Starting phenix.real_space_refine on Thu Feb 5 04:25:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ny4_49919/02_2026/9ny4_49919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ny4_49919/02_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_49919/02_2026/9ny4_49919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ny4_49919/02_2026/9ny4_49919.map" model { file = "/net/cci-nas-00/data/ceres_data/9ny4_49919/02_2026/9ny4_49919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ny4_49919/02_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-2.0-5952/lib/python3.9/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: 2.84, 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: 0.95 Conformation dependent library (CDL) restraints added in 372.7 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: 1.81 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: 2.44 Time building geometry restraints manager: 1.28 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=" N GLY H 50 " pdb=" CA GLY H 50 " ideal model delta sigma weight residual 1.447 1.482 -0.034 9.40e-03 1.13e+04 1.32e+01 bond pdb=" CA PRO U 37 " pdb=" C PRO U 37 " ideal model delta sigma weight residual 1.517 1.547 -0.030 9.30e-03 1.16e+04 1.03e+01 bond pdb=" N VAL U 70 " pdb=" CA VAL U 70 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" CZ ARG G 17 " pdb=" NH2 ARG G 17 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.19e+00 bond pdb=" N ILE C 111 " pdb=" CA ILE C 111 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.25e-02 6.40e+03 9.09e+00 ... (remaining 15784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 14710 1.63 - 3.26: 6029 3.26 - 4.89: 1588 4.89 - 6.52: 214 6.52 - 8.15: 9 Bond angle restraints: 22550 Sorted by residual: angle pdb=" N CYS K 398 " pdb=" CA CYS K 398 " pdb=" C CYS K 398 " ideal model delta sigma weight residual 113.88 107.36 6.52 1.23e+00 6.61e-01 2.81e+01 angle pdb=" O5' DC I 4 " pdb=" C5' DC I 4 " pdb=" C4' DC I 4 " ideal model delta sigma weight residual 110.80 118.35 -7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" N ASP E 81 " pdb=" CA ASP E 81 " pdb=" C ASP E 81 " ideal model delta sigma weight residual 112.47 118.61 -6.14 1.24e+00 6.50e-01 2.45e+01 angle pdb=" CA ASP K 399 " pdb=" CB ASP K 399 " pdb=" CG ASP K 399 " ideal model delta sigma weight residual 112.60 117.51 -4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" OE1 GLN G 84 " pdb=" CD GLN G 84 " pdb=" NE2 GLN G 84 " ideal model delta sigma weight residual 122.60 117.77 4.83 1.00e+00 1.00e+00 2.34e+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: 1967 0.097 - 0.193: 534 0.193 - 0.290: 43 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=" 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 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 -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.87e+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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.490 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 0.044 15789 Z= 0.752 Angle : 1.831 8.148 22550 Z= 1.215 Chirality : 0.083 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 covalent geometry : bond 0.01314 (15789) covalent geometry : angle 1.83125 (22550) hydrogen bonds : bond 0.17779 ( 716) hydrogen bonds : angle 6.79349 ( 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 : 0.412 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: 0.6940 time to fit residues: 244.6261 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 : 0.370 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN B 64 ASN C 110 ASN C 112 GLN G 84 GLN G 112 GLN H 79 HIS K 442 GLN K 556 GLN U 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.129795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086667 restraints weight = 33869.803| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.77 r_work: 0.3247 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15789 Z= 0.181 Angle : 0.674 12.055 22550 Z= 0.390 Chirality : 0.039 0.160 2556 Planarity : 0.004 0.038 1858 Dihedral : 28.122 160.149 4441 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.39 % Allowed : 16.49 % Favored : 78.11 % 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: -0.18 (0.24), residues: 1094 helix: 0.32 (0.21), residues: 579 sheet: -0.91 (0.50), residues: 89 loop : -0.36 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 53 TYR 0.013 0.001 TYR K 555 PHE 0.022 0.002 PHE K 420 TRP 0.009 0.001 TRP K 270 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00382 (15789) covalent geometry : angle 0.67438 (22550) hydrogen bonds : bond 0.05081 ( 716) hydrogen bonds : angle 3.47021 ( 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 231 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8092 (tt0) cc_final: 0.7791 (tt0) REVERT: C 39 TYR cc_start: 0.6358 (m-10) cc_final: 0.5834 (m-80) REVERT: C 71 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.7485 (ttp80) REVERT: D 34 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.7218 (t80) REVERT: D 59 MET cc_start: 0.8924 (tpt) cc_final: 0.8497 (tpt) REVERT: D 82 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8734 (mmtt) REVERT: D 90 GLU cc_start: 0.8424 (mp0) cc_final: 0.7849 (mp0) REVERT: D 102 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: D 120 SER cc_start: 0.8611 (t) cc_final: 0.8256 (p) REVERT: E 76 GLN cc_start: 0.8804 (tt0) cc_final: 0.8512 (tt0) REVERT: G 39 TYR cc_start: 0.6459 (m-80) cc_final: 0.5974 (m-80) REVERT: G 99 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8413 (mmt180) REVERT: H 81 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8354 (OUTLIER) REVERT: K 246 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7449 (tpt170) REVERT: U 1 MET cc_start: 0.5321 (mtm) cc_final: 0.4772 (ptt) REVERT: U 40 GLN cc_start: 0.7095 (mm-40) cc_final: 0.6495 (tm-30) outliers start: 52 outliers final: 18 residues processed: 210 average time/residue: 0.6108 time to fit residues: 139.0281 Evaluate side-chains 170 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 43 VAL 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 119 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 92 GLN 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: 7.9990 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 110 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN F 25 ASN H 46 HIS K 510 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.116791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068512 restraints weight = 32213.019| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.57 r_work: 0.2854 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 15789 Z= 0.366 Angle : 0.771 8.918 22550 Z= 0.440 Chirality : 0.046 0.228 2556 Planarity : 0.006 0.053 1858 Dihedral : 28.651 160.092 4429 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.02 % Allowed : 18.26 % Favored : 75.73 % 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: -0.35 (0.24), residues: 1094 helix: 0.38 (0.20), residues: 608 sheet: -1.15 (0.50), residues: 95 loop : -0.79 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 128 TYR 0.034 0.003 TYR C 39 PHE 0.022 0.002 PHE K 420 TRP 0.005 0.001 TRP K 270 HIS 0.012 0.002 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00864 (15789) covalent geometry : angle 0.77093 (22550) hydrogen bonds : bond 0.08159 ( 716) hydrogen bonds : angle 3.49575 ( 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 181 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7872 (mmm-85) REVERT: A 59 GLU cc_start: 0.8666 (pm20) cc_final: 0.8131 (pm20) REVERT: A 73 GLU cc_start: 0.8585 (tt0) cc_final: 0.8379 (tt0) REVERT: B 45 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8590 (ttt180) REVERT: C 36 LYS cc_start: 0.9058 (mptp) cc_final: 0.8820 (tptm) REVERT: C 71 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7310 (ttp80) REVERT: D 65 ASP cc_start: 0.9145 (t0) cc_final: 0.8794 (t0) REVERT: D 102 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7703 (pp20) REVERT: E 133 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8352 (mt-10) REVERT: F 39 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8648 (mmt-90) REVERT: G 59 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9308 (t) REVERT: G 95 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9166 (ttmm) REVERT: G 99 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8391 (mtp85) REVERT: K 246 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7759 (mmm160) REVERT: K 470 ARG cc_start: 0.6022 (OUTLIER) cc_final: 0.5653 (pmt170) REVERT: U 1 MET cc_start: 0.5330 (mtm) cc_final: 0.4803 (ptt) outliers start: 58 outliers final: 20 residues processed: 167 average time/residue: 0.6910 time to fit residues: 123.6525 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER 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 61 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 81 ASN 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 511 SER 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: 9.9990 chunk 129 optimal weight: 40.0000 chunk 115 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN E 39 HIS K 228 GLN K 518 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.117766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069366 