 93 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP E 171 " pdb=" ND2 ASN E 188 " model vdw 2.253 3.120 nonbonded pdb=" OD2 ASP F1130 " pdb=" OG SER F1132 " model vdw 2.253 3.040 ... (remaining 164866 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 19 through 352) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 630 through 1245) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.730 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 0.125 20444 Z= 0.197 Angle : 0.732 17.504 27778 Z= 0.380 Chirality : 0.047 0.386 2973 Planarity : 0.005 0.099 3609 Dihedral : 19.311 127.444 7803 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.27 % Allowed : 28.56 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2465 helix: 0.47 (0.27), residues: 423 sheet: -0.97 (0.19), residues: 643 loop : -0.80 (0.18), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 886 TYR 0.054 0.002 TYR F 920 PHE 0.021 0.002 PHE D 57 TRP 0.017 0.001 TRP F 847 HIS 0.010 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (20380) covalent geometry : angle 0.70614 / 0.37 (27640) SS BOND : bond 0.00425 / 0.20 ( 54) SS BOND : angle 0.94410 / 0.65 ( 108) hydrogen bonds : bond 0.15740 / 10.28 ( 681) hydrogen bonds : angle 7.68872 / 5.56 ( 1758) link_BETA1-4 : bond 0.01135 / 0.54 ( 3) link_BETA1-4 : angle 2.28214 / 1.15 ( 9) link_NAG-ASN : bond 0.01299 / 0.66 ( 7) link_NAG-ASN : angle 6.80686 / 3.47 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 234 time to evaluate : 0.693 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: B 826 GLU cc_start: 0.7092 (mp0) cc_final: 0.6871 (mp0) REVERT: F 1000 PHE cc_start: 0.3743 (OUTLIER) cc_final: 0.3012 (t80) REVERT: F 1112 ARG cc_start: 0.4841 (mmp80) cc_final: 0.4366 (mmm-85) outliers start: 92 outliers final: 58 residues processed: 300 average time/residue: 0.5368 time to fit residues: 183.7325 Evaluate side-chains 270 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 993 GLN Chi-restraints excluded: chain B residue 995 ASP Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1130 ASP Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1228 CYS Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 128 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 314 ARG Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 323 ARG Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 921 SER Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1000 PHE Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1065 ASN Chi-restraints excluded: chain F residue 1121 SER Chi-restraints excluded: chain F residue 1139 LEU Chi-restraints excluded: chain F residue 1155 ASN Chi-restraints excluded: chain F residue 1182 GLN Chi-restraints excluded: chain F residue 1195 LYS Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain I residue 79 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 GLN B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 966 ASN B1211 ASN E 75 GLN F 718 ASN ** F 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.243157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.205200 restraints weight = 22111.040| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 1.65 r_work: 0.3948 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20444 Z= 0.147 Angle : 0.632 17.789 27778 Z= 0.310 Chirality : 0.045 0.320 2973 Planarity : 0.004 0.061 3609 Dihedral : 10.866 107.297 3184 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.90 % Allowed : 25.59 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2465 helix: 0.68 (0.27), residues: 431 sheet: -0.71 (0.20), residues: 647 loop : -0.77 (0.18), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 775 TYR 0.014 0.001 TYR C 92 PHE 0.013 0.001 PHE B1098 TRP 0.031 0.001 TRP A 333 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (20380) covalent geometry : angle 0.60519 / 0.30 (27640) SS BOND : bond 0.00268 / 0.16 ( 54) SS BOND : angle 1.10206 / 0.72 ( 108) hydrogen bonds : bond 0.03963 / 2.61 ( 681) hydrogen bonds : angle 6.11290 / 4.41 ( 1758) link_BETA1-4 : bond 0.00565 / 0.27 ( 3) link_BETA1-4 : angle 2.08572 / 1.07 ( 9) link_NAG-ASN : bond 0.01118 / 0.57 ( 7) link_NAG-ASN : angle 6.14152 / 3.