Starting phenix.real_space_refine on Sat Oct 11 10:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k36_36845/10_2025/8k36_36845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k36_36845/10_2025/8k36_36845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k36_36845/10_2025/8k36_36845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k36_36845/10_2025/8k36_36845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k36_36845/10_2025/8k36_36845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k36_36845/10_2025/8k36_36845.map" } resolution = 3.48 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= 0.007 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 8892 2.51 5 N 2400 2.21 5 O 2844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14172 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "B" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "C" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "D" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "E" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "F" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "H" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "I" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "J" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "K" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "L" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Time building chain proxies: 3.71, per 1000 atoms: 0.26 Number of scatterers: 14172 At special positions: 0 Unit cell: (110.16, 110.16, 108.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2844 8.00 N 2400 7.00 C 8892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 688.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 32 sheets defined 9.5% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.501A pdb=" N GLN A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.646A pdb=" N ARG A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.649A pdb=" N ARG D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'G' and resid 90 through 102 removed outlier: 3.500A pdb=" N GLN G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.645A pdb=" N ARG G 155 " --> pdb=" O ALA G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'I' and resid 90 through 102 Processing helix chain 'J' and resid 90 through 102 Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.648A pdb=" N ARG J 155 " --> pdb=" O ALA J 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 102 Processing helix chain 'L' and resid 90 through 102 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.534A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS A 142 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 127 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 140 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 129 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 138 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER A 81 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 45 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR A 83 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.534A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 removed outlier: 5.269A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 17 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51 removed outlier: 5.161A pdb=" N VAL B 124 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR B 144 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 138 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 81 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU B 45 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 83 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 76 removed outlier: 5.817A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER C 125 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N SER B 54 " --> pdb=" O TRP C 123 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N TRP C 123 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 14.551A pdb=" N ASP B 56 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 18.179A pdb=" N ARG C 121 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA C 107 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 17 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 76 removed outlier: 5.817A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER C 125 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N SER B 54 " --> pdb=" O TRP C 123 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N TRP C 123 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 14.551A pdb=" N ASP B 56 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 18.179A pdb=" N ARG C 121 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS C 142 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 127 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 140 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS C 129 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR C 138 