Starting phenix.real_space_refine on Fri Jul 3 16:55:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ny4_49919/07_2026/9ny4_49919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ny4_49919/07_2026/9ny4_49919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ny4_49919/07_2026/9ny4_49919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ny4_49919/07_2026/9ny4_49919.map" model { file = "/net/cci-nas-00/data/ceres_data/9ny4_49919/07_2026/9ny4_49919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ny4_49919/07_2026/9ny4_49919.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 31 5.16 5 C 8485 2.51 5 N 2793 2.21 5 O 3339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14936 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2306 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain breaks: 5 Chain: "U" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 2.86, per 1000 atoms: 0.19 Number of scatterers: 14936 At special positions: 0 Unit cell: (133.86, 116.4, 119.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 288 15.00 O 3339 8.00 N 2793 7.00 C 8485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.24 Conformation dependent library (CDL) restraints added in 554.1 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 7 sheets defined 55.8% alpha, 7.0% beta 135 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.695A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.884A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 71 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 113 removed outlier: 3.960A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.979A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.820A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 4.010A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.486A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.839A pdb=" N LEU C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 73 removed outlier: 3.926A pdb=" N LEU C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 4.060A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 86 " --> pdb=" O HIS C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.633A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 4.119A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 Processing helix chain 'D' and resid 61 through 80 removed outlier: 4.101A pdb=" N ASP D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.940A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 120 removed outlier: 3.629A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 52 through 57 Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.745A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 113 removed outlier: 4.534A pdb=" N ALA E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 removed outlier: 3.898A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.620A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 40 removed outlier: 3.760A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.930A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 88 Processing helix chain 'F' and resid 88 through 93 removed outlier: 4.203A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.623A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 73 removed outlier: 3.994A pdb=" N ALA G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 removed outlier: 3.803A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 4.171A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 80 removed outlier: 4.616A pdb=" N SER H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 4.321A pdb=" N VAL H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 119 removed outlier: 4.337A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 110 " --> pdb=" O HIS H 106 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 232 Processing helix chain 'K' and resid 233 through 235 No H-bonds generated for 'chain 'K' and resid 233 through 235' Processing helix chain 'K' and resid 236 through 243 removed outlier: 3.661A pdb=" N ARG K 243 " --> pdb=" O PHE K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 248 Processing helix chain 'K' and resid 257 through 270 Processing helix chain 'K' and resid 280 through 291 removed outlier: 3.525A pdb=" N LYS K 289 " --> pdb=" O ALA K 285 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR K 290 " --> pdb=" O VAL K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 295 Processing helix chain 'K' and resid 301 through 317 Processing helix chain 'K' and resid 356 through 364 Processing helix chain 'K' and resid 415 through 425 Processing helix chain 'K' and resid 430 through 434 Processing