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 213 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 751 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6954 (tmt170) REVERT: B 1154 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: B 1163 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: C 122 MET cc_start: 0.3252 (OUTLIER) cc_final: 0.2807 (mmm) REVERT: D 91 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.1413 (tpt) REVERT: F 1070 TYR cc_start: 0.5851 (m-80) cc_final: 0.5480 (m-80) REVERT: F 1112 ARG cc_start: 0.5923 (mmp80) cc_final: 0.5071 (mmm-85) REVERT: F 1145 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7326 (mt) REVERT: H 92 TYR cc_start: 0.5319 (OUTLIER) cc_final: 0.5067 (t80) REVERT: I 3 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7972 (tt0) outliers start: 127 outliers final: 58 residues processed: 307 average time/residue: 0.4928 time to fit residues: 173.8342 Evaluate side-chains 268 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1130 ASP Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1163 GLN Chi-restraints excluded: chain B residue 1195 LYS Chi-restraints excluded: chain B residue 1201 GLU Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1139 LEU Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1182 GLN Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 120 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 221 optimal weight: 50.0000 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 718 ASN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.239612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.198695 restraints weight = 22183.197| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 1.75 r_work: 0.3808 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20444 Z= 0.182 Angle : 0.639 16.466 27778 Z= 0.313 Chirality : 0.045 0.330 2973 Planarity : 0.004 0.049 3609 Dihedral : 9.085 107.486 3119 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.50 % Allowed : 25.87 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.18), residues: 2465 helix: 0.44 (0.27), residues: 437 sheet: -0.73 (0.20), residues: 651 loop : -0.77 (0.18), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 108 TYR 0.019 0.001 TYR D 52 PHE 0.013 0.001 PHE A 169 TRP 0.020 0.001 TRP F1030 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (20380) covalent geometry : angle 0.61114 / 0.31 (27640) SS BOND : bond 0.00330 / 0.21 ( 54) SS BOND : angle 1.19098 / 0.83 ( 108) hydrogen bonds : bond 0.04189 / 2.74 ( 681) hydrogen bonds : angle 5.92325 / 4.28 ( 1758) link_BETA1-4 : bond 0.00719 / 0.34 ( 3) link_BETA1-4 : angle 2.39791 / 1.23 ( 9) link_NAG-ASN : bond 0.01151 / 0.59 ( 7) link_NAG-ASN : angle 6.16152 / 3.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 214 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.5988 (tt) REVERT: A 259 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8406 (ttt90) REVERT: B 751 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7092 (tmt170) REVERT: B 956 ASP cc_start: 0.8364 (p0) cc_final: 0.7901 (p0) REVERT: B 1115 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7726 (mptm) REVERT: B 1154 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: B 1163 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: C 59 HIS cc_start: 0.5597 (m-70) cc_final: 0.5280 (m-70) REVERT: C 122 MET cc_start: 0.3307 (mpm) cc_final: 0.2841 (mmm) REVERT: E 107 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8050 (ttp80) REVERT: E 301 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8892 (p) REVERT: F 710 MET cc_start: 0.8042 (tpp) cc_final: 0.7758 (tpt) REVERT: F 1070 TYR cc_start: 0.5976 (m-80) cc_final: 0.5493 (m-80) REVERT: F 1145 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7399 (mt) REVERT: H 53 MET cc_start: 0.3159 (mmp) cc_final: 0.2876 (mmm) REVERT: H 91 MET cc_start: 0.4511 (pp-130) cc_final: 0.3482 (tpt) REVERT: H 92 TYR cc_start: 0.5313 (OUTLIER) cc_final: 0.4634 (t80) REVERT: I 3 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: I 71 ARG cc_start: 0.7899 (ttt90) cc_final: 0.7682 (ttt180) outliers start: 140 outliers final: 64 residues processed: 321 average time/residue: 0.4793 time to fit residues: 176.8741 Evaluate side-chains 278 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 203 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 993 GLN Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1130 ASP Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1163 GLN Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1195 LYS Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1139 LEU Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1182 GLN Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 141 GLN Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 241 optimal weight: 0.6980 chunk 131 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 718 