Starting phenix.real_space_refine on Sat Jul 4 09:05:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21kt_67780/07_2026/21kt_67780.cif Found real_map, /net/cci-nas-00/data/ceres_data/21kt_67780/07_2026/21kt_67780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21kt_67780/07_2026/21kt_67780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21kt_67780/07_2026/21kt_67780.map" model { file = "/net/cci-nas-00/data/ceres_data/21kt_67780/07_2026/21kt_67780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21kt_67780/07_2026/21kt_67780.cif" } resolution = 3.33 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= 0.001 sd= 0.018 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 164 5.16 5 C 11900 2.51 5 N 3352 2.21 5 O 3590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s 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: 19006 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 316} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 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: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 316} 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: "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: "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: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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 Time building chain proxies: 3.87, per 1000 atoms: 0.20 Number of scatterers: 19006 At special positions: 0 Unit cell: (132.664, 119.48, 186.224, 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 164 16.00 O 3590 8.00 N 3352 7.00 C 11900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, 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=2.03 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=2.03 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=2.03 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 H 35 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 89 " distance=2.03 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 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=2.02 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=2.03 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 401 " - " ASN A 87 " " NAG B1401 " - " ASN B 692 " " NAG B1402 " - " ASN B1039 " " NAG B1403 " - " ASN B 859 " " NAG I 1 " - " ASN A 298 " " NAG J 1 " - " ASN E 87 " " NAG K 1 " - " ASN E 298 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 642.6 milliseconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 40 sheets defined 22.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 29 through 34 removed outlier: 4.177A pdb=" N SER A 33 " --> pdb=" O GLY A 29 " (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 102 removed outlier: 3.587A pdb=" N VAL A 101 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 106 through 131 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.882A pdb=" N GLY A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 197 Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.004A pdb=" N GLY A 210 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.525A pdb=" N CYS A 311 " --> pdb=" O CYS A 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 4.258A pdb=" N GLY C 45 " --> 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 79 Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 118 through 123 removed outlier: 3.965A pdb=" N MET C 122 " --> pdb=" O CYS C 118 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 123' Processing helix chain 'D' and resid 40 through 45 removed outlier: 4.066A pdb=" N GLY D 45 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 removed outlier: 4.438A pdb=" N ALA D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 107 through 116 Processing helix chain 'E' and resid 21 through 28 removed outlier: 3.548A pdb=" N VAL E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 38 removed outlier: 4.340A pdb=" N SER E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU E 35 " --> pdb=" O GLN E 31 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) 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: 3.952A pdb=" N VAL E 101 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 102 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 104 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 131 removed outlier: 3.556A pdb=" N GLY E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 171 removed outlier: 4.272A pdb=" N GLY E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 198 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 Processing helix chain 'F' and resid 891 through 897 removed outlier: 4.018A pdb=" N SER F 895 " --> pdb=" O ASN F 891 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER F 896 " --> pdb=" O GLU F 892 " (cutoff:3.500A) Processing helix chain 'F' and resid 898 through 900 No H-bonds generated for 'chain 'F' and resid 898 through 900' Processing helix chain 'F' and resid 1066 through 1068 No H-bonds generated for 'chain 'F' and resid 1066 through 1068' Processing helix chain 'F' and resid 1198 through 1204 Processing helix chain 'F' and resid 1209 through 1214 Processing helix chain 'H' and resid 40 through 45 removed outlier: 4.391A pdb=" N GLY H 45 " --> pdb=" O PRO H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 70 Processing helix chain 'H' and resid 71 through 76 Proline residue: H 74 - end of helix No H-bonds generated for 'chain 'H' and resid 71 through 76' Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'H' and resid 108 through 123 removed outlier: 5.746A pdb=" N GLY H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Proline residue: H 120 - end of helix Processing helix chain 'G' and resid 61 through 70 removed outlier: 3.781A pdb=" N ALA G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 removed outlier: 4.008A pdb=" N ILE G 78 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 Processing helix chain 'G' and resid 107 through 125 removed outlier: 4.280A pdb=" N CYS G 111 " --> pdb=" O CYS G 107 " (cutoff:3.500A) Proline residue: G 120 - end of helix Processing helix chain 'B' and resid 891 through 897 removed outlier: 3.542A 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 1205 removed outlier: 3.563A pdb=" N HIS B1205 " --> pdb=" O GLU B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1209 Processing helix chain 'B' and resid 1210 through 1214 Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 206 removed outlier: 4.049A 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: 4.375A pdb=" N HIS A 349 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS A 342 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS A 326 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 344 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG A 324 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR A 346 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG A 322 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 348 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR A 320 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 350 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ALA A 318 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AA6, first strand: chain 'E' and resid 200 through 203 Processing sheet with id=AA7, first strand: chain 'E' and resid 251 through 258 Processing sheet with id=AA8, first strand: chain 'E' and resid 319 through 323 removed outlier: 3.516A pdb=" N TYR E 346 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 653 through 655 removed outlier: 4.063A pdb=" N ASP F 878 " --> pdb=" O SER F 637 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 664 through 668 removed outlier: 4.440A pdb=" N ALA F 666 " --> pdb=" O THR F 679 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE F 686 " --> pdb=" O VAL F 699 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 709 through 713 removed outlier: 3.809A pdb=" N GLY F 709 " --> pdb=" O ALA F 722 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE F 729 " --> pdb=" O LEU F 742 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 762 through 766 Processing sheet with id=AB4, first strand: chain 'F' and resid 793 through 799 removed outlier: 