helix chain 'K' and resid 541 through 547 Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.571A pdb=" N VAL U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.039A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.966A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'K' and resid 390 through 397 removed outlier: 3.555A pdb=" N GLU K 395 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 399 through 402 removed outlier: 6.219A pdb=" N LEU K 400 " --> pdb=" O HIS K 462 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL K 552 " --> pdb=" O LEU K 507 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU K 507 " --> pdb=" O VAL K 552 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE K 554 " --> pdb=" O TYR K 505 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR K 505 " --> pdb=" O ARG K 524 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TRP K 529 " --> pdb=" O VAL K 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'U' and resid 12 through 16 369 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3254 1.33 - 1.45: 4520 1.45 - 1.58: 7394 1.58 - 1.70: 576 1.70 - 1.82: 45 Bond restraints: 15789 Sorted by residual: bond pdb=" C5' DC J 7 " pdb=" C4' DC J 7 " ideal model delta sigma weight residual 1.512 1.546 -0.034 7.00e-03 2.04e+04 2.32e+01 bond pdb=" C5' DA I -45 " pdb=" C4' DA I -45 " ideal model delta sigma weight residual 1.512 1.546 -0.034 7.00e-03 2.04e+04 2.30e+01 bond pdb=" C4 DC J 34 " pdb=" N4 DC J 34 " ideal model delta sigma weight residual 1.335 1.293 0.042 9.00e-03 1.23e+04 2.20e+01 bond pdb=" C5' DG J 4 " pdb=" C4' DG J 4 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.15e+01 bond pdb=" C5' DT I -47 " pdb=" C4' DT I -47 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.12e+01 ... (remaining 15784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 15878 1.79 - 3.58: 5295 3.58 - 5.37: 1254 5.37 - 7.16: 115 7.16 - 8.95: 8 Bond angle restraints: 22550 Sorted by residual: angle pdb=" O5' DC I 4 " pdb=" C5' DC I 4 " pdb=" C4' DC I 4 " ideal model delta sigma weight residual 109.40 118.35 -8.95 8.00e-01 1.56e+00 1.25e+02 angle pdb=" N6 DA J -55 " pdb=" C6 DA J -55 " pdb=" N1 DA J -55 " ideal model delta sigma weight residual 118.60 113.06 5.54 6.00e-01 2.78e+00 8.53e+01 angle pdb=" N6 DA I -67 " pdb=" C6 DA I -67 " pdb=" N1 DA I -67 " ideal model delta sigma weight residual 118.60 113.15 5.45 6.00e-01 2.78e+00 8.24e+01 angle pdb=" N6 DA J -72 " pdb=" C6 DA J -72 " pdb=" N1 DA J -72 " ideal model delta sigma weight residual 118.60 113.27 5.33 6.00e-01 2.78e+00 7.88e+01 angle pdb=" N6 DA J -43 " pdb=" C6 DA J -43 " pdb=" N1 DA J -43 " ideal model delta sigma weight residual 118.60 113.28 5.32 6.00e-01 2.78e+00 7.85e+01 ... (remaining 22545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.37: 7399 31.37 - 62.73: 1352 62.73 - 94.10: 38 94.10 - 125.46: 0 125.46 - 156.83: 1 Dihedral angle restraints: 8790 sinusoidal: 5519 harmonic: 3271 Sorted by residual: dihedral pdb=" CD ARG U 72 " pdb=" NE ARG U 72 " pdb=" CZ ARG U 72 " pdb=" NH1 ARG U 72 " ideal model delta sinusoidal sigma weight residual 0.00 71.74 -71.74 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CA SER H 84 " pdb=" C SER H 84 " pdb=" N THR H 85 " pdb=" CA THR H 85 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual 180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 8787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1920 0.097 - 0.193: 576 0.193 - 0.290: 48 0.290 - 0.386: 9 0.386 - 0.483: 3 Chirality restraints: 2556 Sorted by residual: chirality pdb=" CA LYS B 79 " pdb=" N LYS B 79 " pdb=" C LYS B 79 " pdb=" CB LYS B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.27 -0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 2553 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J -50 " 0.370 2.00e-02 2.50e+03 1.82e-01 8.27e+02 pdb=" N1 DT J -50 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT J -50 " -0.102 2.00e-02 2.50e+03 pdb=" O2 DT J -50 " -0.253 2.00e-02 2.50e+03 pdb=" N3 DT J -50 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT J -50 " 0.095 2.00e-02 2.50e+03 pdb=" O4 DT J -50 " 0.257 2.00e-02 2.50e+03 pdb=" C5 DT J -50 " -0.067 2.00e-02 2.50e+03 pdb=" C7 DT J -50 " -0.161 2.00e-02 2.50e+03 pdb=" C6 DT J -50 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -42 " -0.310 2.00e-02 2.50e+03 1.63e-01 6.62e+02 pdb=" N1 DT I -42 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT I -42 " 0.091 2.00e-02 2.50e+03 pdb=" O2 DT I -42 " 0.246 2.00e-02 2.50e+03 pdb=" N3 DT I -42 " -0.027 2.00e-02 2.50e+03 pdb=" C4 DT I -42 " -0.069 2.00e-02 2.50e+03 pdb=" O4 DT I -42 " -0.236 