ASN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.239602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.195169 restraints weight = 22076.237| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 1.93 r_work: 0.3890 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20444 Z= 0.159 Angle : 0.611 16.131 27778 Z= 0.299 Chirality : 0.045 0.326 2973 Planarity : 0.004 0.043 3609 Dihedral : 8.671 107.538 3113 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.73 % Allowed : 25.27 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.18), residues: 2465 helix: 0.55 (0.27), residues: 431 sheet: -0.72 (0.19), residues: 641 loop : -0.73 (0.18), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 775 TYR 0.016 0.001 TYR C 92 PHE 0.012 0.001 PHE A 169 TRP 0.021 0.001 TRP F1030 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (20380) covalent geometry : angle 0.58405 / 0.29 (27640) SS BOND : bond 0.00291 / 0.18 ( 54) SS BOND : angle 1.06919 / 0.72 ( 108) hydrogen bonds : bond 0.03876 / 2.55 ( 681) hydrogen bonds : angle 5.76272 / 4.17 ( 1758) link_BETA1-4 : bond 0.00520 / 0.25 ( 3) link_BETA1-4 : angle 2.41289 / 1.24 ( 9) link_NAG-ASN : bond 0.01121 / 0.57 ( 7) link_NAG-ASN : angle 6.05827 / 3.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 210 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6005 (tt) REVERT: A 259 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8259 (ttt90) REVERT: B 656 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7795 (mt) REVERT: B 751 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7062 (tmt170) REVERT: B 945 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8418 (m-40) REVERT: B 983 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8048 (t70) REVERT: B 1154 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: C 118 CYS cc_start: 0.2128 (OUTLIER) cc_final: 0.0915 (p) REVERT: C 122 MET cc_start: 0.3153 (mpm) cc_final: 0.2675 (mmm) REVERT: D 91 MET cc_start: 0.2912 (ppp) cc_final: 0.1632 (tpt) REVERT: E 104 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8003 (mppt) REVERT: E 107 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7812 (ttp80) REVERT: E 301 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8869 (p) REVERT: F 1107 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7154 (tt) REVERT: F 1145 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7249 (mt) REVERT: H 53 MET cc_start: 0.3093 (mmp) cc_final: 0.2814 (mmm) REVERT: H 91 MET cc_start: 0.4733 (pp-130) cc_final: 0.3725 (tpt) REVERT: I 3 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: I 71 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7833 (ttt180) outliers start: 145 outliers final: 65 residues processed: 321 average time/residue: 0.4703 time to fit residues: 174.5889 Evaluate side-chains 283 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 204 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 745 LYS Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 993 GLN Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1195 LYS Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1139 LEU Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 141 GLN Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 58 optimal weight: 0.1980 chunk 216 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 230 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 209 optimal weight: 30.0000 chunk 238 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 75 GLN F 718 ASN ** F 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.241945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.198877 restraints weight = 22120.826| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 1.88 r_work: 0.3919 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20444 Z= 0.114 Angle : 0.587 15.643 27778 Z= 0.286 Chirality : 0.044 0.310 2973 Planarity : 0.003 0.039 3609 Dihedral : 8.091 105.976 3093 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.20 % Allowed : 26.94 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.18), residues: 2465 helix: 0.62 (0.27), residues: 437 sheet: -0.62 (0.20), residues: 647 loop : -0.70 (0.18), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 775 TYR 0.017 0.001 TYR C 92 PHE 0.012 0.001 PHE B 636 TRP 0.033 0.001 TRP F1030 HIS 0.004 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (20380) covalent geometry : angle 0.56082 / 0.28 (27640) SS BOND : bond 0.00186 / 0.10 ( 54) SS BOND : angle 0.87952 / 0.61 ( 108) hydrogen bonds : bond 0.03492 / 2.30 ( 681) hydrogen bonds : angle 5.61870 / 4.06 ( 1758) link_BETA1-4 : bond 0.00724 / 0.35 ( 3) link_BETA1-4 : angle 2.38675 / 1.22 ( 9) link_NAG-ASN : bond 0.01109 / 0.56 ( 7) link_NAG-ASN : angle 5.90951 / 3.