restraints weight = 32022.897| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.61 r_work: 0.2875 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15789 Z= 0.217 Angle : 0.598 7.066 22550 Z= 0.350 Chirality : 0.038 0.182 2556 Planarity : 0.004 0.040 1858 Dihedral : 28.149 159.559 4429 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.67 % Allowed : 20.44 % Favored : 74.90 % 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: 0.18 (0.25), residues: 1094 helix: 0.81 (0.21), residues: 603 sheet: -0.95 (0.51), residues: 88 loop : -0.53 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 53 TYR 0.020 0.002 TYR C 39 PHE 0.019 0.002 PHE K 420 TRP 0.006 0.001 TRP K 529 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00497 (15789) covalent geometry : angle 0.59790 (22550) hydrogen bonds : bond 0.05667 ( 716) hydrogen bonds : angle 3.03492 ( 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 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8720 (pm20) cc_final: 0.8232 (pm20) REVERT: C 36 LYS cc_start: 0.9073 (mptp) cc_final: 0.8770 (mptm) REVERT: C 71 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7628 (tmm-80) REVERT: D 65 ASP cc_start: 0.9161 (t0) cc_final: 0.8826 (t0) REVERT: D 102 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: E 133 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: G 59 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9260 (t) REVERT: G 99 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8368 (mtp85) REVERT: K 246 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7770 (mmm160) REVERT: K 470 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.5779 (pmt170) REVERT: U 1 MET cc_start: 0.5230 (mtm) cc_final: 0.4786 (ptt) outliers start: 45 outliers final: 18 residues processed: 149 average time/residue: 0.8260 time to fit residues: 131.3233 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 110 CYS 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 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 309 LEU Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG 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: 5.9990 chunk 44 optimal weight: 0.2980 chunk 101 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 116 optimal weight: 30.0000 chunk 1 optimal weight: 0.1980 chunk 98 optimal weight: 8.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 39 HIS K 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.121706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074491 restraints weight = 32372.702| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.47 r_work: 0.2992 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.6767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15789 Z= 0.131 Angle : 0.525 8.063 22550 Z= 0.308 Chirality : 0.033 0.157 2556 Planarity : 0.003 0.038 1858 Dihedral : 27.887 159.818 4429 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.49 % Allowed : 21.78 % Favored : 75.73 % 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: 0.75 (0.25), residues: 1094 helix: 1.34 (0.21), residues: 602 sheet: -0.70 (0.51), residues: 88 loop : -0.41 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 42 TYR 0.013 0.001 TYR K 555 PHE 0.018 0.001 PHE K 420 TRP 0.003 0.000 TRP K 359 HIS 0.003 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00273 (15789) covalent geometry : angle 0.52454 (22550) hydrogen bonds : bond 0.03432 ( 716) hydrogen bonds : angle 2.68604 ( 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: 24 poor density : 126 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8636 (pm20) cc_final: 0.8255 (pm20) REVERT: A 85 GLN cc_start: 0.8797 (pt0) cc_final: 0.8441 (pt0) REVERT: C 36 LYS cc_start: 0.9020 (mptp) cc_final: 0.8736 (mptm) REVERT: C 71 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7533 (tmm-80) REVERT: D 65 ASP cc_start: 0.9127 (t0) cc_final: 0.8768 (t0) REVERT: D 90 GLU cc_start: 0.9110 (mp0) cc_final: 0.8771 (mp0) REVERT: D 102 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: E 120 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8953 (mtm) REVERT: E 133 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8070 (mt-10) REVERT: F 24 ASP cc_start: 0.7627 (p0) cc_final: 0.7409 (p0) REVERT: F 27 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: G 99 ARG cc_start: 0.8616 (mtp180) cc_final: 0.8373 (mtp85) REVERT: G 116 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (mm) REVERT: K 246 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7731 (mmm160) REVERT: K 310 MET cc_start: 0.4567 (tmm) cc_final: 0.3435 (ptt) REVERT: K 470 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5967 (pmt170) REVERT: U 1 MET cc_start: 0.5131 (mtm) cc_final: 0.4732 (ptt) outliers start: 24 outliers final: 11 residues processed: 142 average time/residue: 0.8273 time to fit residues: 124.7757 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 470 ARG 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: 0.0770 chunk 25 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.0070 overall best weight: 1.