4.289A pdb=" N LEU F 796 " --> pdb=" O TYR F 806 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR F 806 " --> pdb=" O LEU F 796 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE F 798 " --> pdb=" O ARG F 804 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG F 804 " --> pdb=" O ILE F 798 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 835 through 841 removed outlier: 5.915A pdb=" N THR F 848 " --> pdb=" O PHE F 836 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU F 838 " --> pdb=" O TYR F 846 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR F 846 " --> pdb=" O LEU F 838 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN F 840 " --> pdb=" O TYR F 844 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR F 844 " --> pdb=" O GLN F 840 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE F 855 " --> pdb=" O ILE F 869 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 903 through 907 removed outlier: 3.936A pdb=" N LEU F 903 " --> pdb=" O GLY F 915 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 921 through 922 Processing sheet with id=AB8, first strand: chain 'F' and resid 957 through 958 removed outlier: 3.750A pdb=" N LEU F 937 " --> pdb=" O HIS F1192 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER F 939 " --> pdb=" O ASP F1190 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP F1190 " --> pdb=" O SER F 939 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 967 through 972 removed outlier: 4.626A pdb=" N ALA F 969 " --> pdb=" O ILE F 982 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP F 981 " --> pdb=" O ARG F 990 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG F 990 " --> pdb=" O TRP F 981 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE F 989 " --> pdb=" O VAL F1002 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 1016 through 1021 removed outlier: 4.039A pdb=" N ASP F1018 " --> pdb=" O THR F1031 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE F1038 " --> pdb=" O VAL F1050 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL F1050 " --> pdb=" O ILE F1038 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL F1040 " --> pdb=" O VAL F1048 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 1059 through 1065 removed outlier: 4.255A pdb=" N ALA F1061 " --> pdb=" O THR F1074 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F1074 " --> pdb=" O ALA F1061 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG F1085 " --> pdb=" O VAL F1095 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL F1095 " --> pdb=" O ARG F1085 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 1106 through 1110 removed outlier: 4.068A pdb=" N ALA F1106 " --> pdb=" O ALA F1119 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP F1120 " --> pdb=" O ARG F1125 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG F1125 " --> pdb=" O ASP F1120 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER F1128 " --> pdb=" O VAL F1138 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL F1138 " --> pdb=" O SER F1128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 1147 through 1153 removed outlier: 4.355A pdb=" N GLY F1149 " --> pdb=" O ILE F1160 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE F1167 " --> pdb=" O VAL F1181 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 1235 through 1236 Processing sheet with id=AC6, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.772A pdb=" N ARG B 643 " --> pdb=" O PHE B 636 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 636 " --> pdb=" O ARG B 643 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 633 " --> pdb=" O PHE B 882 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP B 878 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 667 through 670 removed outlier: 3.736A pdb=" N ASP B 670 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 675 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE B 686 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 713 removed outlier: 6.534A pdb=" N ILE B 729 " --> pdb=" O LEU B 742 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 754 through 756 Processing sheet with id=AD2, first strand: chain 'B' and resid 793 through 798 removed outlier: 5.417A pdb=" N GLY B 795 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B 808 " --> pdb=" O GLY B 795 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 807 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 835 through 841 removed outlier: 6.155A pdb=" N THR B 848 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 838 " --> pdb=" O TYR B 846 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR B 846 " --> pdb=" O LEU B 838 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN B 840 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 844 " --> pdb=" O GLN B 840 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 845 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 858 " --> pdb=" O ILE B 845 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B 870 " --> pdb=" O ILE B 855 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG B 857 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 868 " --> pdb=" O ARG B 857 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 903 through 907 removed outlier: 3.655A pdb=" N GLY B 915 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 911 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 921 through 922 Processing sheet with id=AD6, first strand: chain 'B' and resid 935 through 940 removed outlier: 3.551A pdb=" N PHE B 935 " --> pdb=" O VAL B1194 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B1194 " --> pdb=" O PHE B 935 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP B1190 " --> pdb=" O SER B 939 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 945 through 946 removed outlier: 3.600A pdb=" N ILE B 957 " --> pdb=" O ARG B 946 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 967 through 973 removed outlier: 6.324A pdb=" N ILE B 982 " --> pdb=" O ARG B 968 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE B 970 " --> pdb=" O TYR B 980 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 980 " --> pdb=" O ILE B 970 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR B 972 " --> pdb=" O GLN B 978 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN B 978 " --> pdb=" O TYR B 972 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 990 " --> pdb=" O TRP B 981 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 989 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1016 through 1022 removed outlier: 4.451A pdb=" N ASP B1018 " --> pdb=" O THR B1031 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1027 " --> pdb=" O ASP B1022 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE B1038 " --> pdb=" O VAL B1051 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B1051 " --> pdb=" O ILE B1038 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B1040 " --> pdb=" O GLY B1049 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B1049 " --> pdb=" O VAL B1040 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG B1042 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER B1047 " --> pdb=" O ARG B1042 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 6.322A pdb=" N ILE B1083 " --> pdb=" O LEU B1096 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1104 through 1109 removed outlier: 3.930A pdb=" N ALA B1106 " --> pdb=" O ALA B1119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B1119 " --> pdb=" O ALA B1106 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B1126 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1147 through 1153 removed outlier: 4.082A pdb=" N GLY B1149 " --> pdb=" O ILE B1160 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS B1169 " --> pdb=" O LYS B1180 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS B1180 " --> pdb=" O LYS B1169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1235 through 1236 586 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6360 1.34 - 1.46: 4519 1.46 - 1.58: 8367 1.58 - 1.71: 0 1.71 - 1.83: 218 Bond restraints: 19464 Sorted by residual: bond pdb=" C SER C 81 " pdb=" N PRO C 82 " ideal model delta sigma weight residual 