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 217 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8216 (ttt90) REVERT: B 751 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7308 (tmt-80) REVERT: B 945 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8377 (m-40) REVERT: B 1115 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7645 (mptm) REVERT: B 1154 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: C 118 CYS cc_start: 0.2071 (OUTLIER) cc_final: 0.0825 (p) REVERT: C 122 MET cc_start: 0.3130 (OUTLIER) cc_final: 0.2711 (mmm) REVERT: D 91 MET cc_start: 0.2933 (ppp) cc_final: 0.1401 (tpt) REVERT: E 107 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7802 (ttp80) REVERT: F 710 MET cc_start: 0.7646 (tpt) cc_final: 0.7164 (tpt) REVERT: F 1070 TYR cc_start: 0.5152 (OUTLIER) cc_final: 0.3803 (m-80) REVERT: F 1145 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7315 (mt) REVERT: H 91 MET cc_start: 0.4797 (pp-130) cc_final: 0.3811 (tpt) outliers start: 112 outliers final: 56 residues processed: 298 average time/residue: 0.4828 time to fit residues: 164.8907 Evaluate side-chains 270 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 204 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 995 ASP Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1070 TYR Chi-restraints excluded: chain F residue 1139 LEU Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 184 optimal weight: 7.9990 chunk 233 optimal weight: 0.0070 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 718 ASN ** F 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.241741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.203136 restraints weight = 22086.812| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 1.65 r_work: 0.3878 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20444 Z= 0.120 Angle : 0.593 15.746 27778 Z= 0.289 Chirality : 0.044 0.309 2973 Planarity : 0.003 0.036 3609 Dihedral : 7.964 105.169 3088 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.71 % Allowed : 26.61 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 2465 helix: 0.74 (0.27), residues: 429 sheet: -0.62 (0.20), residues: 649 loop : -0.68 (0.18), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 108 TYR 0.018 0.001 TYR C 92 PHE 0.017 0.001 PHE B1098 TRP 0.034 0.001 TRP F1030 HIS 0.005 0.000 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (20380) covalent geometry : angle 0.56777 / 0.28 (27640) SS BOND : bond 0.00194 / 0.11 ( 54) SS BOND : angle 0.87880 / 0.61 ( 108) hydrogen bonds : bond 0.03497 / 2.31 ( 681) hydrogen bonds : angle 5.53695 / 4.01 ( 1758) link_BETA1-4 : bond 0.00692 / 0.33 ( 3) link_BETA1-4 : angle 2.34360 / 1.20 ( 9) link_NAG-ASN : bond 0.01115 / 0.56 ( 7) link_NAG-ASN : angle 5.92960 / 3.07 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 205 time to evaluate : 0.559 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: A 259 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8327 (ttt90) REVERT: A 342 CYS cc_start: 0.5404 (OUTLIER) cc_final: 0.5039 (m) REVERT: B 751 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7274 (tmt-80) REVERT: B 864 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6226 (tp40) REVERT: B 945 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8404 (m-40) REVERT: B 983 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7996 (t70) REVERT: B 1115 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7676 (mptm) REVERT: B 1154 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: C 118 CYS cc_start: 0.2179 (OUTLIER) cc_final: 0.0899 (p) REVERT: C 122 MET cc_start: 0.3151 (OUTLIER) cc_final: 0.2721 (mmm) REVERT: C 149 MET cc_start: 0.2180 (mmm) cc_final: 0.1940 (tpt) REVERT: D 91 MET cc_start: 0.2856 (ppp) cc_final: 0.1778 (tpt) REVERT: D 133 MET cc_start: 0.2941 (tpt) cc_final: 0.2135 (mpt) REVERT: E 104 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7934 (mppt) REVERT: E 107 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7844 (ttp80) REVERT: F 710 MET cc_start: 0.7655 (tpt) cc_final: 0.7202 (tpt) REVERT: F 1066 PRO cc_start: 0.4159 (Cg_endo) cc_final: 0.3930 (Cg_exo) REVERT: F 1070 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.3861 (m-80) REVERT: F 1107 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7149 (tt) REVERT: F 1145 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7384 (mt) REVERT: H 67 LEU cc_start: 0.3368 (OUTLIER) cc_final: 0.2737 (pt) REVERT: H 91 MET cc_start: 0.4782 (pp-130) cc_final: 0.3882 (tpt) REVERT: H 149 MET cc_start: 0.4216 (OUTLIER) cc_final: 0.3049 (tmt) REVERT: I 3 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8022 (tt0) outliers start: 123 outliers final: 63 residues processed: 296 average time/residue: 0.5123 time to fit residues: 173.1206 Evaluate side-chains 281 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 200 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 864 GLN Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 993 GLN Chi-restraints excluded: chain B residue 995 ASP Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 686 ILE Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1070 TYR Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1139 LEU Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1182 GLN Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 142 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 195 optimal weight: 30.0000 chunk 238 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 150 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.241081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.201355 restraints weight = 22206.837| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.78 r_work: 0.3872 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20444 Z= 0.156 Angle : 0.617 16.042 27778 Z= 0.300 Chirality : 0.045 0.317 2973 Planarity : 0.004 0.038 3609 Dihedral : 7.953 105.890 3086 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.16 % Allowed : 27.17 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2465 helix: 0.66 (0.27), residues: 429 sheet: -0.66 (0.20), residues: 651 loop : -0.69 (0.18), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 775 TYR 0.016 0.001 TYR I 82 PHE 0.013 0.001 PHE A 224 TRP 0.039 0.001 TRP F1030 HIS 0.004 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (20380) covalent geometry : angle 0.59144 / 0.29 (27640) SS BOND : bond 0.00218 / 0.12 ( 54) SS BOND : angle 0.93320 / 0.63 ( 108) hydrogen bonds : bond 0.03756 / 2.46 ( 681) hydrogen bonds : angle 5.54264 / 4.01 ( 1758) link_BETA1-4 : bond 0.00727 / 0.35 ( 3) link_BETA1-4 : angle 2.37247 / 1.21 ( 9) link_NAG-ASN : bond 0.01134 / 0.58 ( 7) link_NAG-ASN : angle 6.06931 / 3.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 207 time to evaluate : 0.745 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: A 259 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8279 (ttt90) REVERT: B 656 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7776 (mt) REVERT: B 751 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7237 (tmt-80) REVERT: B 945 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8474 (m-40) REVERT: B 983 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8057 (t70) REVERT: B 1115 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7718 (mptm) REVERT: B 1154 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: C 118 CYS cc_start: 0.2153 (OUTLIER) cc_final: 0.0902 (p) REVERT: C 122 MET cc_start: 0.3113 (OUTLIER) cc_final: 0.2706 (mmm) REVERT: D 91 MET cc_start: 0.2925 (OUTLIER) cc_final: 0.1520 (tpt) REVERT: E 104 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7956 (mppt) REVERT: E 107 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7956 (ttp80) REVERT: F 710 MET cc_start: 0.7683 (tpt) cc_final: 0.7117 (tpt) REVERT: F 1066 PRO cc_start: 0.4029 (Cg_endo) cc_final: 0.3762 (Cg_exo) REVERT: F 1070 TYR cc_start: 0.5029 (OUTLIER) cc_final: 0.3837 (m-80) REVERT: F 1145 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7296 (mt) REVERT: G 101 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7619 (tptt) REVERT: H 53 MET cc_start: 0.3040 (mmp) cc_final: 0.2825 (mmm) REVERT: H 67 LEU cc_start: 0.3362 (OUTLIER) cc_final: 0.2733 (pt) REVERT: H 91 MET cc_start: 0.4855 (pp-130) cc_final: 0.3946 (tpt) REVERT: H 149 MET cc_start: 0.4328 (OUTLIER) cc_final: 0.3186 (tmt) REVERT: I 3 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: I 104 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7524 (mm) outliers start: 111 outliers final: 63 residues processed: 287 average time/residue: 0.5135 time to fit residues: 168.6368 Evaluate side-chains 284 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 203 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1172 MET Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1070 TYR Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1182 GLN Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 