2.00e-02 2.50e+03 pdb=" C5 DT I -42 " 0.057 2.00e-02 2.50e+03 pdb=" C7 DT I -42 " 0.177 2.00e-02 2.50e+03 pdb=" C6 DT I -42 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -35 " 0.347 2.00e-02 2.50e+03 1.39e-01 5.82e+02 pdb=" N9 DG J -35 " -0.049 2.00e-02 2.50e+03 pdb=" C8 DG J -35 " -0.135 2.00e-02 2.50e+03 pdb=" N7 DG J -35 " -0.111 2.00e-02 2.50e+03 pdb=" C5 DG J -35 " -0.060 2.00e-02 2.50e+03 pdb=" C6 DG J -35 " 0.054 2.00e-02 2.50e+03 pdb=" O6 DG J -35 " 0.202 2.00e-02 2.50e+03 pdb=" N1 DG J -35 " 0.058 2.00e-02 2.50e+03 pdb=" C2 DG J -35 " -0.040 2.00e-02 2.50e+03 pdb=" N2 DG J -35 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DG J -35 " -0.116 2.00e-02 2.50e+03 pdb=" C4 DG J -35 " -0.110 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 6607 3.01 - 3.48: 14419 3.48 - 3.96: 25627 3.96 - 4.43: 28058 4.43 - 4.90: 38632 Nonbonded interactions: 113343 Sorted by model distance: nonbonded pdb=" N THR K 451 " pdb=" O THR K 451 " model vdw 2.539 2.496 nonbonded pdb=" OE1 GLN A 85 " pdb=" OG1 THR B 82 " model vdw 2.560 3.040 nonbonded pdb=" OG SER D 53 " pdb=" OP2 DA I -54 " model vdw 2.565 3.040 nonbonded pdb=" OG1 THR D 85 " pdb=" OP1 DG I -34 " model vdw 2.565 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.568 3.040 ... (remaining 113338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 113) selection = (chain 'G' and resid 10 through 113) } ncs_group { reference = (chain 'D' and resid 26 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.740 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.013 0.042 15789 Z= 1.195 Angle : 1.848 8.946 22550 Z= 1.823 Chirality : 0.086 0.483 2556 Planarity : 0.033 0.475 1858 Dihedral : 24.651 156.830 6670 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.35 % Allowed : 2.90 % Favored : 95.75 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % 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: -1.76 (0.23), residues: 1094 helix: -1.47 (0.19), residues: 519 sheet: -0.63 (0.63), residues: 63 loop : -0.73 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 36 TYR 0.108 0.018 TYR A 41 PHE 0.054 0.011 PHE K 239 TRP 0.038 0.015 TRP K 529 HIS 0.015 0.003 HIS K 510 Details of bonding type rmsd/Z covalent geometry : bond 0.01342 / 1.20 (15789) covalent geometry : angle 1.84791 / 1.82 (22550) hydrogen bonds : bond 0.17779 / 12.18 ( 716) hydrogen bonds : angle 6.79349 / 4.84 ( 1737) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 317 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 54 THR cc_start: 0.7285 (m) cc_final: 0.7041 (m) REVERT: C 39 TYR cc_start: 0.4279 (m-10) cc_final: 0.4010 (m-80) REVERT: D 65 ASP cc_start: 0.8723 (t70) cc_final: 0.8285 (t0) REVERT: D 82 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8258 (mmtt) REVERT: D 102 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6208 (pp20) REVERT: D 105 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7461 (mtpp) REVERT: D 120 SER cc_start: 0.8289 (t) cc_final: 0.7956 (p) REVERT: K 305 PHE cc_start: 0.8604 (t80) cc_final: 0.7950 (t80) REVERT: K 502 TYR cc_start: 0.0459 (m-80) cc_final: 0.0203 (m-80) REVERT: U 1 MET cc_start: 0.5461 (mtm) cc_final: 0.5075 (ptt) outliers start: 13 outliers final: 7 residues processed: 329 average time/residue: 0.7057 time to fit residues: 249.8133 Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 516 TYR Chi-restraints excluded: chain U residue 72 ARG Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 25 ASN B 64 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 79 HIS H 106 HIS K 442 GLN K 518 HIS K 556 GLN U 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.126548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.081998 restraints weight = 33511.252| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.85 r_work: 0.3146 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15789 Z= 0.267 Angle : 0.957 17.350 22550 Z= 0.528 Chirality : 0.063 0.475 2556 Planarity : 0.007 0.096 1858 Dihedral : 28.691 158.438 4441 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.60 % Allowed : 16.70 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.24), residues: 1094 helix: -0.18 (0.21), residues: 559 sheet: -1.21 (0.47), residues: 92 loop : -0.64 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG U 74 TYR 0.021 0.003 TYR G 57 PHE 0.043 0.003 PHE K 420 TRP 0.010 0.002 TRP K 359 HIS 0.023 0.002 HIS K 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.27 (15789) covalent geometry : angle 0.95746 / 0.53 (22550) hydrogen bonds : bond 0.08200 / 5.45 ( 716) hydrogen bonds : angle 4.07380 / 2.92 ( 1737) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8366 (mtm180) REVERT: A 73 GLU cc_start: 0.8366 (tt0) cc_final: 0.8038 (tt0) REVERT: C 39 TYR cc_start: 0.6471 (m-10) cc_final: 0.6260 (m-80) REVERT: C 56 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7633 (tt0) REVERT: C 71 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7474 (ttp80) REVERT: C 75 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8071 (mmtt) REVERT: C 92 GLU cc_start: 0.7176 (pt0) cc_final: 0.6876 (pt0) REVERT: D 34 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.7353 (t80) REVERT: D 82 LYS cc_start: 0.9160 (mtmm) cc_final: 0.8788 (mmtt) REVERT: D 102 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: D 120 SER cc_start: 0.8611 (t) cc_final: 0.8269 (p) REVERT: E 52 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7756 (mpp-170) REVERT: G 39 TYR cc_start: 0.6479 (m-10) cc_final: 0.6078 (m-80) REVERT: G 99 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8496 (mmt180) REVERT: H 81 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8626 (p0) REVERT: K 246 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7358 (tpm170) REVERT: U 1 MET cc_start: 0.5659 (mtm) cc_final: 0.5092 (ptt) outliers start: 54 outliers final: 21 residues processed: 198 average time/residue: 0.6622 time to fit residues: 141.7706 Evaluate side-chains 167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 chunk 116 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 110 optimal weight: 0.0270 chunk 63 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.123276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077421 restraints weight = 32999.970| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.56 r_work: 0.3056 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15789 Z= 0.179 Angle : 0.756 9.646 22550 Z= 0.426 Chirality : 0.053 0.267 2556 Planarity : 0.005 0.039 1858 Dihedral : 28.802 164.678 4429 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.77 % Allowed : 18.88 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.24), residues: 1094 helix: 0.51 (0.21), residues: 571 sheet: -1.22 (0.47), residues: 90 loop : -0.60 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 53 TYR 0.013 0.002 TYR C 50 PHE 0.027 0.002 PHE K 397 TRP 0.005 0.001 TRP K 359 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (15789) covalent geometry : angle 0.75558 / 0.43 (22550) hydrogen bonds : bond 0.06112 / 4.12 ( 716) hydrogen bonds : angle 3.45322 / 2.46 ( 1737) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8474 (tt0) cc_final: 0.8182 (tt0) REVERT: A 85 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8728 (pt0) REVERT: B 73 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8598 (p) REVERT: B 95 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7465 (ptp90) REVERT: C 39 TYR cc_start: 0.7659 (m-10) cc_final: 0.7391 (m-10) REVERT: C 56 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7995 (tt0) REVERT: C 71 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7524 (ttp80) REVERT: C 92 GLU cc_start: 0.7683 (pt0) cc_final: 0.7427 (pt0) REVERT: D 34 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7345 (t80) REVERT: D 59 MET cc_start: 0.9183 (tpt) cc_final: 0.8665 (tpt) REVERT: D 90 GLU cc_start: 0.8894 (mp0) cc_final: 0.8327 (mp0) REVERT: D 102 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: D 120 SER cc_start: 0.8631 (t) cc_final: 0.8259 (p) REVERT: E 52 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7862 (mpp-170) REVERT: E 76 GLN cc_start: 0.8801 (tt0) cc_final: 0.8527 (tt0) REVERT: E 133 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: F 95 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8506 (ptp90) REVERT: G 95 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9207 (ttmm) REVERT: G 99 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8330 (mmt180) REVERT: H 68 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: H 81 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8692 (p0) REVERT: H 86 ILE cc_start: 0.8006 (pt) cc_final: 0.7797 (mt) REVERT: H 90 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: K 246 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7381 (tpt170) REVERT: K 305 PHE cc_start: 0.8571 (t80) cc_final: 0.8306 (m-80) REVERT: K 558 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6895 (mpt) REVERT: U 1 MET cc_start: 0.5587 (mtm) cc_final: 0.4983 (ptt) outliers start: 46 outliers final: 19 residues processed: 168 average time/residue: 0.7537 time to fit residues: 136.7257 Evaluate side-chains 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 309 LEU Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 558 