Starting phenix.real_space_refine on Thu Mar 5 15:55:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1e_15073/03_2026/8a1e_15073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1e_15073/03_2026/8a1e_15073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a1e_15073/03_2026/8a1e_15073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1e_15073/03_2026/8a1e_15073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a1e_15073/03_2026/8a1e_15073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1e_15073/03_2026/8a1e_15073.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.099 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 6654 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 123 5.16 5 C 11655 2.51 5 N 3150 2.21 5 O 3474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18402 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2678 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 344, 2678 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain breaks: 2 bond proxies already assigned to first conformer: 2736 Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 827 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "B" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 918 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Restraints were copied for chains: F, K, G, L, H, M, I, N, J, O Time building chain proxies: 3.36, per 1000 atoms: 0.18 Number of scatterers: 18402 At special positions: 0 Unit cell: (160.06, 161.12, 96.46, 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 123 16.00 O 3474 8.00 N 3150 7.00 C 11655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 252 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 283 " distance=2.03 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 283 " distance=2.03 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 35 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 159 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 189 " - pdb=" SG CYS F 228 " distance=2.03 Simple disulfide: pdb=" SG CYS K 189 " - pdb=" SG CYS K 228 " distance=2.03 Simple disulfide: pdb=" SG CYS F 223 " - pdb=" SG CYS F 252 " distance=2.04 Simple disulfide: pdb=" SG CYS K 223 " - pdb=" SG CYS K 252 " distance=2.04 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 351 " distance=2.03 Simple disulfide: pdb=" SG CYS K 344 " - pdb=" SG CYS K 351 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 57 sheets defined 11.1% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.560A pdb=" N LEU A 22 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.818A pdb=" N ALA A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.611A pdb=" N ASN A 259 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 294 removed outlier: 3.781A pdb=" N GLU A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.715A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR D 91 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.185A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.560A pdb=" N LEU F 22 " --> pdb=" O ILE F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.818A pdb=" N ALA F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.611A pdb=" N ASN F 259 " --> pdb=" O GLN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 294 removed outlier: 3.781A pdb=" N GLU F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 373 through 380 Processing helix chain 'F' and resid 384 through 388 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.715A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR G 91 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.185A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'K' and resid 18 through 22 removed outlier: 3.560A pdb=" N LEU K 22 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 103 removed outlier: 3.818A pdb=" N ALA K 103 " --> pdb=" O ASN K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 259 removed outlier: 3.611A pdb=" N ASN K 259 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 294 removed outlier: 3.781A pdb=" N GLU K 275 " --> pdb=" O LEU K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 302 Processing helix chain 'K' and resid 303 through 305 No H-bonds generated for 'chain 'K' and resid 303 through 305' Processing helix chain 'K' and resid 373 through 380 Processing helix chain 'K' and resid 384 through 388 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.715A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR L 91 " --> pdb=" O THR L 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.186A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing sheet with id=1, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 322 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR A 5 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS A 328 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 11 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A 326 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 38 through 46 Processing sheet with id=4, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.875A pdb=" N ILE A 177 " --> pdb=" O CYS A 61 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 178 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS A 169 