chunk 52 optimal weight: 0.2980 chunk 228 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.240820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.200765 restraints weight = 22242.619| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.70 r_work: 0.3936 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20444 Z= 0.150 Angle : 0.621 15.926 27778 Z= 0.301 Chirality : 0.044 0.317 2973 Planarity : 0.003 0.037 3609 Dihedral : 7.886 106.276 3083 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.06 % Allowed : 27.45 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2465 helix: 0.66 (0.27), residues: 429 sheet: -0.59 (0.20), residues: 647 loop : -0.68 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 775 TYR 0.017 0.001 TYR C 92 PHE 0.021 0.001 PHE F 633 TRP 0.040 0.001 TRP F1030 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (20380) covalent geometry : angle 0.59510 / 0.30 (27640) SS BOND : bond 0.00210 / 0.12 ( 54) SS BOND : angle 0.90660 / 0.61 ( 108) hydrogen bonds : bond 0.03689 / 2.42 ( 681) hydrogen bonds : angle 5.52420 / 4.00 ( 1758) link_BETA1-4 : bond 0.00734 / 0.35 ( 3) link_BETA1-4 : angle 2.40710 / 1.23 ( 9) link_NAG-ASN : bond 0.01094 / 0.56 ( 7) link_NAG-ASN : angle 6.04228 / 3.13 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 208 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.5845 (tt) REVERT: A 259 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8233 (ttt90) REVERT: A 342 CYS cc_start: 0.5480 (OUTLIER) cc_final: 0.5241 (m) REVERT: B 656 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7762 (mt) REVERT: B 751 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7200 (tmt-80) REVERT: B 864 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6222 (tp40) REVERT: B 945 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8453 (m-40) REVERT: B 983 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8027 (t70) REVERT: B 1115 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7680 (mptm) REVERT: B 1154 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: C 122 MET cc_start: 0.3282 (mpm) cc_final: 0.2898 (mmm) REVERT: D 91 MET cc_start: 0.2775 (OUTLIER) cc_final: 0.1569 (tpt) REVERT: E 104 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7999 (mppt) REVERT: E 107 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7912 (ttp80) REVERT: F 710 MET cc_start: 0.7543 (tpt) cc_final: 0.7198 (tpt) REVERT: F 1004 VAL cc_start: 0.6269 (p) cc_final: 0.5937 (t) REVERT: F 1066 PRO cc_start: 0.3857 (Cg_endo) cc_final: 0.3619 (Cg_exo) REVERT: F 1070 TYR cc_start: 0.4913 (OUTLIER) cc_final: 0.3738 (m-80) REVERT: F 1145 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7246 (mt) REVERT: H 53 MET cc_start: 0.3174 (mmp) cc_final: 0.2945 (mmm) REVERT: H 67 LEU cc_start: 0.3319 (OUTLIER) cc_final: 0.2672 (pt) REVERT: H 91 MET cc_start: 0.4651 (pp-130) cc_final: 0.3811 (tpt) REVERT: H 149 MET cc_start: 0.4382 (OUTLIER) cc_final: 0.3215 (tmt) REVERT: I 3 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: I 104 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7500 (mm) outliers start: 109 outliers final: 67 residues processed: 294 average time/residue: 0.5343 time to fit residues: 179.7196 Evaluate side-chains 290 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 204 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 864 GLN Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 995 ASP Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1130 ASP Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1172 MET Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1070 TYR Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1182 GLN Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 173 optimal weight: 2.9990 chunk 172 optimal weight: 0.0570 chunk 132 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.242017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.202570 restraints weight = 22138.282| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 1.73 r_work: 0.3878 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20444 Z= 0.117 Angle : 0.597 15.605 27778 Z= 0.289 Chirality : 0.044 0.312 2973 Planarity : 0.003 0.038 3609 Dihedral : 7.764 105.398 3083 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.23 % Allowed : 28.24 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2465 helix: 0.77 (0.27), residues: 429 sheet: -0.52 (0.20), residues: 645 loop : -0.65 (0.18), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 775 TYR 0.017 0.001 TYR C 92 PHE 0.018 0.001 