MET Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 100 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 118 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN F 75 HIS H 46 HIS K 533 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.119757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072048 restraints weight = 32330.458| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.59 r_work: 0.2942 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15789 Z= 0.196 Angle : 0.704 7.429 22550 Z= 0.400 Chirality : 0.051 0.265 2556 Planarity : 0.005 0.050 1858 Dihedral : 28.995 161.567 4429 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.33 % Allowed : 17.53 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.24), residues: 1094 helix: 0.77 (0.21), residues: 584 sheet: -0.95 (0.48), residues: 87 loop : -0.66 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 35 TYR 0.016 0.002 TYR K 551 PHE 0.023 0.002 PHE K 420 TRP 0.005 0.001 TRP K 270 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (15789) covalent geometry : angle 0.70368 / 0.40 (22550) hydrogen bonds : bond 0.06435 / 4.32 ( 716) hydrogen bonds : angle 3.31373 / 2.38 ( 1737) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 123 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8258 (pm20) cc_final: 0.8035 (pm20) REVERT: A 73 GLU cc_start: 0.8532 (tt0) cc_final: 0.8259 (tt0) REVERT: B 95 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7523 (ptp90) REVERT: C 56 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8421 (tt0) REVERT: C 71 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7443 (ttp80) REVERT: D 34 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.7587 (t80) REVERT: D 65 ASP cc_start: 0.9184 (t0) cc_final: 0.8798 (t0) REVERT: D 102 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7929 (pp20) REVERT: D 120 SER cc_start: 0.8624 (t) cc_final: 0.8219 (p) REVERT: E 133 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: F 82 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8867 (p) REVERT: G 95 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9185 (ttmm) REVERT: G 99 ARG cc_start: 0.8628 (mtp180) cc_final: 0.8388 (mtp85) REVERT: K 246 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7277 (tpm170) REVERT: K 310 MET cc_start: 0.4790 (tmm) cc_final: 0.3558 (ptp) REVERT: K 470 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5503 (pmt170) REVERT: U 1 MET cc_start: 0.5531 (mtm) cc_final: 0.4970 (ptt) outliers start: 61 outliers final: 20 residues processed: 169 average time/residue: 0.7403 time to fit residues: 134.5917 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 558 MET Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 116 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.121404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074135 restraints weight = 32588.829| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.58 r_work: 0.2988 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 15789 Z= 0.132 Angle : 0.618 10.992 22550 Z= 0.357 Chirality : 0.045 0.245 2556 Planarity : 0.004 0.074 1858 Dihedral : 28.891 165.027 4427 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.32 % Allowed : 20.54 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.25), residues: 1094 helix: 1.09 (0.21), residues: 589 sheet: -0.79 (0.49), residues: 87 loop : -0.48 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 486 TYR 0.011 0.001 TYR K 532 PHE 0.019 0.002 PHE K 222 TRP 0.004 0.001 TRP K 359 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 (15789) covalent geometry : angle 0.61810 / 0.36 (22550) hydrogen bonds : bond 0.04688 / 3.14 ( 716) hydrogen bonds : angle 3.09527 / 2.23 ( 1737) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8169 (pm20) cc_final: 0.7950 (pm20) REVERT: A 73 GLU cc_start: 0.8500 (tt0) cc_final: 0.8217 (tt0) REVERT: B 95 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7427 (ptp90) REVERT: C 92 GLU cc_start: 0.8310 (pt0) cc_final: 0.8036 (pt0) REVERT: D 34 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7596 (t80) REVERT: D 90 GLU cc_start: 0.9036 (mp0) cc_final: 0.8701 (mp0) REVERT: D 102 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7887 (pp20) REVERT: E 133 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: F 82 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8820 (p) REVERT: G 95 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9158 (ttmm) REVERT: G 99 ARG cc_start: 0.8607 (mtp180) cc_final: 0.8395 (mtp85) REVERT: H 30 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.5308 (mmt180) REVERT: H 68 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: K 246 