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=6, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=7, first strand: chain 'A' and resid 358 through 360 removed outlier: 6.648A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.950A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.773A pdb=" N TYR D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.633A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=14, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=15, first strand: chain 'C' and resid 19 through 22 removed outlier: 4.062A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 72 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 65 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 74 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.490A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 85 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.758A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 9 through 10 removed outlier: 6.585A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG B 40 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE B 45 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.504A pdb=" N VAL B 110 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'F' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR F 5 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS F 328 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU F 11 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP F 326 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU F 322 " --> pdb=" O ILE F 17 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'F' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR F 5 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS F 328 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU F 11 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP F 326 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'F' and resid 38 through 46 Processing sheet with id=23, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.875A pdb=" N ILE F 177 " --> pdb=" O CYS F 61 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP F 178 " --> pdb=" O CYS F 169 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS F 169 " --> pdb=" O TRP F 178 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'F' and resid 223 through 227 Processing sheet with id=25, first strand: chain 'F' and resid 295 through 296 Processing sheet with id=26, first strand: chain 'F' and resid 358 through 360 removed outlier: 6.648A pdb=" N ILE F 363 " --> pdb=" O PHE F 359 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=28, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.950A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.774A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.633A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=33, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=34, first strand: chain 'I' and resid 19 through 22 removed outlier: 4.062A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 72 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER I 65 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR I 74 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.490A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.758A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 18 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.585A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG J 40 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE J 45 " --> pdb=" O ARG J 40 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'J' and resid 9 through 10 removed outlier: 3.503A pdb=" N VAL J 110 " --> pdb=" O ILE J 98 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'K' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR K 5 " --> pdb=" O VAL K 332 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS K 328 " --> pdb=" O ASP K 9 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU K 11 " --> pdb=" O ASP K 326 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP K 326 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU K 322 " --> pdb=" O ILE K 17 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'K' and resid 5 through 11 removed outlier: 3.716A pdb=" N TYR K 5 " --> pdb=" O VAL K 332 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS K 328 " --> pdb=" O ASP K 9 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU K 11 " --> pdb=" O ASP K 326 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP K 326 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'K' and resid 38 through 46 Processing sheet with id=42, first strand: chain 'K' and resid 59 through 61 removed outlier: 3.874A pdb=" N ILE K 177 " --> pdb=" O CYS K 61 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP K 178 " --> pdb=" O CYS K 169 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS K 169 " --> pdb=" O TRP K 178 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'K' and resid 223 through 227 Processing sheet with id=44, first strand: chain 'K' and resid 295 through 296 Processing sheet with id=45, first strand: chain 'K' and resid 358 through 360 removed outlier: 6.648A pdb=" N ILE K 363 " --> pdb=" O PHE K 359 