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER C 81 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 45 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 83 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51 removed outlier: 5.345A pdb=" N ALA D 107 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU D 17 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.565A pdb=" N LYS D 142 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE D 127 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR D 140 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS D 129 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR D 138 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER D 81 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU D 45 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR D 83 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AB2, first strand: chain 'D' and resid 50 through 51 removed outlier: 5.270A pdb=" N ALA E 107 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU E 17 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51 removed outlier: 5.160A pdb=" N VAL E 124 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR E 144 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 138 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER E 81 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU E 45 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR E 83 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AB5, first strand: chain 'E' and resid 70 through 76 removed outlier: 5.812A pdb=" N GLU E 53 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS E 75 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR E 51 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER F 125 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N SER E 54 " --> pdb=" O TRP F 123 " (cutoff:3.500A) removed outlier: 12.214A pdb=" N TRP F 123 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 14.548A pdb=" N ASP E 56 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 18.172A pdb=" N ARG F 121 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA F 107 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU F 17 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 70 through 76 removed outlier: 5.812A pdb=" N GLU E 53 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS E 75 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR E 51 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER F 125 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N SER E 54 " --> pdb=" O TRP F 123 " (cutoff:3.500A) removed outlier: 12.214A pdb=" N TRP F 123 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 14.548A pdb=" N ASP E 56 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 18.172A pdb=" N ARG F 121 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS F 142 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE F 127 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR F 140 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS F 129 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR F 138 " --> pdb=" O LYS F 129 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER F 81 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU F 45 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR F 83 " --> pdb=" O LYS F 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 54 through 56 Processing sheet with id=AB8, first strand: chain 'G' and resid 36 through 39 removed outlier: 4.533A pdb=" N LEU G 17 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA G 107 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS G 142 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE G 127 " --> pdb=" O THR G 140 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR G 140 " --> pdb=" O ILE G 127 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS G 129 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR G 138 " --> pdb=" O LYS G 129 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER G 81 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU G 45 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR G 83 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 36 through 39 removed outlier: 4.533A pdb=" N LEU G 17 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA G 107 " --> pdb=" O TYR G 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 50 through 51 removed outlier: 5.270A pdb=" N ALA H 107 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU H 17 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 50 through 51 removed outlier: 5.162A pdb=" N VAL H 124 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR H 144 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR H 138 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N SER H 81 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU H 45 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR H 83 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 