PHE B1098 TRP 0.042 0.001 TRP F1030 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (20380) covalent geometry : angle 0.57243 / 0.28 (27640) SS BOND : bond 0.00210 / 0.11 ( 54) SS BOND : angle 0.83407 / 0.56 ( 108) hydrogen bonds : bond 0.03438 / 2.26 ( 681) hydrogen bonds : angle 5.45963 / 3.95 ( 1758) link_BETA1-4 : bond 0.00694 / 0.33 ( 3) link_BETA1-4 : angle 2.33537 / 1.20 ( 9) link_NAG-ASN : bond 0.01100 / 0.55 ( 7) link_NAG-ASN : angle 5.90017 / 3.05 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 205 time to evaluate : 0.737 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: A 259 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8307 (ttt90) REVERT: A 342 CYS cc_start: 0.5397 (OUTLIER) cc_final: 0.5137 (m) REVERT: B 656 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7749 (mt) REVERT: B 751 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7246 (tmt-80) REVERT: B 864 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.6224 (tp40) REVERT: B 945 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8507 (m-40) REVERT: B 983 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8065 (t70) REVERT: B 1115 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7653 (mptm) REVERT: B 1154 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: B 1163 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: C 91 MET cc_start: 0.6723 (ppp) cc_final: 0.6082 (ptm) REVERT: C 122 MET cc_start: 0.3283 (mpm) cc_final: 0.2905 (mmm) REVERT: D 91 MET cc_start: 0.2847 (OUTLIER) cc_final: 0.1485 (tpt) REVERT: E 104 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7962 (mppt) REVERT: E 107 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7932 (ttp80) REVERT: F 1004 VAL cc_start: 0.6299 (p) cc_final: 0.6002 (t) REVERT: F 1070 TYR cc_start: 0.5102 (OUTLIER) cc_final: 0.3856 (m-80) REVERT: F 1145 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7355 (mt) REVERT: F 1203 ARG cc_start: 0.5591 (pmt-80) cc_final: 0.4942 (tpm-80) REVERT: G 101 LYS cc_start: 0.8358 (mmmt) cc_final: 0.7657 (tptt) REVERT: H 53 MET cc_start: 0.2945 (mmp) cc_final: 0.2728 (mmm) REVERT: H 67 LEU cc_start: 0.3479 (OUTLIER) cc_final: 0.2824 (pt) REVERT: H 91 MET cc_start: 0.4781 (pp-130) cc_final: 0.3890 (tpt) REVERT: H 149 MET cc_start: 0.4271 (OUTLIER) cc_final: 0.3113 (tmt) REVERT: I 3 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8070 (tt0) outliers start: 91 outliers final: 57 residues processed: 275 average time/residue: 0.5127 time to fit residues: 161.9005 Evaluate side-chains 277 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 202 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 864 GLN Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 995 ASP Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1163 GLN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1070 TYR Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1182 GLN Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 118 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 224 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.240491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.196788 restraints weight = 22085.939| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 1.86 r_work: 0.3965 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20444 Z= 0.166 Angle : 0.638 16.070 27778 Z= 0.308 Chirality : 0.045 0.315 2973 Planarity : 0.004 0.042 3609 Dihedral : 7.849 106.173 3083 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.27 % Allowed : 28.29 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2465 helix: 0.65 (0.27), residues: 429 sheet: -0.57 (0.20), residues: 647 loop : -0.65 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 775 TYR 0.018 0.001 TYR C 92 PHE 0.018 0.002 PHE B1098 TRP 0.043 0.001 TRP F1030 HIS 0.006 0.001 HIS B 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (20380) covalent geometry : angle 0.61276 / 0.30 (27640) SS BOND : bond 0.00227 / 0.13 ( 54) SS BOND : angle 0.92436 / 0.62 ( 108) hydrogen bonds : bond 0.03776 / 2.48 ( 681) hydrogen bonds : angle 5.51559 / 3.99 ( 1758) link_BETA1-4 : bond 0.00686 / 0.33 ( 3) link_BETA1-4 : angle 2.39529 / 1.22 ( 9) link_NAG-ASN : bond 0.01102 / 0.56 ( 7) link_NAG-ASN : angle 6.09908 / 3.15 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4930 Ramachandran restraints generated. 