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=47, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.951A pdb=" N MET L 34 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.774A pdb=" N TYR L 108 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.633A pdb=" N SER M 22 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=52, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=53, first strand: chain 'N' and resid 19 through 22 removed outlier: 4.062A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR N 72 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER N 65 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR N 74 " --> pdb=" O THR N 63 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR N 63 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.489A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'O' and resid 3 through 5 removed outlier: 3.758A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET O 18 " --> pdb=" O LEU O 83 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'O' and resid 9 through 10 removed outlier: 6.586A pdb=" N LYS O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP O 47 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG O 40 " --> pdb=" O PHE O 45 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE O 45 " --> pdb=" O ARG O 40 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'O' and resid 9 through 10 removed outlier: 3.504A pdb=" N VAL O 110 " --> pdb=" O ILE O 98 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1554 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: 3.51 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5907 1.34 - 1.46: 4719 1.46 - 1.58: 8055 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 18861 Sorted by residual: bond pdb=" CG1 ILE K 339 " pdb=" CD1 ILE K 339 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.76e-01 bond pdb=" CG1 ILE F 339 " pdb=" CD1 ILE F 339 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.69e-01 bond pdb=" CG1 ILE A 339 " pdb=" CD1 ILE A 339 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.57e-01 bond pdb=" CA THR F 90 " pdb=" CB THR F 90 " ideal model delta sigma weight residual 1.526 1.538 -0.012 1.51e-02 4.39e+03 6.42e-01 bond pdb=" CB PRO E 95 " pdb=" CG PRO E 95 " ideal model delta sigma weight residual 1.506 1.475 0.031 3.90e-02 6.57e+02 6.34e-01 ... (remaining 18856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 24692 1.32 - 2.63: 693 2.63 - 3.95: 157 3.95 - 5.27: 15 5.27 - 6.59: 9 Bond angle restraints: 25566 Sorted by residual: angle pdb=" N VAL G 64 " pdb=" CA VAL G 64 " pdb=" C VAL G 64 " ideal model delta sigma weight residual 112.96 109.95 3.01 1.00e+00 1.00e+00 9.08e+00 angle pdb=" N VAL D 64 " pdb=" CA VAL D 64 " pdb=" C VAL D 64 " ideal model delta sigma weight residual 112.96 109.96 3.00 1.00e+00 1.00e+00 8.98e+00 angle pdb=" N VAL L 64 " pdb=" CA VAL L 64 " pdb=" C VAL L 64 " ideal model delta sigma weight residual 112.96 109.99 2.97 1.00e+00 1.00e+00 8.81e+00 angle pdb=" C SER C 50 " pdb=" N ALA C 51 " pdb=" CA ALA C 51 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.01e+00 angle pdb=" C SER I 50 " pdb=" N ALA I 51 " pdb=" CA ALA I 51 " ideal model delta sigma weight residual 121.54 126.92 -5.38 1.91e+00 2.74e-01 7.92e+00 ... (remaining 25561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 10167 17.27 - 34.54: 861 34.54 - 51.81: 177 51.81 - 69.07: 30 69.07 - 86.34: 9 Dihedral angle restraints: 11244 sinusoidal: 4458 harmonic: 6786 Sorted by residual: dihedral pdb=" CB CYS F 35 " pdb=" SG CYS F 35 " pdb=" SG CYS F 207 " pdb=" CB CYS F 207 " ideal model delta sinusoidal sigma weight residual 93.00 179.34 -86.34 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 35 " pdb=" SG CYS A 35 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual 93.00 179.34 -86.34 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS K 35 " pdb=" SG CYS K 35 " pdb=" SG CYS K 207 " pdb=" CB CYS K 207 " ideal model delta sinusoidal sigma weight residual 93.00 179.34 -86.34 1 1.00e+01 1.00e-02 8.99e+01 ... (remaining 11241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1598 0.028 - 0.056: 752 0.056 - 0.084: 216 0.084 - 0.111: 182 0.111 - 0.139: 36 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CA ILE K 373 " pdb=" N ILE K 373 " pdb=" C ILE K 373 " pdb=" CB ILE K 373 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE F 373 " pdb=" N ILE F 373 " pdb=" C ILE F 373 " pdb=" CB ILE F 373 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 373 " pdb=" N ILE A 373 " pdb=" C ILE A 373 " pdb=" CB ILE A 373 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 2781 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 90 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO F 91 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO F 91 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 91 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 90 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO A 91 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 90 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO K 91 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO K 91 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 91 " 0.024 5.00e-02 