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7163 (tpm170) REVERT: K 305 PHE cc_start: 0.8218 (m-80) cc_final: 0.7937 (m-10) REVERT: K 470 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5664 (pmt170) REVERT: U 1 MET cc_start: 0.5498 (mtm) cc_final: 0.4941 (ptt) outliers start: 32 outliers final: 11 residues processed: 140 average time/residue: 0.7888 time to fit residues: 118.5041 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 133 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.120270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072667 restraints weight = 32338.709| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.59 r_work: 0.2956 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15789 Z= 0.151 Angle : 0.608 8.936 22550 Z= 0.353 Chirality : 0.045 0.265 2556 Planarity : 0.004 0.054 1858 Dihedral : 28.900 164.250 4427 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.63 % Allowed : 20.33 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.25), residues: 1094 helix: 1.17 (0.21), residues: 590 sheet: -0.72 (0.49), residues: 87 loop : -0.47 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.012 0.001 TYR C 39 PHE 0.015 0.001 PHE D 62 TRP 0.003 0.001 TRP K 359 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (15789) covalent geometry : angle 0.60833 / 0.35 (22550) hydrogen bonds : bond 0.05090 / 3.40 ( 716) hydrogen bonds : angle 3.05275 / 2.19 ( 1737) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8243 (pm20) cc_final: 0.7909 (pm20) REVERT: A 73 GLU cc_start: 0.8523 (tt0) cc_final: 0.8235 (tt0) REVERT: B 95 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7477 (ptp90) REVERT: C 15 LYS cc_start: 0.8673 (ptpt) cc_final: 0.8466 (mttm) REVERT: C 71 ARG cc_start: 0.7563 (tmm-80) cc_final: 0.7154 (ttp80) REVERT: D 34 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7533 (t80) REVERT: D 102 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7878 (pp20) REVERT: E 133 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: F 82 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8890 (p) REVERT: G 95 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9155 (ttmm) REVERT: G 99 ARG cc_start: 0.8601 (mtp180) cc_final: 0.8387 (mtp85) REVERT: H 30 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.5877 (mmt180) REVERT: H 81 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8792 (OUTLIER) REVERT: K 222 PHE cc_start: 0.5500 (OUTLIER) cc_final: 0.4687 (p90) REVERT: K 246 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7181 (tpm170) REVERT: K 470 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5629 (pmt170) REVERT: U 1 MET cc_start: 0.5489 (mtm) cc_final: 0.4945 (ptt) outliers start: 35 outliers final: 15 residues processed: 139 average time/residue: 0.7898 time to fit residues: 118.2171 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 222 PHE Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.120565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073040 restraints weight = 32239.381| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.54 r_work: 0.2963 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15789 Z= 0.141 Angle : 0.594 12.649 22550 Z= 0.344 Chirality : 0.043 0.261 2556 Planarity : 0.003 0.040 1858 Dihedral : 28.858 165.052 4427 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.22 % Allowed : 20.64 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.25), residues: 1094 helix: 1.24 (0.21), residues: 588 sheet: -0.68 (0.50), residues: 87 loop : -0.43 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 486 TYR 0.012 0.001 TYR C 39 PHE 0.014 0.001 PHE D 62 TRP 0.003 0.001 TRP K 270 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (15789) covalent geometry : angle 0.59367 / 0.34 (22550) hydrogen bonds : bond 0.04757 / 3.21 ( 716) hydrogen bonds : angle 2.97811 / 2.14 ( 1737) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8318 (pm20) cc_final: 0.7960 (pm20) REVERT: B 84 MET cc_start: 0.8887 (mmp) cc_final: 0.8686 (mmp) REVERT: B 95 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7467 (ptp90) REVERT: C 15 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8493 (mttm) REVERT: C 71 ARG cc_start: 0.7579 (tmm-80) cc_final: 0.7215 (ttp80) REVERT: C 92 GLU cc_start: 0.8419 (pt0) cc_final: 0.8149 (pt0) REVERT: D 34 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7433 (t80) REVERT: D 90 GLU cc_start: 0.9075 (mp0) cc_final: 0.8763 (mp0) REVERT: D 102 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7831 (pp20) REVERT: E 133 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: F 82 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8838 (p) REVERT: G 95 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9130 (ttmm) REVERT: G 99 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8368 (mtp85) REVERT: H 30 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.5916 (mmt180) REVERT: K 246 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7669 (mmm160) REVERT: K 305 PHE cc_start: 0.7218 (m-10) cc_final: 0.6731 (m-10) REVERT: K 470 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5593 (pmt170) REVERT: U 1 MET cc_start: 0.5269 (mtm) cc_final: 0.4735 (ptt) outliers start: 31 outliers final: 13 residues processed: 136 average time/residue: 0.7845 time to fit residues: 114.6809 Evaluate side-chains 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 41 optimal weight: 0.5980 chunk 72 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.120175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072605 restraints weight = 32306.070| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.52 r_work: 0.2951 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15789 Z= 0.141 Angle : 0.587 8.782 22550 Z= 0.340 Chirality : 0.043 0.264 2556 Planarity : 0.003 0.040 1858 Dihedral : 28.794 164.635 4427 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.22 % Allowed : 20.85 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.25), residues: 1094 helix: 1.26 (0.21), residues: 594 sheet: -0.65 (0.50), residues: 88 loop : -0.45 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 486 TYR 0.011 0.001 TYR C 39 PHE 0.014 0.001 PHE D 62 TRP 0.003 0.001 TRP K 529 HIS 0.003 0.001 HIS K 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (15789) covalent geometry : angle 0.58664 / 0.34 (22550) hydrogen bonds : bond 0.04954 / 3.36 ( 716) hydrogen bonds : angle 2.91816 / 2.08 ( 1737) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8413 (pm20) cc_final: 0.8060 (pm20) REVERT: B 84 MET cc_start: 0.8899 (mmp) cc_final: 0.8630 (mmp) REVERT: B 95 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7455 (ptp90) REVERT: C 71 ARG cc_start: 0.7608 (tmm-80) cc_final: 0.7249 (ttp80) REVERT: C 92 GLU cc_start: 0.8326 (pt0) cc_final: 0.8032 (pt0) REVERT: D 34 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7463 (t80) REVERT: D 65 ASP cc_start: 0.9196 (t0) cc_final: 0.8791 (t0) REVERT: D 90 GLU cc_start: 0.9107 (mp0) cc_final: 0.8643 (mp0) REVERT: D 102 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7792 (pp20) REVERT: E 133 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: G 95 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9072 (ttmm) REVERT: G 99 ARG cc_start: 0.8578 (mtp180) cc_final: 0.8368 (mtp85) REVERT: H 30 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6105 (mmt180) REVERT: K 222 PHE cc_start: 0.5735 (OUTLIER) cc_final: 0.4840 (p90) REVERT: K 246 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7730 (mmm160) REVERT: K 305 PHE cc_start: 0.7237 (m-80) cc_final: 0.6809 (m-10) REVERT: K 310 MET cc_start: 0.4689 (tmm) cc_final: 0.3298 (ptp) REVERT: K 470 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5564 (pmt170) REVERT: U 1 MET cc_start: 0.5316 (mtm) cc_final: 0.4841 (ptt) outliers start: 31 outliers final: 13 residues processed: 136 average time/residue: 0.7862 time to fit residues: 114.8694 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 222 PHE Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.0050 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 overall best weight: 3.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.117376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068884 restraints weight = 31994.225| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.52 r_work: 0.2865 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15789 Z= 0.209 Angle : 0.675 8.668 22550 Z= 0.382 Chirality : 0.049 0.292 2556 Planarity : 0.004 0.041 1858 Dihedral : 28.817 163.673 4427 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.05 % Allowed : 20.75 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.24), residues: 1094 helix: 0.93 (0.21), residues: 601 sheet: -0.73 (0.50), residues: 88 loop : -0.74 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 128 TYR 0.027 0.002 TYR C 39 PHE 0.023 0.002 PHE D 62 TRP 0.006 0.001 TRP K 270 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (15789) covalent geometry : angle 0.67482 / 0.38 (22550) hydrogen bonds : bond 0.07308 / 5.06 ( 716) hydrogen bonds : angle 3.11363 / 2.24 ( 1737) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8635 (pm20) cc_final: 0.8329 (pm20) REVERT: B 95 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7676 (ptp90) REVERT: C 36 