54 through 56 Processing sheet with id=AC4, first strand: chain 'H' and resid 70 through 76 removed outlier: 5.816A pdb=" N GLU H 53 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS H 75 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR H 51 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER I 125 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER H 54 " --> pdb=" O TRP I 123 " (cutoff:3.500A) removed outlier: 12.212A pdb=" N TRP I 123 " --> pdb=" O SER H 54 " (cutoff:3.500A) removed outlier: 14.552A pdb=" N ASP H 56 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 18.180A pdb=" N ARG I 121 " --> pdb=" O ASP H 56 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA I 107 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU I 17 " --> pdb=" O LEU I 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 70 through 76 removed outlier: 5.816A pdb=" N GLU H 53 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS H 75 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR H 51 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER I 125 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER H 54 " --> pdb=" O TRP I 123 " (cutoff:3.500A) removed outlier: 12.212A pdb=" N TRP I 123 " --> pdb=" O SER H 54 " (cutoff:3.500A) removed outlier: 14.552A pdb=" N ASP H 56 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 18.180A pdb=" N ARG I 121 " --> pdb=" O ASP H 56 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS I 142 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE I 127 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR I 140 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS I 129 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR I 138 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER I 81 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU I 45 " --> pdb=" O SER I 81 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR I 83 " --> pdb=" O LYS I 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 50 through 51 removed outlier: 5.345A pdb=" N ALA J 107 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU J 17 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 50 through 51 removed outlier: 6.565A pdb=" N LYS J 142 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE J 127 " --> pdb=" O THR J 140 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR J 140 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS J 129 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR J 138 " --> pdb=" O LYS J 129 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER J 81 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU J 45 " --> pdb=" O SER J 81 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR J 83 " --> pdb=" O LYS J 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 54 through 56 Processing sheet with id=AC9, first strand: chain 'J' and resid 50 through 51 removed outlier: 5.270A pdb=" N ALA K 107 " --> pdb=" O TYR K 20 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU K 17 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 50 through 51 removed outlier: 5.160A pdb=" N VAL K 124 " --> pdb=" O THR K 144 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR K 144 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR K 138 " --> pdb=" O ALA K 130 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER K 81 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU K 45 " --> pdb=" O SER K 81 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR K 83 " --> pdb=" O LYS K 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 54 through 56 Processing sheet with id=AD3, first strand: chain 'K' and resid 70 through 76 removed outlier: 5.811A pdb=" N GLU K 53 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS K 75 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR K 51 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER L 125 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER K 54 " --> pdb=" O TRP L 123 " (cutoff:3.500A) removed outlier: 12.213A pdb=" N TRP L 123 " --> pdb=" O SER K 54 " (cutoff:3.500A) removed outlier: 14.546A pdb=" N ASP K 56 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 18.171A pdb=" N ARG L 121 " --> pdb=" O ASP K 56 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA L 107 " --> pdb=" O TYR L 20 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU L 17 " --> pdb=" O LEU L 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 70 through 76 removed outlier: 5.811A pdb=" N GLU K 53 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS K 75 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR K 51 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER L 125 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER K 54 " --> pdb=" O TRP L 123 " (cutoff:3.500A) removed outlier: 12.213A pdb=" N TRP L 123 " --> pdb=" O SER K 54 " (cutoff:3.500A) removed outlier: 14.546A pdb=" N ASP K 56 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 