4.00e+02 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.30: 51 2.30 - 2.95: 8256 2.95 - 3.60: 25729 3.60 - 4.25: 44068 4.25 - 4.90: 75612 Nonbonded interactions: 153716 Sorted by model distance: nonbonded pdb=" SD MET A 291 " pdb=" CE MET F 385 " model vdw 1.655 3.820 nonbonded pdb=" SD MET F 291 " pdb=" CE MET K 385 " model vdw 1.655 3.820 nonbonded pdb=" CE MET A 385 " pdb=" SD MET K 291 " model vdw 1.655 3.820 nonbonded pdb=" O SER A 379 " pdb=" NH1 ARG K 264 " model vdw 1.826 3.120 nonbonded pdb=" NH1 ARG A 264 " pdb=" O SER F 379 " model vdw 1.827 3.120 ... (remaining 153711 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'O' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.900 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 0.033 18894 Z= 0.140 Angle : 0.541 6.587 25632 Z= 0.288 Chirality : 0.042 0.139 2784 Planarity : 0.004 0.043 3264 Dihedral : 12.784 82.462 6807 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2325 helix: 0.13 (0.39), residues: 159 sheet: -0.26 (0.19), residues: 720 loop : -0.38 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 54 TYR 0.013 0.001 TYR D 105 PHE 0.009 0.001 PHE J 45 TRP 0.010 0.001 TRP D 109 HIS 0.003 0.001 HIS N 91 Details of bonding type rmsd covalent geometry : bond 0.00325 (18861) covalent geometry : angle 0.53946 (25566) SS BOND : bond 0.00203 ( 33) SS BOND : angle 1.01815 ( 66) hydrogen bonds : bond 0.22707 ( 579) hydrogen bonds : angle 9.36187 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.8822 (tt) cc_final: 0.8620 (tm) REVERT: B 34 MET cc_start: 0.7402 (tpp) cc_final: 0.7155 (tpp) REVERT: F 44 MET cc_start: 0.8828 (mtm) cc_final: 0.8558 (mtm) REVERT: F 376 MET cc_start: 0.9136 (ttp) cc_final: 0.8828 (ttm) REVERT: I 87 TYR cc_start: 0.7932 (m-80) cc_final: 0.7710 (m-80) REVERT: J 34 MET cc_start: 0.7333 (tpp) cc_final: 0.7034 (tpp) REVERT: K 278 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8171 (tttp) REVERT: K 376 MET cc_start: 0.9049 (ttp) cc_final: 0.8634 (ttm) REVERT: N 4 MET cc_start: 0.7571 (mmt) cc_final: 0.7238 (mmt) REVERT: O 34 MET cc_start: 0.7391 (tpp) cc_final: 0.7162 (tpp) REVERT: O 94 TYR cc_start: 0.7746 (m-10) cc_final: 0.7277 (m-10) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.4816 time to fit residues: 158.0601 Evaluate side-chains 247 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS A 261 HIS E 93 ASN C 38 GLN F 150 HIS F 261 HIS F 356 ASN G 3 GLN K 261 HIS K 356 ASN M 93 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.186718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120108 restraints weight = 31803.784| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.78 r_work: 0.3112 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18894 Z= 0.194 Angle : 0.630 9.257 25632 Z= 0.323 Chirality : 0.045 0.179 2784 Planarity : 0.005 0.050 3264 Dihedral : 4.955 25.168 2565 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.89 % Allowed : 9.62 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2325 helix: -0.00 (0.40), residues: 159 sheet: -0.02 (0.20), residues: 666 loop : -0.55 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 199 TYR 0.012 0.002 TYR D 105 PHE 0.012 0.002 PHE M 83 TRP 0.010 0.001 TRP D 109 HIS 0.011 0.001 HIS F 150 Details of bonding type rmsd covalent geometry : bond 0.00453 (18861) covalent geometry : angle 0.62844 (25566) SS BOND : bond 0.00279 ( 33) SS BOND : angle 0.98467 ( 66) hydrogen bonds : bond 0.04703 ( 579) hydrogen bonds : angle 6.36363 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 0.694 Fit side-chains REVERT: A 231 LEU cc_start: 0.8836 (tt) cc_final: 0.8424 (tm) REVERT: F 44 MET cc_start: 0.9357 (mtm) cc_final: 0.8741 (mtm) REVERT: I 4 MET cc_start: 0.7427 (mmt) cc_final: 0.7150 (mmt) REVERT: I 87 TYR cc_start: 0.7979 (m-80) cc_final: 0.7749 (m-80) REVERT: J 34 MET cc_start: 0.7378 (tpp) cc_final: 0.7036 (tpp) REVERT: K 102 MET cc_start: 0.2870 (ppp) cc_final: 0.2064 (pmt) REVERT: K 376 MET cc_start: 0.9241 (ttp) cc_final: 0.8789 (ttm) REVERT: N 4 MET cc_start: 0.7521 (mmt) cc_final: 0.7217 (mmp) REVERT: O 18 MET cc_start: 0.7475 (ppp) cc_final: 0.6982 (pmm) REVERT: O 34 MET cc_start: 0.7423 (tpp) cc_final: 0.7124 (tpp) REVERT: O 94 TYR cc_start: 0.7537 (m-10) cc_final: 0.7052 (m-10) outliers start: 18 outliers final: 12 residues processed: 253 average time/residue: 0.4900 time to fit residues: 142.0945 Evaluate side-chains 248 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 150 HIS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 95 optimal weight: 0.0070 chunk 91 optimal weight: 0.0170 chunk 110 optimal weight: 0.0470 chunk 177 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 172 optimal weight: 0.1980 chunk 129 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 overall best weight: 0.