1.334 1.353 -0.020 8.40e-03 1.42e+04 5.60e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C PRO D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.34e-02 5.57e+03 2.71e+00 bond pdb=" C GLU A 248 " pdb=" N SER A 249 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.30e-02 5.92e+03 2.71e+00 bond pdb=" N LEU G 88 " pdb=" CA LEU G 88 " ideal model delta sigma weight residual 1.459 1.440 0.020 1.19e-02 7.06e+03 2.70e+00 ... (remaining 19459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 26047 2.30 - 4.60: 290 4.60 - 6.90: 46 6.90 - 9.20: 14 9.20 - 11.50: 5 Bond angle restraints: 26402 Sorted by residual: angle pdb=" O PRO D 105 " pdb=" C PRO D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 121.31 123.27 -1.96 4.60e-01 4.73e+00 1.82e+01 angle pdb=" CB MET E 241 " pdb=" CG MET E 241 " pdb=" SD MET E 241 " ideal model delta sigma weight residual 112.70 124.20 -11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C SER C 81 " pdb=" N PRO C 82 " pdb=" CA PRO C 82 " ideal model delta sigma weight residual 120.83 117.18 3.65 1.02e+00 9.61e-01 1.28e+01 angle pdb=" CB MET F1172 " pdb=" CG MET F1172 " pdb=" SD MET F1172 " ideal model delta sigma weight residual 112.70 122.63 -9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C VAL G 69 " pdb=" N HIS G 70 " pdb=" CA HIS G 70 " ideal model delta sigma weight residual 122.31 115.76 6.55 2.00e+00 2.50e-01 1.07e+01 ... (remaining 26397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 10562 23.01 - 46.03: 1146 46.03 - 69.04: 203 69.04 - 92.05: 38 92.05 - 115.07: 16 Dihedral angle restraints: 11965 sinusoidal: 5071 harmonic: 6894 Sorted by residual: dihedral pdb=" CB CYS E 327 " pdb=" SG CYS E 327 " pdb=" SG CYS E 342 " pdb=" CB CYS E 342 " ideal model delta sinusoidal sigma weight residual -86.00 -3.54 -82.46 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS B1214 " pdb=" SG CYS B1214 " pdb=" SG CYS B1228 " pdb=" CB CYS B1228 " ideal model delta sinusoidal sigma weight residual -86.00 -167.20 81.20 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS E 138 " pdb=" SG CYS E 138 " pdb=" SG CYS E 155 " pdb=" CB CYS E 155 " ideal model delta sinusoidal sigma weight residual -86.00 -11.16 -74.84 1 1.00e+01 1.00e-02 7.09e+01 ... (remaining 11962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2280 0.051 - 0.101: 442 0.101 - 0.151: 109 0.151 - 0.202: 4 0.202 - 0.252: 1 Chirality restraints: 2836 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 87 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU H 67 " pdb=" CB LEU H 67 " pdb=" CD1 LEU H 67 " pdb=" CD2 LEU H 67 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C1 NAG B1403 " pdb=" ND2 ASN B 859 " pdb=" C2 NAG B1403 " pdb=" O5 NAG B1403 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 2833 not shown) Planarity restraints: 3459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 73 " 0.015 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP H 73 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP H 73 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 73 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 73 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 73 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 73 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 73 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 73 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 73 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 172 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.22e+00 pdb=" C ALA E 172 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA E 172 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG E 173 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 73 " -0.013 2.00e-02 2.50e+03 1.12e-02 3.15e+00 pdb=" CG TRP G 73 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP G 73 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP G 73 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 73 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 73 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 73 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 73 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 73 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 73 " 0.000 2.00e-02 2.50e+03 ... (remaining 3456 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2077 2.75 - 3.28: 19457 3.28 - 3.82: 32674 3.82 - 4.36: 36611 4.36 - 4.90: 62854 Nonbonded interactions: 153673 Sorted by model distance: nonbonded pdb=" OH TYR B1024 " pdb=" OE2 GLU B1201 " model vdw 2.208 3.040 nonbonded pdb=" OD2 ASP F 723 " pdb=" OG1 THR F 726 " model vdw 2.221 3.040 nonbonded pdb=" OG SER A 94 " pdb=" O ALA A 96 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP B 723 " pdb=" OG1 THR B 726 " model vdw 2.234 3.040 nonbonded pdb=" O LEU E 41 " pdb=" OG SER E 44 " model vdw 2.235 3.040 ... (remaining 153668 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 'I' selection = chain 'J' selection = chain 'K' } 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: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.880 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19527 Z= 0.141 Angle : 0.642 15.745 26538 Z= 0.314 Chirality : 0.043 0.252 2836 Planarity : 0.003 0.035 3452 Dihedral : 18.636 115.067 7370 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.87 % Allowed : 32.80 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.18), residues: 2360 helix: 0.75 (0.27), residues: 410 sheet: -1.09 (0.26), residues: 446 loop : -1.09 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.014 0.001 TYR E 32 PHE 0.009 0.001 PHE G 86 TRP 0.035 0.001 TRP H 73 HIS 0.006 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (19464) covalent geometry : angle 0.62722 / 0.31 (26402) SS BOND : bond 0.00243 / 0.15 ( 53) SS BOND : angle 0.72647 / 0.51 ( 106) hydrogen bonds : bond 0.24065 / 15.99 ( 586) hydrogen bonds : angle 9.21172 / 6.74 ( 1515) link_BETA1-4 : bond 0.00719 / 0.35 ( 3) link_BETA1-4 : angle 1.81738 / 0.94 ( 9) link_NAG-ASN : bond 0.00842 / 0.43 ( 7) link_NAG-ASN : angle 4.62947 / 2.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 399 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.6107 (tpp80) cc_final: 0.5721 (mmt-90) REVERT: C 57 PHE cc_start: 0.7643 (m-80) cc_final: 0.7336 (m-10) REVERT: C 121 LEU cc_start: 0.6177 (tt) cc_final: 0.5342 (mt) REVERT: D 53 MET cc_start: 0.6416 (ptm) cc_final: 0.6115 (ptp) REVERT: D 101 LYS cc_start: 0.3215 (OUTLIER) cc_final: 0.2184 (tptp) REVERT: D 133 MET cc_start: 0.7391 (tmm) cc_final: 0.7135 (tmm) REVERT: D 149 MET cc_start: 0.4715 (ttp) cc_final: 0.1967 (mmm) REVERT: E 61 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7067 (tp30) REVERT: E 63 MET cc_start: 0.5717 (mtp) cc_final: 0.5382 (mmp) REVERT: E 76 GLU cc_start: 0.7480 (tp30) cc_final: 0.6920 (tp30) REVERT: E 189 GLU cc_start: 0.6589 (tp30) cc_final: 0.5630 (mt-10) REVERT: E 287 THR cc_start: 0.7053 (t) cc_final: 0.5869 (m) REVERT: E 292 THR cc_start: 0.7974 (t) cc_final: 0.6376 (p) REVERT: F 652 ASN cc_start: 0.6013 (t0) cc_final: 0.5794 (t0) REVERT: F 669 PHE cc_start: 0.7537 (p90) cc_final: 0.7195 (p90) REVERT: F 761 PHE cc_start: 0.5949 (m-80) cc_final: 0.5629 (m-80) REVERT: F 816 GLU cc_start: 0.6419 (tt0) cc_final: 0.6115 (tt0) REVERT: F 957 ILE cc_start: 0.8074 (tt) cc_final: 0.7752 (tp) REVERT: F 1176 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6599 (tp30) REVERT: H 133 MET cc_start: 0.6106 (ppp) cc_final: 0.4624 (tmm) REVERT: H 149 MET cc_start: -0.0613 (pmm) cc_final: -0.4046 (mmt) REVERT: G 53 MET cc_start: 0.6933 (mpp) cc_final: 0.6381 (mmt) REVERT: G 70 HIS cc_start: 0.5463 (m-70) cc_final: 0.5034 (m-70) REVERT: G 91 MET cc_start: 0.7813 (mmp) cc_final: 0.6939 (mtp) REVERT: G 102 LYS cc_start: 0.8015 (tttt) cc_final: 0.6911 (mttt) REVERT: B 770 LYS cc_start: 0.7028 (tptt) cc_final: 0.6774 (ttpt) REVERT: B 802 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7788 (tptp) REVERT: B 849 ASP cc_start: 0.6799 (t70) cc_final: 0.6141 (t0) REVERT: B 856 GLU cc_start: 0.6405 (mp0) cc_final: 0.5940 (mp0) REVERT: B 913 VAL cc_start: 0.6354 (p) cc_final: 0.6129 (m) REVERT: B 1067 GLU cc_start: 0.7702 (tp30) cc_final: 0.7046 (pt0) REVERT: B 1156 TRP cc_start: 0.6911 (m100) cc_final: 0.6584 (m100) REVERT: B 1164 GLN cc_start: 0.7472 (tp40) cc_final: 0.7188 (tt0) outliers start: 18 outliers final: 2 residues processed: 411 average time/residue: 0.1361 time to fit residues: 82.1256 Evaluate side-chains 259 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 256 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain F residue 1038 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0060 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1163 GLN G 59 HIS ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.232370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.192512 restraints weight = 25134.902| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 1.94 r_work: 0.3953 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19527 Z= 0.140 Angle : 0.687 15.113 26538 Z= 0.343 Chirality : 0.047 0.308 2836 Planarity : 0.005 0.061 3452 Dihedral : 9.218 102.740 2843 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.73 % Allowed : 29.94 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.18), residues: 2360 helix: 0.55 (0.27), residues: 441 sheet: -1.14 (0.23), residues: 512 loop : -1.20 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1125 TYR 0.022 0.002 TYR F1029 PHE 0.018 0.001 PHE B1000 TRP 0.020 0.001 TRP B1118 HIS 0.006 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (19464) covalent geometry : angle 0.67161 / 0.34 (26402) SS BOND : bond 0.00421 / 0.19 ( 53) SS BOND : angle 1.19135 / 0.77 ( 106) hydrogen bonds : bond 0.04727 / 3.15 ( 586) hydrogen bonds : angle 6.82272 / 5.02 ( 1515) link_BETA1-4 : bond 0.00736 / 0.38 ( 3) link_BETA1-4 : angle 2.00371 / 1.01 ( 9) link_NAG-ASN : bond 0.01050 / 0.52 ( 7) link_NAG-ASN : angle 4.47539 / 1.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 257 time to evaluate : 0.459 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: C 121 LEU cc_start: 0.6383 (tt) cc_final: 0.5811 (mt) REVERT: D 88 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6902 (pt) REVERT: D 101 LYS cc_start: 0.2325 (OUTLIER) cc_final: 0.2019 (mttt) REVERT: D 149 MET cc_start: 0.4659 (ttp) cc_final: 0.1731 (mmm) REVERT: E 130 GLU cc_start: 0.7090 (tt0) cc_final: 0.6855 (mt-10) REVERT: E 152 TRP cc_start: 0.7761 (m-90) cc_final: 0.7470 (m-90) REVERT: E 189 GLU cc_start: 0.7100 (tp30) cc_final: 0.6716 (mt-10) REVERT: E 292 THR cc_start: 0.8682 (t) cc_final: 0.8358 (m) REVERT: F 691 MET cc_start: 0.8048 (tpp) cc_final: 0.7805 (mmm) REVERT: F 753 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6836 (tp) REVERT: F 1017 TYR cc_start: 0.6001 (t80) cc_final: 0.5793 (m-80) REVERT: H 53 MET cc_start: 0.2616 (OUTLIER) cc_final: 0.2110 (ppp) REVERT: H 133 MET cc_start: 0.5240 (ppp) cc_final: 0.4590 (tmm) REVERT: H 149 MET cc_start: -0.0314 (pmm) cc_final: -0.3945 (mmt) REVERT: G 70 HIS cc_start: 0.5802 (m-70) cc_final: 0.5425 (m-70) REVERT: B 782 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7015 (tm-30) REVERT: B 849 ASP cc_start: 0.6866 (t70) cc_final: 0.6626 (t0) REVERT: B 856 GLU cc_start: 0.6684 (mp0) cc_final: 0.6291 (mt-10) REVERT: B 913 VAL cc_start: 0.7278 (p) cc_final: 0.7064 (m) REVERT: B 941 LYS cc_start: 0.7429 (tttp) cc_final: 0.6744 (tttm) REVERT: B 945 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7337 (m-40) REVERT: B 988 MET cc_start: 0.4530 (ppp) cc_final: 0.4284 (ppp) REVERT: B 1094 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.4827 (pt0) outliers start: 77 outliers final: 24 residues processed: 318 average time/residue: 0.1180 time to fit residues: 58.4307 Evaluate side-chains 241 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 800 TYR Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 929 CYS Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1117 PHE Chi-restraints excluded: chain F residue 1179 THR Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 182 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 ASN ** F 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 840 GLN ** G 71 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 = 0.4659 r_free = 0.4659 target = 0.226280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.193523 restraints weight = 25267.041| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 1.89 r_work: 0.3933 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19527 Z= 0.250 Angle : 0.772 15.880 26538 Z= 0.389 Chirality : 0.050 0.301 2836 Planarity : 0.006 0.074 3452 Dihedral : 7.627 97.667 2840 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 6.83 % Allowed : 26.99 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2360 helix: -0.14 (0.24), residues: 470 sheet: -1.51 (0.23), residues: 510 loop : -1.40 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 751 TYR 0.026 0.002 TYR E 59 PHE 0.022 0.002 PHE F 669 TRP 0.031 0.002 TRP B1156 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (19464) covalent geometry : angle 0.75452 / 0.39 (26402) SS BOND : bond 0.00476 / 0.31 ( 53) SS BOND : angle 1.25315 / 0.80 ( 106) hydrogen bonds : bond 0.05088 / 3.43 ( 586) hydrogen bonds : angle 6.60889 / 4.87 ( 1515) link_BETA1-4 : bond 0.00655 / 0.31 ( 3) link_BETA1-4 : angle 2.07249 / 1.08 ( 9) link_NAG-ASN : bond 0.01366 / 0.70 ( 7) link_NAG-ASN : angle 5.30055 / 2.43 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 251 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8491 (mtpp) REVERT: A 152 TRP cc_start: 0.7452 (m100) cc_final: 0.7137 (m100) REVERT: A 168 GLU cc_start: 0.8348 (mp0) cc_final: 0.8057 (mp0) REVERT: A 202 LYS cc_start: 0.7280 (tptt) cc_final: 0.6954 (tppt) REVERT: D 149 MET cc_start: 0.4481 (ttp) cc_final: 0.2028 (mmm) REVERT: E 130 GLU cc_start: 0.7807 (tt0) cc_final: 0.7569 (mt-10) REVERT: E 150 TRP cc_start: 0.5772 (p-90) cc_final: 0.5259 (p90) REVERT: E 227 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7976 (mt) REVERT: F 787 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7827 (t) REVERT: F 802 LYS cc_start: 0.7589 (pttt) cc_final: 0.6801 (tttt) REVERT: F 819 ASN cc_start: 0.6879 (t0) cc_final: 0.5932 (p0) REVERT: F 919 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7614 (m-70) REVERT: F 1201 GLU cc_start: 0.6391 (tm-30) cc_final: 0.5831 (tt0) REVERT: H 53 MET cc_start: 0.2553 (OUTLIER) cc_final: 0.2022 (ppp) REVERT: H 149 MET cc_start: -0.0296 (pmm) cc_final: -0.3811 (mmt) REVERT: G 70 HIS cc_start: 0.5914 (m-70) cc_final: 0.5479 (m-70) REVERT: G 102 LYS cc_start: 0.7953 (tttt) cc_final: 0.7084 (mttt) REVERT: B 643 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7602 (mtt90) REVERT: B 652 ASN cc_start: 0.6509 (t0) cc_final: 0.6065 (m-40) REVERT: B 753 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8524 (tp) REVERT: B 849 ASP cc_start: 0.7604 (t70) cc_final: 0.7294 (t0) REVERT: B 856 GLU cc_start: 0.6912 (mp0) cc_final: 0.6560 (mp0) REVERT: B 985 ARG cc_start: 0.6611 (tpp-160) cc_final: 0.6332 (ttp-170) REVERT: B 1072 TYR cc_start: 0.6834 (m-80) cc_final: 0.6533 (m-80) REVERT: B 1103 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.7023 (ttpp) REVERT: B 1118 TRP cc_start: 0.6669 (p90) cc_final: 0.6259 (p90) outliers start: 141 outliers final: 64 residues processed: 364 average time/residue: 0.1181 time to fit residues: 66.6107 Evaluate side-chains 272 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 333 TRP Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 686 ILE Chi-restraints excluded: chain F residue 787 VAL Chi-restraints excluded: chain F residue 808 THR Chi-restraints excluded: chain F residue 840 GLN Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 880 LEU Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 919 HIS Chi-restraints excluded: chain F residue 929 CYS Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 964 LEU Chi-restraints excluded: chain F residue 967 VAL Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1019 LEU Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1107 LEU Chi-restraints excluded: chain F residue 1117 PHE Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1103 LYS Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 209 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 840 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN B 824 ASN B1187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.227181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.189572 restraints weight = 25087.161| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 1.96 r_work: 0.3871 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19527 Z= 0.164 Angle : 0.689 16.867 26538 Z= 0.343 Chirality : 0.047 0.283 2836 Planarity : 0.005 0.107 3452 Dihedral : 7.221 95.935 2836 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.36 % Favored : 93.60 % Rotamer: Outliers : 4.46 % Allowed : 29.02 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2360 helix: -0.04 (0.25), residues: 464 sheet: -1.33 (0.23), residues: 502 loop : -1.39 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 108 TYR 0.023 0.002 TYR B 844 PHE 0.017 0.002 PHE B 761 TRP 0.021 0.002 TRP B1156 HIS 0.005 0.001 HIS E 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (19464) covalent geometry : angle 0.66780 / 0.34 (26402) SS BOND : bond 0.00400 / 0.24 ( 53) SS BOND : angle 1.53141 / 0.97 ( 106) hydrogen bonds : bond 0.04100 / 2.70 ( 586) hydrogen bonds : angle 6.20924 / 4.60 ( 1515) link_BETA1-4 : bond 0.00471 / 0.23 ( 3) link_BETA1-4 : angle 1.96604 / 1.01 ( 9) link_NAG-ASN : bond 0.01043 / 0.54 ( 7) link_NAG-ASN : angle 5.12056 / 2.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 213 time to evaluate : 0.493 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: A 104 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8540 (ttpt) REVERT: A 126 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7255 (mmt-90) REVERT: A 168 GLU cc_start: 0.8389 (mp0) cc_final: 0.8132 (mp0) REVERT: A 202 LYS cc_start: 0.7400 (tptt) cc_final: 0.6918 (tppt) REVERT: D 149 MET cc_start: 0.4487 (ttp) cc_final: 0.1999 (mmm) REVERT: E 130 GLU cc_start: 0.7850 (tt0) cc_final: 0.7627 (mt-10) REVERT: E 195 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7661 (tt) REVERT: E 227 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7815 (mt) REVERT: F 802 LYS cc_start: 0.7702 (pttt) cc_final: 0.6977 (tttt) REVERT: F 819 ASN cc_start: 0.7130 (t0) cc_final: 0.5998 (p0) REVERT: F 1071 MET cc_start: 0.4668 (ppp) cc_final: 0.4251 (ppp) REVERT: H 53 MET cc_start: 0.2590 (OUTLIER) cc_final: 0.2145 (ppp) REVERT: H 68 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6985 (mm-30) REVERT: H 133 MET cc_start: 0.5571 (pmm) cc_final: 0.2821 (tpp) REVERT: H 137 ARG cc_start: 0.4061 (OUTLIER) cc_final: 0.2503 (mtt180) REVERT: H 149 MET cc_start: -0.0175 (pmm) cc_final: -0.3829 (mmt) REVERT: G 70 HIS cc_start: 0.5753 (m-70) cc_final: 0.5245 (m-70) REVERT: G 84 LEU cc_start: 0.6875 (mm) cc_final: 0.6333 (pt) REVERT: B 643 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7596 (mtt90) REVERT: B 708 GLU cc_start: 0.7948 (mp0) cc_final: 0.7651 (mm-30) REVERT: B 753 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8521 (tp) REVERT: B 802 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7397 (mmtp) REVERT: B 803 ARG cc_start: 0.6461 (tpt170) cc_final: 0.5205 (tpt90) REVERT: B 849 ASP cc_start: 0.7523 (t70) cc_final: 0.7216 (t0) REVERT: B 985 ARG cc_start: 0.6751 (tpp-160) cc_final: 0.6429 (ttp-170) REVERT: B 1076 LEU cc_start: 0.7442 (tt) cc_final: 0.7232 (mt) REVERT: B 1094 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6414 (pp20) REVERT: B 1103 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6940 (ttpp) REVERT: B 1118 TRP cc_start: 0.6889 (p90) cc_final: 0.6473 (p90) outliers start: 92 outliers final: 56 residues processed: 289 average time/residue: 0.1290 time to fit residues: 57.1193 Evaluate side-chains 260 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 333 TRP Chi-restraints excluded: chain F residue 686 ILE Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 773 ILE Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 880 LEU Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 929 CYS Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1019 LEU Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1117 PHE Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 111 CYS Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain B residue 1103 LYS Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 146 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 864 GLN G 36 GLN B 674 ASN B 737 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.233794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.182043 restraints weight = 26648.203| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.19 r_work: 0.3892 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 19527 Z= 0.144 Angle : 0.656 16.577 26538 Z= 0.327 Chirality : 0.045 0.290 2836 Planarity : 0.004 0.075 3452 Dihedral : 7.006 93.404 2836 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.09 % Allowed : 28.20 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2360 helix: 0.06 (0.25), residues: 464 sheet: -1.30 (0.23), residues: 498 loop : -1.37 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 638 TYR 0.018 0.001 TYR B 844 PHE 0.014 0.002 PHE B1073 TRP 0.014 0.001 TRP B1030 HIS 0.003 0.001 HIS F 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (19464) covalent geometry : angle 0.63472 / 0.32 (26402) SS BOND : bond 0.00529 / 0.35 ( 53) SS BOND : angle 1.43957 / 0.93 ( 106) hydrogen bonds : bond 0.03717 / 2.45 ( 586) hydrogen bonds : angle 6.11272 / 4.54 ( 1515) link_BETA1-4 : bond 0.00555 / 0.27 ( 3) link_BETA1-4 : angle 1.94211 / 1.01 ( 9) link_NAG-ASN : bond 0.00984 / 0.51 ( 7) link_NAG-ASN : angle 5.10183 / 2.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 209 time to evaluate : 0.605 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: A 202 LYS cc_start: 0.7458 (tptt) cc_final: 0.6934 (tppt) REVERT: C 91 MET cc_start: 0.6956 (mtm) cc_final: 0.6735 (mmm) REVERT: C 121 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4747 (mt) REVERT: C 122 MET cc_start: -0.0004 (tpp) cc_final: -0.0326 (tpp) REVERT: D 53 MET cc_start: 0.6323 (tmm) cc_final: 0.5060 (mtt) REVERT: D 149 MET cc_start: 0.4410 (ttp) cc_final: 0.1901 (mmm) REVERT: E 130 GLU cc_start: 0.8018 (tt0) cc_final: 0.7774 (mt-10) REVERT: E 173 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7710 (mtm-85) REVERT: E 195 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7581 (tt) REVERT: E 227 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7855 (mt) REVERT: F 753 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7726 (tp) REVERT: F 942 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8382 (t) REVERT: F 978 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7410 (mm-40) REVERT: F 1071 MET cc_start: 0.4262 (ppp) cc_final: 0.3820 (ppp) REVERT: F 1201 GLU cc_start: 0.6714 (tm-30) cc_final: 0.5859 (tt0) REVERT: H 53 MET cc_start: 0.2706 (OUTLIER) cc_final: 0.2292 (ppp) REVERT: H 68 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7234 (mm-30) REVERT: H 91 MET cc_start: 0.6012 (ptp) cc_final: 0.5653 (ptp) REVERT: H 133 MET cc_start: 0.5666 (pmm) cc_final: 0.3055 (tpt) REVERT: H 137 ARG cc_start: 0.4128 (OUTLIER) cc_final: 0.2780 (ptp-170) REVERT: H 149 MET cc_start: -0.0329 (pmm) cc_final: -0.3952 (mmt) REVERT: G 70 HIS cc_start: 0.5540 (m-70) cc_final: 0.4993 (m-70) REVERT: G 84 LEU cc_start: 0.6834 (mm) cc_final: 0.6340 (pt) REVERT: G 102 LYS cc_start: 0.7961 (tttm) cc_final: 0.6786 (mttt) REVERT: B 643 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7701 (mtt90) REVERT: B 753 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8507 (tp) REVERT: B 1094 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6421 (pp20) REVERT: B 1103 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6874 (ttpp) REVERT: B 1118 TRP cc_start: 0.6837 (p90) cc_final: 0.6470 (p90) outliers start: 105 outliers final: 66 residues processed: 296 average time/residue: 0.1275 time to fit residues: 58.9078 Evaluate side-chains 270 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 194 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 333 TRP Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 880 LEU Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 929 CYS Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 967 VAL Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1019 