18.171A pdb=" N ARG L 121 " --> pdb=" O ASP K 56 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS L 142 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE L 127 " --> pdb=" O THR L 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR L 140 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS L 129 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR L 138 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER L 81 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU L 45 " --> pdb=" O SER L 81 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR L 83 " --> pdb=" O LYS L 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 54 through 56 526 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2515 1.31 - 1.44: 3915 1.44 - 1.56: 8018 1.56 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 14520 Sorted by residual: bond pdb=" CA GLY I 103 " pdb=" C GLY I 103 " ideal model delta sigma weight residual 1.519 1.461 0.057 9.70e-03 1.06e+04 3.50e+01 bond pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 1.519 1.462 0.057 9.70e-03 1.06e+04 3.45e+01 bond pdb=" CA GLU C 102 " pdb=" C GLU C 102 " ideal model delta sigma weight residual 1.525 1.454 0.071 1.29e-02 6.01e+03 3.01e+01 bond pdb=" CA GLU I 102 " pdb=" C GLU I 102 " ideal model delta sigma weight residual 1.525 1.454 0.071 1.29e-02 6.01e+03 3.00e+01 bond pdb=" CA GLN G 91 " pdb=" C GLN G 91 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.35e-02 5.49e+03 1.86e+01 ... (remaining 14515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 19225 1.98 - 3.96: 487 3.96 - 5.93: 49 5.93 - 7.91: 29 7.91 - 9.89: 10 Bond angle restraints: 19800 Sorted by residual: angle pdb=" N ASP F 61 " pdb=" CA ASP F 61 " pdb=" C ASP F 61 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" N ASP L 61 " pdb=" CA ASP L 61 " pdb=" C ASP L 61 " ideal model delta sigma weight residual 111.28 116.78 -5.50 1.09e+00 8.42e-01 2.55e+01 angle pdb=" N ASP I 61 " pdb=" CA ASP I 61 " pdb=" C ASP I 61 " ideal model delta sigma weight residual 111.28 116.75 -5.47 1.09e+00 8.42e-01 2.52e+01 angle pdb=" N ASP C 61 " pdb=" CA ASP C 61 " pdb=" C ASP C 61 " ideal model delta sigma weight residual 111.28 116.74 -5.46 1.09e+00 8.42e-01 2.51e+01 angle pdb=" N ASP C 62 " pdb=" CA ASP C 62 " pdb=" C ASP C 62 " ideal model delta sigma weight residual 110.24 117.04 -6.80 1.41e+00 5.03e-01 2.32e+01 ... (remaining 19795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7886 17.75 - 35.51: 532 35.51 - 53.26: 74 53.26 - 71.01: 14 71.01 - 88.77: 14 Dihedral angle restraints: 8520 sinusoidal: 3288 harmonic: 5232 Sorted by residual: dihedral pdb=" C GLU I 102 " pdb=" N GLU I 102 " pdb=" CA GLU I 102 " pdb=" CB GLU I 102 " ideal model delta harmonic sigma weight residual -122.60 -112.62 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C GLU C 102 " pdb=" N GLU C 102 " pdb=" CA GLU C 102 " pdb=" CB GLU C 102 " ideal model delta harmonic sigma weight residual -122.60 -112.62 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C ARG E 139 " pdb=" N ARG E 139 " pdb=" CA ARG E 139 " pdb=" CB ARG E 139 " ideal model delta harmonic sigma weight residual -122.60 -113.61 -8.99 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1900 0.087 - 0.175: 228 0.175 - 0.262: 14 0.262 - 0.349: 0 0.349 - 0.436: 6 Chirality restraints: 2148 Sorted by residual: chirality pdb=" CA ASP F 62 " pdb=" N ASP F 62 " pdb=" C ASP F 62 " pdb=" CB ASP F 62 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ASP I 62 " pdb=" N ASP I 62 " pdb=" C ASP I 62 " pdb=" CB ASP I 62 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ASP C 62 " pdb=" N ASP C 62 " pdb=" C ASP C 62 " pdb=" CB ASP C 62 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 2145 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 90 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C GLU G 90 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU G 90 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN G 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 90 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C GLU A 90 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU A 90 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN A 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 31 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C LEU A 31 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 31 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 32 " 0.012 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3173 2.78 - 3.31: 11954 3.31 - 3.84: 20948 3.84 - 4.37: 24600 4.37 - 4.90: 46736 Nonbonded interactions: 107411 Sorted by model distance: nonbonded pdb=" OH TYR F 108 " pdb=" OD1 ASN F 145 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR L 108 " pdb=" OD1 ASN L 145 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR I 108 " pdb=" OD1 ASN I 145 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR C 108 " pdb=" OD1 