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 HIS F 356 ASN G 3 GLN K 356 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.191653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125427 restraints weight = 26803.738| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.31 r_work: 0.3241 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18894 Z= 0.099 Angle : 0.543 8.342 25632 Z= 0.275 Chirality : 0.042 0.210 2784 Planarity : 0.004 0.051 3264 Dihedral : 4.575 21.515 2565 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.23 % Allowed : 11.93 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2325 helix: 0.37 (0.40), residues: 159 sheet: 0.05 (0.20), residues: 660 loop : -0.49 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 199 TYR 0.010 0.001 TYR C 53 PHE 0.009 0.001 PHE I 98 TRP 0.010 0.001 TRP J 36 HIS 0.024 0.001 HIS F 150 Details of bonding type rmsd covalent geometry : bond 0.00216 (18861) covalent geometry : angle 0.54241 (25566) SS BOND : bond 0.00185 ( 33) SS BOND : angle 0.65236 ( 66) hydrogen bonds : bond 0.03353 ( 579) hydrogen bonds : angle 5.53123 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.674 Fit side-chains REVERT: A 376 MET cc_start: 0.9102 (ttp) cc_final: 0.8663 (ttp) REVERT: D 5 VAL cc_start: 0.8727 (t) cc_final: 0.8458 (m) REVERT: D 59 ASP cc_start: 0.8700 (m-30) cc_final: 0.8445 (m-30) REVERT: C 11 MET cc_start: 0.6211 (mmp) cc_final: 0.5809 (mmt) REVERT: F 44 MET cc_start: 0.9224 (mtm) cc_final: 0.8741 (mtm) REVERT: H 6 GLN cc_start: 0.8635 (tt0) cc_final: 0.8429 (tt0) REVERT: I 4 MET cc_start: 0.7389 (mmt) cc_final: 0.7112 (mmt) REVERT: I 87 TYR cc_start: 0.7833 (m-80) cc_final: 0.7596 (m-80) REVERT: J 18 MET cc_start: 0.6819 (pp-130) cc_final: 0.6561 (pp-130) REVERT: J 34 MET cc_start: 0.7151 (tpp) cc_final: 0.6788 (tpp) REVERT: K 324 GLU cc_start: 0.8719 (pt0) cc_final: 0.8484 (pt0) REVERT: K 376 MET cc_start: 0.9134 (ttp) cc_final: 0.8893 (ttp) REVERT: N 4 MET cc_start: 0.7428 (mmt) cc_final: 0.7130 (mmt) REVERT: N 11 MET cc_start: 0.5902 (mmp) cc_final: 0.5542 (mmt) REVERT: O 94 TYR cc_start: 0.7443 (m-10) cc_final: 0.7001 (m-10) REVERT: O 100 LEU cc_start: 0.8324 (mm) cc_final: 0.7869 (mt) outliers start: 25 outliers final: 8 residues processed: 257 average time/residue: 0.5015 time to fit residues: 147.3662 Evaluate side-chains 241 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 233 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 129 optimal weight: 0.0980 chunk 191 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN I 38 GLN K 356 ASN N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.188081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124842 restraints weight = 26752.757| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.53 r_work: 0.3163 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18894 Z= 0.155 Angle : 0.573 8.462 25632 Z= 0.288 Chirality : 0.043 0.155 2784 Planarity : 0.004 0.051 3264 Dihedral : 4.662 23.575 2565 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.82 % Allowed : 13.36 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2325 helix: 0.31 (0.41), residues: 159 sheet: -0.05 (0.19), residues: 660 loop : -0.51 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 199 TYR 0.011 0.001 TYR D 105 PHE 0.011 0.001 PHE M 83 TRP 0.013 0.001 TRP C 35 HIS 0.008 0.001 HIS F 397 Details of bonding type rmsd covalent geometry : bond 0.00365 (18861) covalent geometry : angle 0.57226 (25566) SS BOND : bond 0.00277 ( 33) SS BOND : angle 0.83866 ( 66) hydrogen bonds : bond 0.03461 ( 579) hydrogen bonds : angle 5.44493 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.473 Fit side-chains REVERT: D 5 VAL cc_start: 0.8739 (t) cc_final: 0.8409 (m) REVERT: F 44 MET cc_start: 0.9327 (mtm) cc_final: 0.8764 (mtm) REVERT: F 376 MET cc_start: 0.9142 (ttp) cc_final: 0.8869 (ttm) REVERT: G 77 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8104 (m-40) REVERT: H 6 GLN cc_start: 0.8758 (tt0) cc_final: 0.8500 (tt0) REVERT: I 4 MET cc_start: 0.7358 (mmt) cc_final: 0.7128 (mmt) REVERT: I 87 TYR cc_start: 0.7872 (m-80) cc_final: 0.7632 (m-80) REVERT: J 34 MET cc_start: 0.7281 (tpp) cc_final: 0.6863 (tpp) REVERT: K 376 MET cc_start: 0.9145 (ttp) cc_final: 0.8823 (ttp) REVERT: L 89 GLU cc_start: 0.8232 (pm20) cc_final: 0.8006 (pm20) REVERT: N 4 MET cc_start: 0.7386 (mmt) cc_final: 0.7051 (mmt) REVERT: O 18 MET cc_start: 0.7161 (pp-130) cc_final: 0.6540 (pmm) REVERT: O 94 TYR cc_start: 0.7483 (m-10) cc_final: 0.7087 (m-10) outliers start: 37 outliers final: 19 residues processed: 258 average time/residue: 0.4509 time to fit residues: 134.4842 Evaluate side-chains 254 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 HIS F 356 ASN G 3 GLN K 356 ASN M 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.185711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120813 restraints weight = 32992.897| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.74 r_work: 0.3096 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18894 Z= 0.202 Angle : 0.613 8.830 25632 Z= 0.309 Chirality : 0.045 0.170 2784 Planarity : 0.005 0.049 3264 Dihedral : 4.916 26.175 2565 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.56 % Allowed : 13.41 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2325 helix: 0.12 (0.41), residues: 159 sheet: -0.11 (0.18), residues: 714 loop : -0.59 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 305 TYR 0.012 0.002 TYR M 32 PHE 0.012 0.002 PHE J 45 TRP 0.012 0.002 TRP D 109 HIS 0.010 0.001 HIS F 150 Details of bonding type rmsd covalent geometry : bond 0.00479 (18861) covalent geometry : angle 0.61181 (25566) SS BOND : bond 