2465 Oldfield, 0 Emsley, 2465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 196 time to evaluate : 0.726 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: A 41 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.5754 (tt) REVERT: A 259 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8405 (ttt90) REVERT: A 342 CYS cc_start: 0.5552 (OUTLIER) cc_final: 0.5344 (m) REVERT: B 656 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7892 (mt) REVERT: B 751 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7291 (tmt170) REVERT: B 864 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6260 (tp40) REVERT: B 945 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8392 (m-40) REVERT: B 979 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8063 (tp) REVERT: B 983 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8144 (t70) REVERT: B 1115 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7979 (mptm) REVERT: B 1154 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: B 1163 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: C 122 MET cc_start: 0.3243 (mpm) cc_final: 0.2852 (mmm) REVERT: D 91 MET cc_start: 0.2714 (OUTLIER) cc_final: 0.1443 (tpt) REVERT: E 104 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8129 (mppt) REVERT: E 107 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: E 319 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8308 (ttp-170) REVERT: F 1004 VAL cc_start: 0.6209 (p) cc_final: 0.5928 (t) REVERT: F 1070 TYR cc_start: 0.5010 (OUTLIER) cc_final: 0.3804 (m-80) REVERT: F 1145 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7137 (mt) REVERT: F 1203 ARG cc_start: 0.5471 (pmt-80) cc_final: 0.4865 (tpm-80) REVERT: G 101 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7626 (tptt) REVERT: H 53 MET cc_start: 0.3131 (mmp) cc_final: 0.2880 (mmm) REVERT: H 67 LEU cc_start: 0.3484 (OUTLIER) cc_final: 0.2729 (pt) REVERT: H 91 MET cc_start: 0.4961 (pp-130) cc_final: 0.3817 (tpt) REVERT: H 149 MET cc_start: 0.4554 (OUTLIER) cc_final: 0.3460 (tmt) REVERT: I 3 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8173 (tt0) outliers start: 92 outliers final: 61 residues processed: 267 average time/residue: 0.4957 time to fit residues: 151.5707 Evaluate side-chains 275 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 193 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 751 ARG Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 864 GLN Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 952 GLN Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1115 LYS Chi-restraints excluded: chain B residue 1130 ASP Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1163 GLN Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 319 ARG Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain F residue 706 TYR Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 838 LEU Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1064 VAL Chi-restraints excluded: chain F residue 1070 TYR Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1182 GLN Chi-restraints excluded: chain F residue 1230 CYS Chi-restraints excluded: chain G residue 80 CYS Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.0050 chunk 158 optimal weight: 5.9990 chunk 217 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.4652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 653 ASN F 718 ASN ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.242614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.204182 restraints weight = 22285.826| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 1.68 r_work: 0.3891 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20444 Z= 0.110 Angle : 0.607 15.472 27778 Z= 0.291 Chirality : 0.043 0.310 2973 Planarity : 0.003 0.039 3609 Dihedral : 7.672 104.959 3083 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.53 % Allowed : 29.03 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2465 helix: 0.81 (0.28), residues: 429 sheet: -0.48 (0.20), residues: 645 loop : -0.60 (0.18), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 775 TYR 0.020 0.001 TYR C 92 PHE 0.016 0.001 PHE F 633 TRP 0.043 0.001 TRP F1030 HIS 0.005 0.000 HIS B 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20380) covalent geometry : angle 0.58316 / 0.29 (27640) SS BOND : bond 0.00188 / 0.12 ( 54) SS BOND : angle 0.75911 / 0.52 ( 108) hydrogen bonds : bond 0.03294 / 2.17 ( 681) hydrogen bonds : angle 5.42076 / 3.92 ( 1758) link_BETA1-4 : bond 0.00691 / 0.33 ( 3) link_BETA1-4 : angle 2.33772 / 1.20 ( 9) link_NAG-ASN : bond 0.01088 / 0.55 ( 7) link_NAG-ASN : angle 5.81316 / 3.00 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5599.64 seconds wall clock time: 96 minutes 20.91 seconds (5780.91 seconds total)