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8810 (tptm) REVERT: D 34 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7312 (t80) REVERT: D 65 ASP cc_start: 0.9215 (t0) cc_final: 0.8861 (t0) REVERT: D 102 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7822 (pp20) REVERT: E 133 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: G 95 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9090 (ttmm) REVERT: G 99 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8364 (mtp85) REVERT: H 30 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6049 (mmt180) REVERT: K 222 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.4701 (p90) REVERT: K 246 ARG cc_start: 0.8057 (mtm180) cc_final: 0.7678 (mmm160) REVERT: K 305 PHE cc_start: 0.7215 (m-80) cc_final: 0.6801 (m-10) REVERT: K 310 MET cc_start: 0.4654 (tmm) cc_final: 0.3283 (ptp) REVERT: K 470 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5619 (pmt170) REVERT: U 1 MET cc_start: 0.5193 (mtm) cc_final: 0.4737 (ptt) outliers start: 39 outliers final: 14 residues processed: 139 average time/residue: 0.7645 time to fit residues: 113.7921 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 222 PHE Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 112 optimal weight: 40.0000 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.0070 chunk 97 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 121 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.116622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067933 restraints weight = 32020.443| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.56 r_work: 0.2844 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15789 Z= 0.278 Angle : 0.713 7.842 22550 Z= 0.399 Chirality : 0.051 0.302 2556 Planarity : 0.005 0.050 1858 Dihedral : 28.816 163.997 4427 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.80 % Allowed : 22.10 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.24), residues: 1094 helix: 0.73 (0.21), residues: 601 sheet: -0.70 (0.50), residues: 87 loop : -0.81 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 42 TYR 0.032 0.002 TYR C 39 PHE 0.025 0.002 PHE D 62 TRP 0.007 0.001 TRP K 270 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.28 (15789) covalent geometry : angle 0.71332 / 0.40 (22550) hydrogen bonds : bond 0.07577 / 5.19 ( 716) hydrogen bonds : angle 3.16854 / 2.28 ( 1737) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8699 (pm20) cc_final: 0.8390 (pm20) REVERT: B 95 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7796 (ptp90) REVERT: C 36 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8836 (tptm) REVERT: C 71 ARG cc_start: 0.7598 (tmm-80) cc_final: 0.7236 (tmm-80) REVERT: D 65 ASP cc_start: 0.9223 (t0) cc_final: 0.8878 (t0) REVERT: D 102 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7655 (pp20) REVERT: E 120 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8852 (mtm) REVERT: E 133 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: G 95 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9108 (ttmm) REVERT: H 30 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6064 (mmt180) REVERT: K 246 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7687 (mmm160) REVERT: K 305 PHE cc_start: 0.7255 (m-80) cc_final: 0.6814 (m-10) REVERT: K 310 MET cc_start: 0.4668 (tmm) cc_final: 0.3306 (ptp) REVERT: U 1 MET cc_start: 0.5246 (mtm) cc_final: 0.4797 (ptt) outliers start: 27 outliers final: 17 residues processed: 129 average time/residue: 0.8214 time to fit residues: 113.3033 Evaluate side-chains 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.118764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070848 restraints weight = 31850.509| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.42 r_work: 0.2910 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15789 Z= 0.133 Angle : 0.612 8.048 22550 Z= 0.353 Chirality : 0.044 0.244 2556 Planarity : 0.003 0.042 1858 Dihedral : 28.695 165.004 4427 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.28 % Allowed : 22.41 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.25), residues: 1094 helix: 1.08 (0.21), residues: 604 sheet: -0.67 (0.50), residues: 87 loop : -0.67 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 42 TYR 0.010 0.001 TYR D 34 PHE 0.014 0.001 PHE K 222 TRP 0.004 0.001 TRP K 529 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (15789) covalent geometry : angle 0.61193 / 0.35 (22550) hydrogen bonds : bond 0.05221 / 3.56 ( 716) hydrogen bonds : angle 2.96594 / 2.13 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5486.87 seconds wall clock time: 93 minutes 53.51 seconds (5633.51 seconds total)