ASN C 145 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP D 44 " pdb=" N LEU D 45 " model vdw 2.266 3.120 ... (remaining 107406 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.750 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.008 0.071 14520 Z= 0.436 Angle : 0.812 9.889 19800 Z= 0.463 Chirality : 0.057 0.436 2148 Planarity : 0.004 0.030 2580 Dihedral : 12.359 88.766 5184 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.80 % Allowed : 0.80 % Favored : 98.40 % 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 aren not related in a simple way. whole: -0.90 (0.17), residues: 1824 helix: 1.22 (0.47), residues: 144 sheet: -0.16 (0.17), residues: 864 loop : -1.37 (0.15), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 148 TYR 0.012 0.002 TYR K 20 PHE 0.017 0.002 PHE B 120 TRP 0.016 0.002 TRP I 18 Details of bonding type rmsd covalent geometry : bond 0.00830 (14520) covalent geometry : angle 0.81227 (19800) hydrogen bonds : bond 0.20235 ( 462) hydrogen bonds : angle 9.68250 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 370 time to evaluate : 0.541 Fit side-chains REVERT: A 61 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: A 134 LYS cc_start: 0.9186 (mtpt) cc_final: 0.8831 (mtmt) REVERT: B 27 TYR cc_start: 0.8889 (m-10) cc_final: 0.8634 (m-80) REVERT: C 11 LYS cc_start: 0.9427 (mttp) cc_final: 0.9182 (mttm) REVERT: C 41 LYS cc_start: 0.9401 (mttm) cc_final: 0.9165 (mttt) REVERT: C 43 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8300 (mtpp) REVERT: C 61 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: C 87 MET cc_start: 0.9238 (mtp) cc_final: 0.8941 (mtp) REVERT: C 114 ASN cc_start: 0.8767 (t0) cc_final: 0.8554 (t0) REVERT: C 134 LYS cc_start: 0.9273 (mtmt) cc_final: 0.9069 (mtmt) REVERT: D 44 ASP cc_start: 0.7826 (t0) cc_final: 0.7591 (t70) REVERT: D 118 ASP cc_start: 0.7839 (t0) cc_final: 0.7493 (t0) REVERT: E 11 LYS cc_start: 0.9337 (mttp) cc_final: 0.9106 (mttm) REVERT: F 61 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: F 87 MET cc_start: 0.9037 (mtp) cc_final: 0.8756 (mtp) REVERT: G 27 TYR cc_start: 0.8997 (m-10) cc_final: 0.8748 (m-10) REVERT: G 53 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7447 (mp0) REVERT: G 101 ASN cc_start: 0.8676 (m-40) cc_final: 0.8451 (m-40) REVERT: I 43 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8341 (mptt) REVERT: K 43 LYS cc_start: 0.9091 (mtpp) cc_final: 0.7670 (mmtt) REVERT: L 43 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8105 (mptt) REVERT: L 121 ARG cc_start: 0.8551 (mtp-110) cc_final: 0.8162 (ttm-80) outliers start: 12 outliers final: 0 residues processed: 372 average time/residue: 0.1502 time to fit residues: 76.8058 Evaluate side-chains 218 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain F residue 61 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN G 101 ASN J 101 ASN K 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.081006 restraints weight = 20095.025| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.62 r_work: 0.2649 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14520 Z= 0.100 Angle : 0.501 4.688 19800 Z= 0.266 Chirality : 0.044 0.147 2148 Planarity : 0.003 0.025 2580 Dihedral : 4.654 56.763 1986 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.60 % Allowed : 8.07 % Favored : 90.33 % 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 aren not related in a simple way. whole: -0.77 (0.16), residues: 1824 helix: 1.56 (0.43), residues: 144 sheet: -0.39 (0.15), residues: 948 loop : -0.94 (0.15), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 148 TYR 0.011 0.001 TYR G 108 PHE 0.012 0.001 PHE B 120 TRP 0.008 0.001 TRP A 36 Details of bonding type rmsd covalent geometry : bond 0.00227 (14520) covalent geometry : angle 0.50093 (19800) hydrogen bonds : bond 0.03266 ( 462) hydrogen bonds : angle 6.30629 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 275 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8822 (mtpp) REVERT: A 134 LYS cc_start: 0.9229 (mtpt) cc_final: 0.8873 (mtmt) REVERT: B 61 ASP cc_start: 0.8656 (m-30) cc_final: 0.8339 (m-30) REVERT: B 151 MET cc_start: 0.9143 (mmp) cc_final: 0.8778 (mmp) REVERT: C 11 LYS cc_start: 0.9418 (mttp) cc_final: 0.9175 (mttm) REVERT: C 43 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8235 (mtpp) REVERT: C 44 ASP cc_start: 0.7963 (m-30) cc_final: 0.7664 (m-30) REVERT: C 61 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8277 (m-30) REVERT: C 87 MET cc_start: 0.9132 (mtp) cc_final: 0.8839 (mtp) REVERT: C 114 ASN cc_start: 0.8740 (t0) cc_final: 0.8539 (t0) REVERT: C 129 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8894 (ttmm) REVERT: D 20 TYR cc_start: 0.9436 (t80) cc_final: 0.9033 (t80) REVERT: F 5 ASN cc_start: 0.8715 (t0) cc_final: 0.8361 (t0) REVERT: F 61 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: F 87 MET cc_start: 0.9035 (mtp) cc_final: 0.8748 (mtp) REVERT: G 53 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8071 (mp0) REVERT: G 118 ASP cc_start: 0.7651 (t0) cc_final: 0.7408 (t0) REVERT: H 20 TYR cc_start: 0.9105 (t80) cc_final: 0.8827 (t80) REVERT: H 135 GLU cc_start: 0.8474 (mp0) cc_final: 0.8210 (mp0) REVERT: I 20 TYR cc_start: 0.8966 (t80) cc_final: 0.8517 (t80) REVERT: I 32 SER cc_start: 0.8919 (t) cc_final: 0.8630 (m) REVERT: I 43 LYS cc_start: 0.9193 (mtpt) cc_final: 0.7760 (mptt) REVERT: I 97 LEU cc_start: 0.8849 (mt) cc_final: 0.8539 (mt) REVERT: I 101 ASN cc_start: 0.8232 (m-40) cc_final: 0.7991 (m-40) REVERT: J 135 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8419 (mp0) REVERT: K 5 ASN cc_start: 0.8933 (t0) cc_final: 0.8608 (t0) REVERT: K 74 GLN cc_start: 0.9068 (tt0) cc_final: 0.8782 (tt0) REVERT: K 135 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8099 (mp0) REVERT: L 20 TYR cc_start: 0.9070 (t80) cc_final: 0.8797 (t80) REVERT: L 29 ASN cc_start: 0.9372 (t0) cc_final: 0.9139 (t0) REVERT: L 101 ASN cc_start: 0.8881 (m-40) cc_final: 0.8520 (m-40) REVERT: L 121 ARG cc_start: 0.8726 (mtp-110) cc_final: 0.8201 (ttm-80) outliers start: 24 outliers final: 17 residues processed: 293 average time/residue: 0.1457 time to fit residues: 59.7451 Evaluate side-chains 217 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 101 ASN K 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.090402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.075793 restraints weight = 20551.959| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 1.60 r_work: 0.2559 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14520 Z= 0.143 Angle : 0.516 4.409 19800 Z= 0.273 Chirality : 0.045 0.153 2148 Planarity : 0.003 0.026 2580 Dihedral : 4.619 52.587 1984 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.93 % Allowed : 10.73 % Favored : 86.33 % 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 aren not related in a simple way. whole: -0.54 (0.17), residues: 1824 helix: 1.85 (0.42), residues: 144 sheet: -0.29 (0.16), residues: 936 loop : -0.74 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 121 TYR 0.013 0.001 TYR C 108 PHE 0.012 0.002 PHE J 120 TRP 0.010 0.001 TRP A 36 Details of bonding type rmsd covalent geometry : bond 0.00348 (14520) covalent geometry : angle 0.51554 (19800) hydrogen bonds : bond 0.03249 ( 462) hydrogen bonds : angle 5.57617 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.466 Fit side-chains REVERT: A 10 VAL cc_start: 0.9226 (p) cc_final: 0.8838 (m) REVERT: A 61 ASP cc_start: 0.8787 (t0) cc_final: 0.8565 (t0) REVERT: A 102 GLU cc_start: 0.8255 (pp20) cc_final: 0.8004 (pp20) REVERT: A 134 LYS cc_start: 0.9254 (mtpt) cc_final: 0.8929 (mtmt) REVERT: B 61 ASP cc_start: 0.8767 (m-30) cc_final: 0.8386 (m-30) REVERT: C 11 LYS cc_start: 0.9433 (mttp) cc_final: 0.9196 (mttt) REVERT: C 43 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8277 (mtpp) REVERT: C 44 ASP cc_start: 0.8113 (m-30) cc_final: 0.7701 (m-30) REVERT: C 61 ASP cc_start: 0.8762 (t0) cc_final: 0.8429 (m-30) REVERT: C 87 MET cc_start: 0.9321 (mtp) cc_final: 0.9113 (mtp) REVERT: F 10 VAL cc_start: 0.9313 (p) cc_final: 0.8900 (m) REVERT: F 41 LYS cc_start: 0.9292 (mttt) cc_final: 0.9068 (mmtt) REVERT: F 87 MET cc_start: 0.9253 (mtp) cc_final: 0.8999 (mtp) REVERT: G 5 ASN cc_start: 0.8947 (t0) cc_final: 0.8666 (t0) REVERT: G 53 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8179 (mp0) REVERT: G 102 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7323 (tm-30) REVERT: H 20 TYR cc_start: 0.9096 (t80) cc_final: 0.8681 (t80) REVERT: H 135 GLU cc_start: 0.8614 (mp0) cc_final: 0.8276 (mp0) REVERT: I 20 TYR cc_start: 0.9080 (t80) cc_final: 0.8465 (t80) REVERT: I 32 SER cc_start: 0.8935 (t) cc_final: 0.8656 (m) REVERT: I 43 LYS cc_start: 0.9032 (mtpt) cc_final: 0.7845 (mptt) REVERT: J 101 ASN cc_start: 0.8702 (m-40) cc_final: 0.8488 (m110) REVERT: K 5 ASN cc_start: 0.8673 (t0) cc_final: 0.8323 (t0) REVERT: K 118 ASP cc_start: 0.8115 (t0) cc_final: 0.7854 (t0) REVERT: L 29 ASN cc_start: 0.9310 (t0) cc_final: 0.9086 (t0) REVERT: L 101 ASN cc_start: 0.8962 (m-40) cc_final: 0.8540 (m-40) REVERT: L 121 ARG cc_start: 0.8694 (mtp-110) cc_final: 0.8275 (ttm-80) outliers start: 44 outliers final: 38 residues processed: 243 average time/residue: 0.1399 time to fit residues: 47.7769 Evaluate side-chains 228 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 51 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.086776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.071929 restraints weight = 20838.496| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 1.64 r_work: 0.2499 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2368 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14520 Z= 0.201 Angle : 0.553 4.868 19800 Z= 0.292 Chirality : 0.046 0.160 2148 Planarity : 0.004 0.033 2580 Dihedral : 4.637 17.973 1980 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.73 % Allowed : 10.47 % Favored : 84.80 % 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 