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 39 HIS K 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.119241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071218 restraints weight = 31659.706| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.43 r_work: 0.2918 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15789 Z= 0.155 Angle : 0.539 7.082 22550 Z= 0.317 Chirality : 0.035 0.176 2556 Planarity : 0.003 0.038 1858 Dihedral : 27.942 159.960 4429 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.53 % Allowed : 21.16 % 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: 0.85 (0.25), residues: 1094 helix: 1.47 (0.21), residues: 603 sheet: -0.61 (0.52), residues: 88 loop : -0.48 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.011 0.001 TYR K 555 PHE 0.015 0.001 PHE K 420 TRP 0.002 0.001 TRP K 270 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00341 (15789) covalent geometry : angle 0.53926 (22550) hydrogen bonds : bond 0.04594 ( 716) hydrogen bonds : angle 2.70896 ( 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 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8728 (pm20) cc_final: 0.8309 (pm20) REVERT: A 64 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8871 (mttp) REVERT: B 45 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.6561 (ttm170) REVERT: C 36 LYS cc_start: 0.9040 (mptp) cc_final: 0.8760 (mptm) REVERT: C 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8798 (tt0) REVERT: C 71 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7568 (tmm-80) REVERT: D 65 ASP cc_start: 0.9177 (t0) cc_final: 0.8884 (t0) REVERT: D 102 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: E 133 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: F 27 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: G 99 ARG cc_start: 0.8603 (mtp180) cc_final: 0.8358 (mtp85) REVERT: G 116 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8283 (mm) REVERT: K 222 PHE cc_start: 0.5146 (OUTLIER) cc_final: 0.4663 (p90) REVERT: K 246 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7702 (mmm160) REVERT: K 470 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6251 (pmt170) REVERT: K 478 VAL cc_start: 0.4308 (OUTLIER) cc_final: 0.3859 (t) REVERT: U 1 MET cc_start: 0.5109 (mtm) cc_final: 0.4710 (ptt) REVERT: U 73 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6333 (mt) outliers start: 34 outliers final: 12 residues processed: 143 average time/residue: 0.7461 time to fit residues: 113.9415 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 222 PHE Chi-restraints excluded: chain K residue 390 ARG 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: 2.9990 chunk 62 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 39 HIS K 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.120277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072616 restraints weight = 31554.749| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.43 r_work: 0.2950 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15789 Z= 0.140 Angle : 0.521 8.862 22550 Z= 0.306 Chirality : 0.034 0.171 2556 Planarity : 0.003 0.039 1858 Dihedral : 27.791 159.926 4429 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.90 % Allowed : 21.68 % Favored : 75.41 % 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: 1.01 (0.25), residues: 1094 helix: 1.60 (0.21), residues: 604 sheet: -0.53 (0.52), residues: 88 loop : -0.41 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.011 0.001 TYR K 555 PHE 0.014 0.001 PHE K 420 TRP 0.002 0.000 TRP K 270 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00303 (15789) covalent geometry : angle 0.52107 (22550) hydrogen bonds : bond 0.03870 ( 716) hydrogen bonds : angle 2.61251 ( 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 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8713 (pm20) cc_final: 0.8326 (pm20) REVERT: C 15 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8259 (mttm) REVERT: C 36 LYS cc_start: 0.9031 (mptp) cc_final: 0.8749 (mptm) REVERT: C 71 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7614 (tmm-80) REVERT: D 65 ASP cc_start: 0.9203 (t0) cc_final: 0.8825 (t0) REVERT: D 102 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7408 (pp20) REVERT: E 133 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8109 (mt-10) REVERT: F 27 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: G 99 ARG cc_start: 0.8604 (mtp180) cc_final: 0.8356 (mtp85) REVERT: G 116 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8305 (mm) REVERT: K 222 PHE cc_start: 0.5230 (OUTLIER) cc_final: 0.4278 (p90) REVERT: K 246 ARG cc_start: 0.8138 (mtm180) cc_final: 0.7722 (mmm160) REVERT: K 310 MET cc_start: 0.4700 (tmm) cc_final: 0.3490 (ptt) REVERT: K 470 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6404 (pmt170) REVERT: U 1 MET cc_start: 0.5052 (mtm) cc_final: 0.4601 (ptt) REVERT: U 73 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6166 (mt) outliers start: 28 outliers final: 10 residues processed: 142 average time/residue: 0.8093 time to fit residues: 122.6560 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 222 PHE Chi-restraints excluded: chain K residue 390 ARG 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: 6.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 6 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 40.0000 chunk 98 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 39 HIS K 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.119883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072826 restraints weight = 31109.032| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.36 r_work: 0.3001 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15789 Z= 0.178 Angle : 0.556 7.755 22550 Z= 0.326 Chirality : 0.036 0.192 2556 Planarity : 0.003 0.040 1858 Dihedral : 27.905 159.972 4429 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.59 % Allowed : 21.99 % Favored : 75.41 % 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: 0.96 (0.25), residues: 1094 helix: 1.54 (0.21), residues: 603 sheet: -0.58 (0.52), residues: 89 loop : -0.40 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.011 0.001 TYR C 39 PHE 0.015 0.001 PHE K 305 TRP 0.003 0.001 TRP K 270 HIS 0.004 0.001 HIS K 510 Details of bonding type rmsd covalent geometry : bond 0.00401 (15789) covalent geometry : angle 0.55633 (22550) hydrogen bonds : bond 0.05070 ( 716) hydrogen bonds : angle 2.72467 ( 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 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8958 (pm20) cc_final: 0.8622 (pm20) REVERT: B 45 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.6791 (ttm170) REVERT: C 36 LYS cc_start: 0.9177 (mptp) cc_final: 0.8928 (mptm) REVERT: C 56 GLU cc_start: 0.9002 (tt0) cc_final: 0.8779 (tt0) REVERT: D 65 ASP cc_start: 0.9343 (t0) cc_final: 0.9042 (t0) REVERT: E 133 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: F 27 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.8331 (mp10) REVERT: K 305 PHE cc_start: 0.6918 (m-10) cc_final: 0.6291 (m-10) REVERT: K 470 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.5895 (pmt170) REVERT: U 1 MET cc_start: 0.5109 (mtm) cc_final: 0.4657 (ptt) REVERT: U 73 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6202 (mt) outliers start: 25 outliers final: 14 residues processed: 134 average time/residue: 0.8167 time to fit residues: 116.8344 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU 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: 5.9990 chunk 96 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN K 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.118312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.071104 restraints weight = 31158.118| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.41 r_work: 0.2958 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15789 Z= 0.231 Angle : 0.611 9.338 22550 Z= 0.354 Chirality : 0.039 0.202 2556 Planarity : 0.004 0.040 1858 Dihedral : 27.991 159.764 4424 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.90 % Allowed : 21.78 % 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: 0.75 (0.25), residues: 1094 helix: 1.33 (0.21), residues: 607 sheet: -0.67 (0.51), residues: 89 loop : -0.43 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 42 TYR 0.015 0.002 TYR C 39 PHE 0.018 0.002 PHE D 62 TRP 0.005 0.001 TRP K 529 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00534 (15789) covalent geometry : angle 0.61070 (22550) hydrogen bonds : bond 0.06069 ( 716) hydrogen bonds : angle 2.87171 ( 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 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9027 (pm20) cc_final: 0.8676 (pm20) REVERT: B 45 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.6845 (ttm170) REVERT: C 36 LYS cc_start: 0.9213 (mptp) cc_final: 0.8962 (mptm) REVERT: C 56 GLU cc_start: 0.9048 (tt0) cc_final: 