LEU Chi-restraints excluded: chain F residue 1028 ILE Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1117 PHE Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain B residue 1103 LYS Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 76 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 153 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 738 HIS F1163 GLN B 674 ASN B 737 GLN B1187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.231520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.183047 restraints weight = 26070.231| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.29 r_work: 0.3896 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19527 Z= 0.131 Angle : 0.642 16.645 26538 Z= 0.320 Chirality : 0.045 0.298 2836 Planarity : 0.004 0.066 3452 Dihedral : 6.800 91.334 2836 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.60 % Allowed : 28.44 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2360 helix: 0.15 (0.25), residues: 464 sheet: -1.19 (0.22), residues: 516 loop : -1.34 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 638 TYR 0.018 0.001 TYR F 980 PHE 0.014 0.001 PHE B1000 TRP 0.018 0.001 TRP E 152 HIS 0.010 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (19464) covalent geometry : angle 0.62135 / 0.31 (26402) SS BOND : bond 0.00549 / 0.37 ( 53) SS BOND : angle 1.32648 / 0.85 ( 106) hydrogen bonds : bond 0.03627 / 2.40 ( 586) hydrogen bonds : angle 5.90972 / 4.38 ( 1515) link_BETA1-4 : bond 0.00511 / 0.25 ( 3) link_BETA1-4 : angle 1.86815 / 0.96 ( 9) link_NAG-ASN : bond 0.00999 / 0.51 ( 7) link_NAG-ASN : angle 5.02898 / 2.23 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 205 time to evaluate : 0.676 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: A 202 LYS cc_start: 0.7412 (tptt) cc_final: 0.7030 (tppt) REVERT: C 91 MET cc_start: 0.6884 (mtm) cc_final: 0.6537 (mmm) REVERT: C 121 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.4882 (mt) REVERT: C 149 MET cc_start: 0.4418 (tpt) cc_final: 0.3683 (mtt) REVERT: D 91 MET cc_start: 0.5012 (mtp) cc_final: 0.2792 (ppp) REVERT: D 149 MET cc_start: 0.4341 (ttp) cc_final: 0.1983 (mmm) REVERT: E 20 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.4864 (m-80) REVERT: E 130 GLU cc_start: 0.7850 (tt0) cc_final: 0.7614 (mt-10) REVERT: E 151 LYS cc_start: 0.7493 (mmmt) cc_final: 0.7278 (mmmt) REVERT: E 195 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7321 (tt) REVERT: E 227 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7660 (mt) REVERT: F 753 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7723 (tp) REVERT: F 787 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7738 (t) REVERT: F 942 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8231 (t) REVERT: F 1071 MET cc_start: 0.3966 (ppp) cc_final: 0.3589 (ppp) REVERT: F 1201 GLU cc_start: 0.6540 (tm-30) cc_final: 0.5759 (tt0) REVERT: H 53 MET cc_start: 0.2643 (OUTLIER) cc_final: 0.2185 (ppp) REVERT: H 133 MET cc_start: 0.5357 (pmm) cc_final: 0.3210 (tmm) REVERT: H 137 ARG cc_start: 0.3741 (OUTLIER) cc_final: 0.2582 (ptp-170) REVERT: H 149 MET cc_start: -0.0169 (pmm) cc_final: -0.3963 (mmt) REVERT: G 70 HIS cc_start: 0.5638 (m-70) cc_final: 0.5044 (m-70) REVERT: G 84 LEU cc_start: 0.6979 (mm) cc_final: 0.6455 (pp) REVERT: G 91 MET cc_start: 0.7797 (mmp) cc_final: 0.7055 (mtp) REVERT: G 102 LYS cc_start: 0.7954 (tttm) cc_final: 0.6781 (mttt) REVERT: B 643 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7406 (mtt90) REVERT: B 694 SER cc_start: 0.6382 (p) cc_final: 0.6121 (t) REVERT: B 753 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8428 (tp) REVERT: B 810 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 985 ARG cc_start: 0.7533 (tpp-160) cc_final: 0.7035 (tmm-80) REVERT: B 988 MET cc_start: 0.5676 (ppp) cc_final: 0.5280 (ppp) REVERT: B 1094 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6403 (pp20) outliers start: 95 outliers final: 58 residues processed: 287 average time/residue: 0.1303 time to fit residues: 57.8710 Evaluate side-chains 258 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 188 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 333 TRP Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 773 ILE Chi-restraints excluded: chain F residue 787 VAL Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 880 LEU Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 929 CYS Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1019 LEU Chi-restraints excluded: chain F residue 1028 ILE Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1117 PHE Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 90 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 143 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 164 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN C 141 GLN E 198 HIS F1146 GLN G 36 GLN B 737 GLN ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1192 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.225225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.178330 restraints weight = 26117.802| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.34 r_work: 0.3818 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19527 Z= 0.229 Angle : 0.727 16.768 26538 Z= 0.364 Chirality : 0.048 0.344 2836 Planarity : 0.005 0.057 3452 Dihedral : 6.796 87.508 2836 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.75 % Allowed : 28.29 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2360 helix: -0.17 (0.25), residues: 467 sheet: -1.39 (0.22), residues: 524 loop : -1.46 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 675 TYR 0.020 0.002 TYR A 32 PHE 0.016 0.002 PHE E 161 TRP 0.018 0.002 TRP F 721 HIS 0.007 0.001 HIS F 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (19464) covalent geometry : angle 0.70526 / 0.36 (26402) SS BOND : bond 0.00423 / 0.26 ( 53) SS BOND : angle 1.39887 / 0.90 ( 106) hydrogen bonds : bond 0.04342 / 2.89 ( 586) hydrogen bonds : angle 6.09039 / 4.53 ( 1515) link_BETA1-4 : bond 0.00639 / 0.31 ( 3) link_BETA1-4 : angle 2.43565 / 1.25 ( 9) link_NAG-ASN : bond 0.01234 / 0.64 ( 7) link_NAG-ASN : angle 5.45490 / 2.48 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 205 time to evaluate : 0.742 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 202 LYS cc_start: 0.7570 (tptt) cc_final: 0.7196 (tppt) REVERT: A 257 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7915 (ttp80) REVERT: C 91 MET cc_start: 0.6919 (mtm) cc_final: 0.6613 (mmm) REVERT: C 121 LEU cc_start: 0.5433 (OUTLIER) cc_final: 0.4898 (mt) REVERT: C 122 MET cc_start: -0.0157 (tpp) cc_final: -0.0582 (tpp) REVERT: C 149 MET cc_start: 0.4379 (tpt) cc_final: 0.3703 (mtt) REVERT: D 149 MET cc_start: 0.4353 (ttp) cc_final: 0.1943 (mmm) REVERT: E 20 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.4966 (m-80) REVERT: E 130 GLU cc_start: 0.8037 (tt0) cc_final: 0.7789 (mt-10) REVERT: E 195 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7860 (tt) REVERT: E 227 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7787 (mt) REVERT: F 798 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5571 (mm) REVERT: F 802 LYS cc_start: 0.7814 (pttt) cc_final: 0.7169 (tttt) REVERT: F 978 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7362 (mm-40) REVERT: F 1117 PHE cc_start: 0.5050 (OUTLIER) cc_final: 0.4841 (m-80) REVERT: F 1201 GLU cc_start: 0.6557 (tm-30) cc_final: 0.5779 (tt0) REVERT: H 53 MET cc_start: 0.2748 (OUTLIER) cc_final: 0.2372 (ppp) REVERT: H 61 THR cc_start: 0.0063 (OUTLIER) cc_final: -0.0194 (t) REVERT: H 137 ARG cc_start: 0.3722 (OUTLIER) cc_final: 0.2635 (ptp-170) REVERT: H 149 MET cc_start: 0.0197 (pmm) cc_final: -0.3634 (mmt) REVERT: G 70 HIS cc_start: 0.5708 (m-70) cc_final: 0.5137 (m-70) REVERT: B 643 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7470 (mtt90) REVERT: B 753 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8527 (tp) REVERT: B 810 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8409 (mt) REVERT: B 1094 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6535 (pp20) outliers start: 98 outliers final: 71 residues processed: 285 average time/residue: 0.1261 time to fit residues: 56.7843 Evaluate side-chains 277 