aren not related in a simple way. whole: -0.66 (0.17), residues: 1824 helix: 1.63 (0.42), residues: 144 sheet: -0.36 (0.16), residues: 936 loop : -0.79 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 121 TYR 0.011 0.002 TYR E 108 PHE 0.013 0.002 PHE J 120 TRP 0.011 0.002 TRP E 36 Details of bonding type rmsd covalent geometry : bond 0.00493 (14520) covalent geometry : angle 0.55285 (19800) hydrogen bonds : bond 0.03406 ( 462) hydrogen bonds : angle 5.58735 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 0.473 Fit side-chains REVERT: A 134 LYS cc_start: 0.9282 (mtpt) cc_final: 0.9008 (mtmt) REVERT: B 61 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: C 11 LYS cc_start: 0.9483 (mttp) cc_final: 0.9262 (mttt) REVERT: C 43 LYS cc_start: 0.9085 (mtpt) cc_final: 0.8230 (mtpp) REVERT: C 44 ASP cc_start: 0.8243 (m-30) cc_final: 0.7992 (m-30) REVERT: C 61 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: C 87 MET cc_start: 0.9509 (mtp) cc_final: 0.9267 (mtp) REVERT: D 58 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8107 (p) REVERT: F 8 MET cc_start: 0.9052 (mmm) cc_final: 0.8528 (mtm) REVERT: F 10 VAL cc_start: 0.9344 (p) cc_final: 0.8950 (m) REVERT: F 114 ASN cc_start: 0.9029 (t0) cc_final: 0.8782 (t0) REVERT: G 53 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8186 (mp0) REVERT: G 102 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7540 (tm-30) REVERT: I 20 TYR cc_start: 0.9057 (t80) cc_final: 0.8644 (t80) REVERT: I 32 SER cc_start: 0.9005 (t) cc_final: 0.8677 (m) REVERT: I 43 LYS cc_start: 0.9081 (mtpt) cc_final: 0.7658 (mptt) REVERT: J 8 MET cc_start: 0.8694 (mmp) cc_final: 0.8480 (mmt) REVERT: J 101 ASN cc_start: 0.8845 (m-40) cc_final: 0.8589 (m110) REVERT: K 5 ASN cc_start: 0.8673 (t0) cc_final: 0.8264 (t0) REVERT: L 29 ASN cc_start: 0.9230 (t0) cc_final: 0.8960 (t0) REVERT: L 101 ASN cc_start: 0.8969 (m-40) cc_final: 0.8543 (m-40) outliers start: 71 outliers final: 56 residues processed: 253 average time/residue: 0.1436 time to fit residues: 50.6325 Evaluate side-chains 240 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.087676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.072785 restraints weight = 20599.938| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 1.63 r_work: 0.2511 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2379 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14520 Z= 0.165 Angle : 0.520 5.642 19800 Z= 0.274 Chirality : 0.045 0.158 2148 Planarity : 0.003 0.034 2580 Dihedral : 4.459 16.362 1980 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.13 % Allowed : 11.13 % Favored : 83.73 % 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 aren not related in a simple way. whole: -0.64 (0.17), residues: 1824 helix: 1.68 (0.42), residues: 144 sheet: -0.37 (0.16), residues: 936 loop : -0.77 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 121 TYR 0.010 0.001 TYR C 108 PHE 0.011 0.002 PHE J 120 TRP 0.010 0.001 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00404 (14520) covalent geometry : angle 0.51981 (19800) hydrogen bonds : bond 0.03173 ( 462) hydrogen bonds : angle 5.35543 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 184 time to evaluate : 0.558 Fit side-chains REVERT: A 134 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8977 (mtmt) REVERT: C 11 LYS cc_start: 0.9472 (mttp) cc_final: 0.9249 (mttt) REVERT: C 43 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8183 (mtpp) REVERT: C 61 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8375 (t70) REVERT: C 87 MET cc_start: 0.9480 (mtp) cc_final: 0.9243 (mtp) REVERT: D 58 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8078 (p) REVERT: F 8 MET cc_start: 0.8978 (mmm) cc_final: 0.8489 (mtm) REVERT: F 10 VAL cc_start: 0.9326 (p) cc_final: 0.8970 (m) REVERT: F 114 ASN cc_start: 0.8998 (t0) cc_final: 0.8722 (t0) REVERT: G 53 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8145 (mp0) REVERT: G 118 ASP cc_start: 0.7947 (m-30) cc_final: 0.7613 (m-30) REVERT: H 42 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8796 (t) REVERT: I 32 SER cc_start: 0.9010 (t) cc_final: 0.8672 (m) REVERT: I 43 LYS cc_start: 0.9084 (mtpt) cc_final: 0.7649 (mptt) REVERT: I 97 LEU cc_start: 0.8864 (mt) cc_final: 0.8619 (mt) REVERT: J 101 ASN cc_start: 0.8864 (m-40) cc_final: 0.8615 (m110) REVERT: K 5 ASN cc_start: 0.8642 (t0) cc_final: 0.8155 (t0) REVERT: K 118 ASP cc_start: 0.8168 (t0) cc_final: 0.7952 (t0) REVERT: K 135 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8149 (mp0) REVERT: L 29 ASN cc_start: 0.9284 (t0) cc_final: 0.8956 (t0) REVERT: L 101 ASN cc_start: 0.8971 (m-40) cc_final: 0.8578 (m-40) REVERT: L 118 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8260 (t0) outliers start: 77 outliers final: 58 residues processed: 251 average time/residue: 0.1312 time to fit residues: 46.9337 Evaluate side-chains 244 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0670 