0.8832 (tt0) REVERT: D 65 ASP cc_start: 0.9362 (t0) cc_final: 0.9058 (t0) REVERT: E 133 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: F 27 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: H 73 GLU cc_start: 0.9054 (tp30) cc_final: 0.8748 (mm-30) REVERT: K 305 PHE cc_start: 0.6697 (m-10) cc_final: 0.6006 (m-10) REVERT: K 310 MET cc_start: 0.4708 (tmm) cc_final: 0.3457 (ptt) REVERT: K 470 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6723 (pmt170) REVERT: U 1 MET cc_start: 0.4991 (mtm) cc_final: 0.4549 (ptt) outliers start: 28 outliers final: 17 residues processed: 134 average time/residue: 0.8333 time to fit residues: 119.4907 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 : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL 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 K residue 552 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: 3.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 50.0000 chunk 97 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 40.0000 chunk 121 optimal weight: 40.0000 chunk 73 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 39 HIS K 228 GLN K 300 GLN U 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.113781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.064107 restraints weight = 31880.293| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.54 r_work: 0.2747 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 15789 Z= 0.397 Angle : 0.741 9.270 22550 Z= 0.424 Chirality : 0.046 0.216 2556 Planarity : 0.005 0.045 1858 Dihedral : 28.329 159.156 4424 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.70 % Allowed : 21.68 % Favored : 75.62 % 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: 0.78 (0.21), residues: 607 sheet: -0.96 (0.48), residues: 89 loop : -0.76 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 92 TYR 0.022 0.003 TYR C 39 PHE 0.027 0.002 PHE D 62 TRP 0.013 0.002 TRP K 529 HIS 0.008 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00933 (15789) covalent geometry : angle 0.74113 (22550) hydrogen bonds : bond 0.08429 ( 716) hydrogen bonds : angle 3.21828 ( 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 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8944 (pm20) cc_final: 0.8401 (pm20) REVERT: B 45 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.6556 (ttm170) REVERT: C 36 LYS cc_start: 0.9028 (mptp) cc_final: 0.8750 (mptm) REVERT: C 56 GLU cc_start: 0.9167 (tt0) cc_final: 0.8960 (tt0) REVERT: C 92 GLU cc_start: 0.8938 (pt0) cc_final: 0.8677 (pt0) REVERT: D 65 ASP cc_start: 0.9229 (t0) cc_final: 0.8902 (t0) REVERT: E 133 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: F 24 ASP cc_start: 0.7569 (p0) cc_final: 0.7266 (p0) REVERT: F 27 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8318 (mp10) REVERT: H 32 GLU cc_start: 0.8379 (tp30) cc_final: 0.8070 (mm-30) REVERT: H 73 GLU cc_start: 0.8863 (tp30) cc_final: 0.8507 (mm-30) REVERT: K 305 PHE cc_start: 0.6501 (m-10) cc_final: 0.5778 (m-10) REVERT: K 310 MET cc_start: 0.4536 (tmm) cc_final: 0.3331 (ptt) REVERT: K 470 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5574 (pmt170) REVERT: U 1 MET cc_start: 0.5125 (mtm) cc_final: 0.4712 (ptt) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 0.8496 time to fit residues: 117.8062 Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL 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 552 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: 2.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 0.0050 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.121063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074837 restraints weight = 31195.527| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.45 r_work: 0.3049 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15789 Z= 0.139 Angle : 0.548 8.803 22550 Z= 0.321 Chirality : 0.034 0.157 2556 Planarity : 0.004 0.042 1858 Dihedral : 27.786 159.434 4424 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.97 % Allowed : 22.10 % 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: 0.77 (0.25), residues: 1094 helix: 1.46 (0.21), residues: 604 sheet: -0.79 (0.50), residues: 89 loop : -0.57 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.011 0.001 TYR K 555 PHE 0.037 0.001 PHE K 287 TRP 0.003 0.000 TRP K 529 HIS 0.003 0.000 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00293 (15789) covalent geometry : angle 0.54829 (22550) hydrogen bonds : bond 0.03857 ( 716) hydrogen bonds : angle 2.63538 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5600.27 seconds wall clock time: 95 minutes 42.73 seconds (5742.73 seconds total)