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 194 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 333 TRP Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 715 LEU Chi-restraints excluded: chain F residue 726 THR Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 773 ILE Chi-restraints excluded: chain F residue 798 ILE Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 880 LEU Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 967 VAL Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1019 LEU Chi-restraints excluded: chain F residue 1028 ILE Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1117 PHE Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 111 CYS Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 72 optimal weight: 0.5980 chunk 47 optimal weight: 40.0000 chunk 228 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 198 HIS G 36 GLN B 674 ASN ** B 993 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 = 0.4743 r_free = 0.4743 target = 0.231571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.180664 restraints weight = 26721.407| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.26 r_work: 0.3846 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19527 Z= 0.157 Angle : 0.681 16.967 26538 Z= 0.336 Chirality : 0.046 0.311 2836 Planarity : 0.004 0.054 3452 Dihedral : 6.705 85.440 2836 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.51 % Allowed : 28.97 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.17), residues: 2360 helix: 0.06 (0.25), residues: 454 sheet: -1.38 (0.22), residues: 516 loop : -1.42 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 866 TYR 0.017 0.001 TYR G 52 PHE 0.013 0.002 PHE F 938 TRP 0.015 0.001 TRP F 721 HIS 0.005 0.001 HIS F 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (19464) covalent geometry : angle 0.65725 / 0.33 (26402) SS BOND : bond 0.00547 / 0.35 ( 53) SS BOND : angle 1.42135 / 0.90 ( 106) hydrogen bonds : bond 0.03830 / 2.54 ( 586) hydrogen bonds : angle 5.94369 / 4.42 ( 1515) link_BETA1-4 : bond 0.00617 / 0.30 ( 3) link_BETA1-4 : angle 2.14422 / 1.10 ( 9) link_NAG-ASN : bond 0.01074 / 0.56 ( 7) link_NAG-ASN : angle 5.47482 / 2.50 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 0.718 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: A 202 LYS cc_start: 0.7561 (tptt) cc_final: 0.7229 (tppt) REVERT: C 91 MET cc_start: 0.7002 (mtm) cc_final: 0.6690 (mmm) REVERT: C 149 MET cc_start: 0.4433 (tpt) cc_final: 0.3742 (mtt) REVERT: D 53 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.3670 (mtt) REVERT: D 149 MET cc_start: 0.4323 (ttp) cc_final: 0.1907 (mmm) REVERT: E 20 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.5214 (m-80) REVERT: E 91 VAL cc_start: 0.8387 (t) cc_final: 0.8121 (m) REVERT: E 130 GLU cc_start: 0.8262 (tt0) cc_final: 0.7981 (mt-10) REVERT: E 195 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7670 (tt) REVERT: E 227 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7901 (mt) REVERT: F 753 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7763 (mt) REVERT: F 798 ILE cc_start: 0.6110 (mm) cc_final: 0.5831 (mm) REVERT: F 802 LYS cc_start: 0.7881 (pttt) cc_final: 0.7225 (tttt) REVERT: F 942 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8449 (t) REVERT: F 949 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6867 (mp) REVERT: F 978 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7478 (mm-40) REVERT: F 1071 MET cc_start: 0.4423 (ppp) cc_final: 0.3911 (ppp) REVERT: F 1201 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6240 (pp20) REVERT: H 53 MET cc_start: 0.2770 (OUTLIER) cc_final: 0.2470 (ppp) REVERT: H 61 THR cc_start: 0.0172 (OUTLIER) cc_final: -0.0067 (t) REVERT: H 137 ARG cc_start: 0.4252 (OUTLIER) cc_final: 0.3009 (ptp-170) REVERT: H 149 MET cc_start: 0.0047 (pmm) cc_final: -0.3727 (mmt) REVERT: G 70 HIS cc_start: 0.5568 (m-70) cc_final: 0.4988 (m-70) REVERT: G 84 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6405 (pp) REVERT: G 91 MET cc_start: 0.7875 (mmp) cc_final: 0.6985 (mtp) REVERT: G 95 ILE cc_start: 0.8464 (mp) cc_final: 0.8226 (tp) REVERT: B 643 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7720 (mtt90) REVERT: B 753 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8489 (tp) REVERT: B 810 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8436 (mt) REVERT: B 977 LYS cc_start: 0.7387 (mmmt) cc_final: 0.7184 (mmmt) outliers start: 93 outliers final: 65 residues processed: 275 average time/residue: 0.1277 time to fit residues: 54.5535 Evaluate side-chains 268 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 190 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 333 TRP Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 715 LEU Chi-restraints excluded: chain F residue 726 THR Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 773 ILE Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 880 LEU Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 949 ILE Chi-restraints excluded: chain F residue 967 VAL Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1019 LEU Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1028 ILE Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 111 CYS Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 168 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 204 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 172 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 143 ASN E 198 HIS B 674 ASN ** B 993 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 = 0.227093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.181647 restraints weight = 25600.671| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.04 r_work: 0.3908 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19527 Z= 0.132 Angle : 0.669 16.864 26538 Z= 0.330 Chirality : 0.046 0.307 2836 Planarity : 0.004 0.052 3452 Dihedral : 6.534 82.998 2836 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.12 % Allowed : 29.17 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2360 helix: 0.24 (0.25), residues: 453 sheet: -1.24 (0.22), residues: 530 loop : -1.42 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 675 TYR 0.021 0.001 TYR C 92 PHE 0.012 0.001 PHE F 938 TRP 0.020 0.001 TRP B1118 HIS 0.005 0.001 HIS F 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (19464) covalent geometry : angle 0.64760 / 0.32 (26402) SS BOND : bond 0.00377 / 0.23 ( 53) SS BOND : angle 1.33036 / 0.85 ( 106) hydrogen bonds : bond 0.03573 / 2.37 ( 586) hydrogen bonds : angle 5.90132 / 4.38 ( 1515) link_BETA1-4 : bond 0.00649 / 0.31 ( 3) link_BETA1-4 : angle 2.05171 / 1.05 ( 9) link_NAG-ASN : bond 0.01037 / 0.53 ( 7) link_NAG-ASN : angle 5.28218 / 2.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 202 time to evaluate : 0.453 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: A 202 LYS cc_start: 0.7486 (tptt) cc_final: 0.7252 (tppt) REVERT: A 257 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7872 (ttp80) REVERT: C 121 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.4897 (mt) REVERT: C 149 MET cc_start: 0.4405 (tpt) cc_final: 0.3730 (mtt) REVERT: D 53 MET cc_start: 0.5258 (OUTLIER) cc_final: 0.3697 (mtt) REVERT: D 149 MET cc_start: 0.4351 (ttp) cc_final: 0.1928 (mmm) REVERT: E 20 TYR cc_start: 0.6100 (OUTLIER) cc_final: 0.5165 (m-80) REVERT: E 91 VAL cc_start: 0.8430 (t) cc_final: 0.8190 (m) REVERT: E 130 GLU cc_start: 0.8196 (tt0) cc_final: 0.7930 (mt-10) REVERT: E 151 LYS cc_start: 0.7378 (mmmt) cc_final: 0.6803 (mtmt) REVERT: E 227 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7832 (mt) REVERT: F 753 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7568 (tp) REVERT: F 798 ILE cc_start: 0.6109 (mm) cc_final: 0.5792 (mm) REVERT: F 802 LYS cc_start: 0.7883 (pttt) cc_final: 0.7215 (tttt) REVERT: F 942 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8448 (t) REVERT: F 949 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6944 (mp) REVERT: F 978 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7466 (mm-40) REVERT: F 1071 MET cc_start: 0.4725 (ppp) cc_final: 0.4237 (ppp) REVERT: F 1163 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: F 1168 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6844 (mm-30) REVERT: F 1201 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6156 (pp20) REVERT: H 53 MET cc_start: 0.2677 (OUTLIER) cc_final: 0.2344 (ppp) REVERT: H 61 THR cc_start: 0.0041 (OUTLIER) cc_final: -0.0214 (t) REVERT: H 133 MET cc_start: 0.5674 (pmm) cc_final: 0.3670 (tmm) REVERT: H 137 ARG cc_start: 0.4383 (OUTLIER) cc_final: 0.3062 (mtt180) REVERT: H 149 MET cc_start: 0.0021 (pmm) cc_final: -0.3715 (mmt) REVERT: G 70 HIS cc_start: 0.5559 (m-70) cc_final: 0.4972 (m-70) REVERT: G 84 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6436 (pp) REVERT: G 91 MET cc_start: 0.7869 (mmp) cc_final: 0.7047 (mtp) REVERT: G 95 ILE cc_start: 0.8486 (mp) cc_final: 0.8275 (tp) REVERT: B 643 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7556 (mtm-85) REVERT: B 753 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8464 (tp) REVERT: B 802 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7787 (mmmt) outliers start: 85 outliers final: 62 residues processed: 269 average time/residue: 0.1202 time to fit residues: 50.6522 Evaluate side-chains 268 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 193 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 333 TRP Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 715 LEU Chi-restraints excluded: chain F residue 726 THR Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 773 ILE Chi-restraints excluded: chain F residue 808 THR Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 880 LEU Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 949 ILE Chi-restraints excluded: chain F residue 1019 LEU Chi-restraints excluded: chain F residue 1027 TYR Chi-restraints excluded: chain F residue 1028 ILE Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1117 PHE Chi-restraints excluded: chain F residue 1163 GLN Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 111 CYS Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 58 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 20.0000 chunk 8 optimal weight: 0.0970 chunk 221 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS ** F 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN G 36 GLN B 674 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.227291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.180666 restraints weight = 25667.562| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.11 r_work: 0.3902 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19527 Z= 0.135 Angle : 0.672 16.772 26538 Z= 0.332 Chirality : 0.046 0.323 2836 Planarity : 0.004 0.050 3452 Dihedral : 6.300 78.671 2836 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.73 % Allowed : 29.55 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2360 helix: 0.33 (0.25), residues: 451 sheet: -1.11 (0.22), residues: 526 loop : -1.43 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 866 TYR 0.016 0.001 TYR C 92 PHE 0.012 0.001 PHE F 938 TRP 0.025 0.001 TRP E 152 HIS 0.006 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (19464) covalent geometry : angle 0.65194 / 0.33 (26402) SS BOND : bond 0.00361 / 0.22 ( 53) SS BOND : angle 1.27247 / 0.79 ( 106) hydrogen bonds : bond 0.03543 / 2.36 ( 586) hydrogen bonds : angle 5.82971 / 4.32 ( 1515) link_BETA1-4 : bond 0.00622 / 0.30 ( 3) link_BETA1-4 : angle 2.17307 / 1.11 ( 9) link_NAG-ASN : bond 0.01064 / 0.55 ( 7) link_NAG-ASN : angle 5.17522 / 2.34 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 194 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 LEU cc_start: 0.5477 (OUTLIER) cc_final: 0.4965 (mt) REVERT: C 149 MET cc_start: 0.4338 (tpt) cc_final: 0.3717 (mtt) REVERT: D 53 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.3726 (mtt) REVERT: D 57 PHE cc_start: 0.1192 (OUTLIER) cc_final: 0.0448 (m-80) REVERT: D 149 MET cc_start: 0.4315 (ttp) cc_final: 0.1898 (mmm) REVERT: E 20 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5267 (m-80) REVERT: E 91 VAL cc_start: 0.8362 (t) cc_final: 0.8153 (m) REVERT: E 130 GLU cc_start: 0.8241 (tt0) cc_final: 0.7944 (mt-10) REVERT: E 227 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7815 (mt) REVERT: F 753 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7914 (tp) REVERT: F 798 ILE cc_start: 0.6127 (mm) cc_final: 0.5798 (mm) REVERT: F 802 LYS cc_start: 0.7887 (pttt) cc_final: 0.7261 (tttt) REVERT: F 942 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8391 (t) REVERT: F 949 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6955 (mp) REVERT: F 1071 MET cc_start: 0.4872 (ppp) cc_final: 0.4361 (ppp) REVERT: F 1163 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: F 1168 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7220 (mm-30) REVERT: F 1201 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6128 (pp20) REVERT: H 53 MET cc_start: 0.2555 (OUTLIER) cc_final: 0.2204 (ppp) REVERT: H 61 THR cc_start: 0.0064 (OUTLIER) cc_final: -0.0220 (t) REVERT: H 133 MET cc_start: 0.5544 (pmm) cc_final: 0.3646 (tmm) REVERT: H 137 ARG cc_start: 0.4287 (OUTLIER) cc_final: 0.3071 (mtt180) REVERT: H 149 MET cc_start: 0.0174 (pmm) cc_final: -0.3631 (mmt) REVERT: G 70 HIS cc_start: 0.5672 (m-70) cc_final: 0.4996 (m-70) REVERT: G 84 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6455 (pp) REVERT: G 91 MET cc_start: 0.7834 (mmp) cc_final: 0.7042 (mtp) REVERT: G 95 ILE cc_start: 0.8517 (mp) cc_final: 0.8312 (tp) REVERT: B 643 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7544 (mtm-85) REVERT: B 753 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8463 (tp) REVERT: B 810 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8361 (mt) outliers start: 77 outliers final: 58 residues processed: 255 average time/residue: 0.1296 time to fit residues: 51.1863 Evaluate side-chains 259 residues out of total 2068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 186 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 57 PHE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 333 TRP Chi-restraints excluded: chain F residue 635 LEU Chi-restraints excluded: chain F residue 715 LEU Chi-restraints excluded: chain F residue 726 THR Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 773 ILE Chi-restraints excluded: chain F residue 808 THR Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 880 LEU Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 949 ILE Chi-restraints excluded: chain F residue 1019 LEU Chi-restraints excluded: chain F residue 1028 ILE Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1117 PHE Chi-restraints excluded: chain F residue 1163 GLN Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1228 CYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 111 CYS Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1243 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 93 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 219 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN B 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.226062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.188473 restraints weight = 24685.596| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 1.88 r_work: 0.3868 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19527 Z= 0.135 Angle : 0.676 16.819 26538 Z= 0.330 Chirality : 0.046 0.335 2836 Planarity : 0.004 0.047 3452 Dihedral : 6.137 74.634 2836 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.88 % Allowed : 29.80 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 2360 helix: 0.37 (0.26), residues: 451 sheet: -1.26 (0.22), residues: 530 loop : -1.35 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 866 TYR 0.026 0.001 TYR H 92 PHE 0.012 0.001 PHE F 938 TRP 0.020 0.001 TRP B1118 HIS 0.004 0.001 HIS F 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (19464) covalent geometry : angle 0.65618 / 0.33 (26402) SS BOND : bond 0.00354 / 0.22 ( 53) SS BOND : angle 1.24478 / 0.77 ( 106) hydrogen bonds : bond 0.03495 / 2.33 ( 586) hydrogen bonds : angle 5.82601 / 4.32 ( 1515) link_BETA1-4 : bond 0.00809 / 0.39 ( 3) link_BETA1-4 : angle 2.30116 / 1.18 ( 9) link_NAG-ASN : bond 0.01067 / 0.54 ( 7) link_NAG-ASN : angle 5.13198 / 2.30 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4996.56 seconds wall clock time: 86 minutes 3.61 seconds (5163.61 seconds total)