0.00324 ( 33) SS BOND : angle 0.89604 ( 66) hydrogen bonds : bond 0.03623 ( 579) hydrogen bonds : angle 5.56772 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 291 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6690 (mmm) REVERT: C 11 MET cc_start: 0.6246 (mmp) cc_final: 0.5870 (mmt) REVERT: F 44 MET cc_start: 0.9367 (mtm) cc_final: 0.8755 (mtm) REVERT: F 263 PHE cc_start: 0.5479 (OUTLIER) cc_final: 0.5135 (m-10) REVERT: F 385 MET cc_start: 0.8420 (tpp) cc_final: 0.7786 (ttp) REVERT: G 77 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8114 (m-40) REVERT: H 6 GLN cc_start: 0.8826 (tt0) cc_final: 0.8523 (tt0) REVERT: H 107 LYS cc_start: 0.6834 (pttm) cc_final: 0.6603 (pmtt) REVERT: I 4 MET cc_start: 0.7228 (mmt) cc_final: 0.7021 (mmt) REVERT: I 87 TYR cc_start: 0.7953 (m-80) cc_final: 0.7716 (m-80) REVERT: J 18 MET cc_start: 0.6844 (pp-130) cc_final: 0.6248 (pmm) REVERT: J 34 MET cc_start: 0.7418 (tpp) cc_final: 0.7055 (tpp) REVERT: K 263 PHE cc_start: 0.5422 (OUTLIER) cc_final: 0.5096 (m-10) REVERT: K 376 MET cc_start: 0.9154 (ttp) cc_final: 0.8810 (ttp) REVERT: L 87 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7186 (ptp-170) REVERT: N 4 MET cc_start: 0.7378 (mmt) cc_final: 0.7048 (mmt) REVERT: N 11 MET cc_start: 0.5947 (mmp) cc_final: 0.5466 (mmt) REVERT: O 18 MET cc_start: 0.7095 (pp-130) cc_final: 0.6218 (pmm) REVERT: O 94 TYR cc_start: 0.7531 (m-10) cc_final: 0.7139 (m-10) outliers start: 52 outliers final: 31 residues processed: 268 average time/residue: 0.4805 time to fit residues: 148.4209 Evaluate side-chains 270 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 196 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS F 356 ASN G 3 GLN I 91 HIS ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN N 91 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.186021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116356 restraints weight = 35987.987| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.61 r_work: 0.3120 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18894 Z= 0.183 Angle : 0.594 8.897 25632 Z= 0.300 Chirality : 0.044 0.154 2784 Planarity : 0.005 0.049 3264 Dihedral : 4.921 25.700 2565 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.27 % Allowed : 14.45 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2325 helix: -0.42 (0.39), residues: 177 sheet: -0.13 (0.18), residues: 711 loop : -0.60 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 18 TYR 0.012 0.001 TYR M 32 PHE 0.013 0.002 PHE M 83 TRP 0.018 0.001 TRP N 35 HIS 0.008 0.001 HIS F 397 Details of bonding type rmsd covalent geometry : bond 0.00435 (18861) covalent geometry : angle 0.59324 (25566) SS BOND : bond 0.00288 ( 33) SS BOND : angle 0.84218 ( 66) hydrogen bonds : bond 0.03420 ( 579) hydrogen bonds : angle 5.47399 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6528 (mmm) REVERT: C 11 MET cc_start: 0.6222 (mmp) cc_final: 0.5822 (mmt) REVERT: F 44 MET cc_start: 0.9333 (mtm) cc_final: 0.8730 (mtm) REVERT: F 236 MET cc_start: 0.8781 (ttp) cc_final: 0.8549 (ttp) REVERT: F 263 PHE cc_start: 0.5399 (OUTLIER) cc_final: 0.5080 (m-10) REVERT: F 385 MET cc_start: 0.8478 (tpp) cc_final: 0.7762 (ttp) REVERT: G 77 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8042 (m-40) REVERT: I 87 TYR cc_start: 0.7949 (m-80) cc_final: 0.7688 (m-80) REVERT: J 18 MET cc_start: 0.6798 (pp-130) cc_final: 0.6411 (pmm) REVERT: J 34 MET cc_start: 0.7368 (tpp) cc_final: 0.6999 (tpp) REVERT: K 236 MET cc_start: 0.8800 (mtm) cc_final: 0.8416 (ttp) REVERT: K 263 PHE cc_start: 0.5397 (OUTLIER) cc_final: 0.5010 (m-10) REVERT: K 376 MET cc_start: 0.9181 (ttp) cc_final: 0.8812 (ttp) REVERT: L 87 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7001 (ptp-170) REVERT: N 4 MET cc_start: 0.7350 (mmt) cc_final: 0.7109 (mmt) REVERT: N 11 MET cc_start: 0.6055 (mmp) cc_final: 0.5710 (mmt) REVERT: O 18 MET cc_start: 0.7053 (pp-130) cc_final: 0.6240 (pmm) REVERT: O 94 TYR cc_start: 0.7472 (m-10) cc_final: 0.7123 (m-10) outliers start: 46 outliers final: 34 residues processed: 263 average time/residue: 0.4833 time to fit residues: 146.3211 Evaluate side-chains 272 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 185 optimal weight: 0.5980 chunk 212 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 HIS ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.186112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122570 restraints weight = 26707.942| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.58 r_work: 0.3141 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18894 Z= 0.176 Angle : 0.594 8.681 25632 Z= 0.299 Chirality : 0.044 0.153 2784 Planarity : 0.005 0.048 3264 Dihedral : 4.908 25.426 2565 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.42 % Allowed : 14.50 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.17), residues: 2325 helix: -0.39 (0.40), residues: 177 sheet: -0.29 (0.18), residues: 744 loop : -0.57 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.010 0.001 TYR D 80 PHE 0.013 0.002 PHE M 83 TRP 0.011 0.001 TRP D 109 HIS 0.012 0.001 HIS F 150 Details of bonding type rmsd covalent geometry : bond 0.00417 (18861) covalent geometry : angle 0.59305 (25566) SS BOND : bond 0.00277 ( 33) SS BOND : angle 0.83268 ( 66) hydrogen bonds : bond 0.03359 ( 579) hydrogen bonds : angle 5.42512 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 MET cc_start: 0.6216 (mmp) cc_final: 0.5835 (mmt) REVERT: F 44 MET cc_start: 0.9322 (mtm) cc_final: 0.8735 (mtm) REVERT: F 263 PHE cc_start: 0.5458 (OUTLIER) cc_final: 0.5126 (m-10) REVERT: F 385 MET cc_start: 0.8475 (tpp) cc_final: 0.7804 (ttp) REVERT: G 77 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: I 87 TYR cc_start: 0.7944 (m-80) cc_final: 0.7643 (m-80) REVERT: K 236 MET cc_start: 0.8799 (mtm) cc_final: 0.8386 (ttp) REVERT: K 263 PHE cc_start: 0.5309 (OUTLIER) cc_final: 0.4917 (m-10) REVERT: K 376 MET cc_start: 0.9188 (ttp) cc_final: 0.8816 (ttp) REVERT: L 87 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7125 (ptp-170) REVERT: M 107 LYS cc_start: 0.7036 (pttm) cc_final: 0.6762 (pmtt) REVERT: N 4 MET cc_start: 0.7360 (mmt) cc_final: 0.7122 (mmt) REVERT: N 11 MET cc_start: 0.6027 (mmp) cc_final: 0.5599 (mmt) REVERT: O 94 TYR cc_start: 0.7474 (m-10) cc_final: 0.7121 (m-10) outliers start: 49 outliers final: 37 residues processed: 263 average time/residue: 0.4750 time to fit residues: 144.3011 Evaluate side-chains 273 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain K residue 355 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 39 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 13 optimal weight: 0.0000 chunk 43 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 155 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.189632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.124540 restraints weight = 32238.199| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.77 r_work: 0.3159 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18894 Z= 0.104 Angle : 0.536 8.394 25632 Z= 0.271 Chirality : 0.042 0.152 2784 Planarity : 0.004 0.048 3264 Dihedral : 4.617 21.920 2565 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.73 % Allowed : 15.29 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2325 helix: -0.14 (0.40), residues: 177 sheet: -0.09 (0.20), residues: 642 loop : -0.55 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.011 0.001 TYR D 105 PHE 0.010 0.001 PHE M 83 TRP 0.011 0.001 TRP N 35 HIS 0.009 0.001 HIS F 397 Details of bonding type rmsd covalent geometry : bond 0.00238 (18861) covalent geometry : angle 0.53580 (25566) SS BOND : bond 0.00184 ( 33) SS BOND : angle 0.66256 ( 66) hydrogen bonds : bond 0.02873 ( 579) hydrogen bonds : angle 5.09881 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 274 GLU cc_start: 0.7710 (tp30) cc_final: 0.7510 (mm-30) REVERT: D 5 VAL cc_start: 0.8752 (t) cc_final: 0.8440 (m) REVERT: C 4 MET cc_start: 0.7239 (mmt) cc_final: 0.6752 (tpp) REVERT: C 11 MET cc_start: 0.6206 (mmp) cc_final: 0.5826 (mmt) REVERT: B 18 MET cc_start: 0.6284 (pp-130) cc_final: 0.5982 (pmm) REVERT: F 44 MET cc_start: 0.9305 (mtm) cc_final: 0.8793 (mtm) REVERT: F 385 MET cc_start: 0.8267 (tpp) cc_final: 0.7747 (ttp) REVERT: G 77 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: H 107 LYS cc_start: 0.6846 (pttm) cc_final: 0.6591 (pmtt) REVERT: I 87 TYR cc_start: 0.7957 (m-80) cc_final: 0.7693 (m-80) REVERT: K 236 MET cc_start: 0.8708 (mtm) cc_final: 0.8344 (ttp) REVERT: K 263 PHE cc_start: 0.5273 (OUTLIER) cc_final: 0.4871 (m-10) REVERT: K 291 MET cc_start: 0.7360 (mmt) cc_final: 0.7036 (mmm) REVERT: K 376 MET cc_start: 0.9195 (ttp) cc_final: 0.8948 (ttp) REVERT: K 396 MET cc_start: 0.6971 (ttt) cc_final: 0.6578 (ttp) REVERT: M 33 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8962 (tp) REVERT: N 4 MET cc_start: 0.7260 (mmt) cc_final: 0.7057 (mmt) REVERT: N 11 MET cc_start: 0.5892 (mmp) cc_final: 0.5495 (mmt) REVERT: N 95 PRO cc_start: 0.8103 (Cg_endo) cc_final: 0.7843 (Cg_exo) REVERT: O 18 MET cc_start: 0.7257 (pp-130) cc_final: 0.6264 (pmm) REVERT: O 94 TYR cc_start: 0.7624 (m-10) cc_final: 0.7227 (m-10) outliers start: 35 outliers final: 16 residues processed: 261 average time/residue: 0.4516 time to fit residues: 136.2556 Evaluate side-chains 254 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 101 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN I 8 HIS ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.186382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119621 restraints weight = 35819.887| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.95 r_work: 0.3106 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18894 Z= 0.187 Angle : 0.602 10.188 25632 Z= 0.302 Chirality : 0.044 0.153 2784 Planarity : 0.005 0.047 3264 Dihedral : 4.807 24.964 2565 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.53 % Allowed : 15.68 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2325 helix: -0.25 (0.40), residues: 177 sheet: -0.28 (0.18), residues: 738 loop : -0.56 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 18 TYR 0.014 0.002 TYR G 80 PHE 0.011 0.002 PHE M 83 TRP 0.022 0.002 TRP C 35 HIS 0.006 0.001 HIS F 397 Details of bonding type rmsd covalent geometry : bond 0.00448 (18861) covalent geometry : angle 0.60152 (25566) SS BOND : bond 0.00287 ( 33) SS BOND : angle 0.85833 ( 66) hydrogen bonds : bond 0.03348 ( 579) hydrogen bonds : angle 5.29924 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.7754 (tpp) cc_final: 0.7435 (tpt) REVERT: D 5 VAL cc_start: 0.8744 (t) cc_final: 0.8399 (m) REVERT: C 11 MET cc_start: 0.6302 (mmp) cc_final: 0.5917 (mmt) REVERT: B 18 MET cc_start: 0.6298 (pp-130) cc_final: 0.6042 (pmm) REVERT: F 44 MET cc_start: 0.9355 (mtm) cc_final: 0.8801 (mtm) REVERT: F 376 MET cc_start: 0.9208 (ttp) cc_final: 0.8795 (ttm) REVERT: G 77 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8134 (m-40) REVERT: I 87 TYR cc_start: 0.8001 (m-80) cc_final: 0.7690 (m-80) REVERT: K 236 MET cc_start: 0.8847 (mtm) cc_final: 0.8447 (ttp) REVERT: K 263 PHE cc_start: 0.5304 (OUTLIER) cc_final: 0.4866 (m-10) REVERT: K 376 MET cc_start: 0.9167 (ttp) cc_final: 0.8818 (ttp) REVERT: L 87 ARG cc_start: 0.7632 (ptp-170) cc_final: 0.7307 (ptp-170) REVERT: N 4 MET cc_start: 0.7349 (mmt) cc_final: 0.7103 (mmt) REVERT: N 11 MET cc_start: 0.5991 (mmp) cc_final: 0.5570 (mmt) REVERT: O 18 MET cc_start: 0.7270 (pp-130) cc_final: 0.6320 (pmm) REVERT: O 94 TYR cc_start: 0.7632 (m-10) cc_final: 0.7197 (m-10) outliers start: 31 outliers final: 22 residues processed: 258 average time/residue: 0.4535 time to fit residues: 135.7287 Evaluate side-chains 252 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 225 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN H 37 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.186930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124644 restraints weight = 25307.698| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.33 r_work: 0.3196 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18894 Z= 0.160 Angle : 0.600 10.434 25632 Z= 0.299 Chirality : 0.044 0.152 2784 Planarity : 0.005 0.050 3264 Dihedral : 4.822 24.489 2565 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.43 % Allowed : 15.83 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.17), residues: 2325 helix: -0.24 (0.40), residues: 177 sheet: -0.36 (0.19), residues: 693 loop : -0.56 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 18 TYR 0.014 0.001 TYR O 27 PHE 0.011 0.001 PHE M 83 TRP 0.020 0.001 TRP C 35 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00380 (18861) covalent geometry : angle 0.59755 (25566) SS BOND : bond 0.00302 ( 33) SS BOND : angle 1.15961 ( 66) hydrogen bonds : bond 0.03194 ( 579) hydrogen bonds : angle 5.27213 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.7629 (tp30) cc_final: 0.7374 (mm-30) REVERT: D 5 VAL cc_start: 0.8728 (t) cc_final: 0.8405 (m) REVERT: C 11 MET cc_start: 0.6249 (mmp) cc_final: 0.5860 (mmt) REVERT: F 44 MET cc_start: 0.9306 (mtm) cc_final: 0.8737 (mtm) REVERT: F 263 PHE cc_start: 0.5304 (OUTLIER) cc_final: 0.5031 (m-10) REVERT: F 376 MET cc_start: 0.9166 (ttp) cc_final: 0.8740 (ttm) REVERT: F 385 MET cc_start: 0.8405 (tpp) cc_final: 0.7873 (ttp) REVERT: F 396 MET cc_start: 0.6547 (tmt) cc_final: 0.6315 (tmm) REVERT: G 77 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8067 (m-40) REVERT: I 87 TYR cc_start: 0.7957 (m-80) cc_final: 0.7632 (m-80) REVERT: K 236 MET cc_start: 0.8791 (mtm) cc_final: 0.8402 (ttp) REVERT: K 263 PHE cc_start: 0.5243 (OUTLIER) cc_final: 0.4832 (m-10) REVERT: K 376 MET cc_start: 0.9183 (ttp) cc_final: 0.8822 (ttp) REVERT: N 4 MET cc_start: 0.7330 (mmt) cc_final: 0.7098 (mmt) REVERT: N 11 MET cc_start: 0.5885 (mmp) cc_final: 0.5484 (mmt) REVERT: N 95 PRO cc_start: 0.8136 (Cg_endo) cc_final: 0.7876 (Cg_exo) REVERT: O 18 MET cc_start: 0.7297 (pp-130) cc_final: 0.6425 (pmm) REVERT: O 94 TYR cc_start: 0.7555 (m-10) cc_final: 0.7130 (m-10) outliers start: 29 outliers final: 23 residues processed: 250 average time/residue: 0.4681 time to fit residues: 135.3482 Evaluate side-chains 257 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain F residue 263 PHE Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 263 PHE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 116 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 chunk 184 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 71 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN G 3 GLN ** K 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.187856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121715 restraints weight = 31067.634| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.55 r_work: 0.3183 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18894 Z= 0.135 Angle : 0.592 11.879 25632 Z= 0.294 Chirality : 0.043 0.150 2784 Planarity : 0.005 0.062 3264 Dihedral : 4.727 23.839 2565 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.58 % Allowed : 15.78 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2325 helix: -0.20 (0.40), residues: 177 sheet: -0.34 (0.19), residues: 693 loop : -0.54 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 18 TYR 0.011 0.001 TYR D 105 PHE 0.010 0.001 PHE M 83 TRP 0.019 0.001 TRP C 35 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00321 (18861) covalent geometry : angle 0.58989 (25566) SS BOND : bond 0.00244 ( 33) SS BOND : angle 1.12733 ( 66) hydrogen bonds : bond 0.03022 ( 579) hydrogen bonds : angle 5.16974 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8415.33 seconds wall clock time: 143 minutes 18.26 seconds (8598.26 seconds total)