chunk 161 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 73 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.090986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.076265 restraints weight = 20409.149| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 1.62 r_work: 0.2581 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14520 Z= 0.090 Angle : 0.460 6.153 19800 Z= 0.239 Chirality : 0.043 0.158 2148 Planarity : 0.003 0.029 2580 Dihedral : 3.917 16.177 1980 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.93 % Allowed : 12.67 % Favored : 83.40 % 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 aren not related in a simple way. whole: -0.42 (0.17), residues: 1824 helix: 1.95 (0.40), residues: 144 sheet: -0.22 (0.16), residues: 936 loop : -0.64 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 121 TYR 0.009 0.001 TYR B 108 PHE 0.008 0.001 PHE B 120 TRP 0.007 0.001 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00211 (14520) covalent geometry : angle 0.46033 (19800) hydrogen bonds : bond 0.02680 ( 462) hydrogen bonds : angle 4.89943 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 205 time to evaluate : 0.574 Fit side-chains REVERT: A 10 VAL cc_start: 0.9288 (p) cc_final: 0.8915 (m) REVERT: A 134 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8943 (mtmt) REVERT: B 61 ASP cc_start: 0.8559 (m-30) cc_final: 0.8105 (m-30) REVERT: C 10 VAL cc_start: 0.9364 (p) cc_final: 0.9066 (m) REVERT: C 11 LYS cc_start: 0.9423 (mttp) cc_final: 0.9177 (mttm) REVERT: C 43 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8594 (mtpp) REVERT: C 87 MET cc_start: 0.9351 (mtp) cc_final: 0.9151 (mtp) REVERT: D 58 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8088 (p) REVERT: F 10 VAL cc_start: 0.9282 (p) cc_final: 0.8960 (m) REVERT: H 135 GLU cc_start: 0.8491 (mp0) cc_final: 0.8110 (mp0) REVERT: I 32 SER cc_start: 0.8977 (t) cc_final: 0.8635 (m) REVERT: I 43 LYS cc_start: 0.8951 (mtpt) cc_final: 0.7656 (mptt) REVERT: K 5 ASN cc_start: 0.8571 (t0) cc_final: 0.8070 (t0) REVERT: K 118 ASP cc_start: 0.8107 (t0) cc_final: 0.7744 (t0) REVERT: L 29 ASN cc_start: 0.9285 (t0) cc_final: 0.8880 (t0) REVERT: L 101 ASN cc_start: 0.8745 (m-40) cc_final: 0.8475 (m-40) outliers start: 59 outliers final: 50 residues processed: 253 average time/residue: 0.1423 time to fit residues: 50.7295 Evaluate side-chains 243 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 34 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 47 optimal weight: 0.4980 chunk 94 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.084924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.070089 restraints weight = 21016.953| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 1.65 r_work: 0.2466 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2335 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14520 Z= 0.266 Angle : 0.607 6.891 19800 Z= 0.320 Chirality : 0.048 0.167 2148 Planarity : 0.004 0.037 2580 Dihedral : 4.803 19.354 1980 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.00 % Allowed : 12.13 % Favored : 82.87 % 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 aren not related in a simple way. whole: -0.74 (0.17), residues: 1824 helix: 1.61 (0.43), residues: 144 sheet: -0.40 (0.16), residues: 936 loop : -0.87 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 121 TYR 0.011 0.002 TYR C 108 PHE 0.018 0.002 PHE C 120 TRP 0.013 0.002 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00660 (14520) covalent geometry : angle 0.60682 (19800) hydrogen bonds : bond 0.03676 ( 462) hydrogen bonds : angle 5.47919 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 0.561 Fit side-chains REVERT: A 134 LYS cc_start: 0.9279 (mtpt) cc_final: 0.9025 (mtmt) REVERT: C 11 LYS cc_start: 0.9475 (mttp) cc_final: 0.9263 (mttt) REVERT: D 58 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8088 (p) REVERT: F 8 MET cc_start: 0.9003 (mmm) cc_final: 0.8398 (mtm) REVERT: F 10 VAL cc_start: 0.9341 (p) cc_final: 0.8964 (m) REVERT: G 102 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8159 (tm-30) REVERT: G 118 ASP cc_start: 0.8119 (m-30) cc_final: 0.7838 (m-30) REVERT: I 32 SER cc_start: 0.9005 (t) cc_final: 0.8681 (m) REVERT: I 43 LYS cc_start: 0.9095 (mtpt) cc_final: 0.7781 (mptt) REVERT: K 5 ASN cc_start: 0.8757 (t0) cc_final: 0.8210 (t0) REVERT: L 29 ASN cc_start: 0.9276 (t0) cc_final: 0.8898 (t0) REVERT: L 41 LYS cc_start: 0.9068 (mttm) cc_final: 0.6871 (tptp) REVERT: L 101 ASN cc_start: 0.8954 (m-40) cc_final: 0.8495 (m-40) REVERT: L 153 GLU cc_start: 0.8958 (pm20) cc_final: 0.8654 (pm20) outliers start: 75 outliers final: 61 residues processed: 250 average time/residue: 0.1383 time to fit residues: 49.2739 Evaluate side-chains 242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.087914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.073217 restraints weight = 20712.348| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 1.63 r_work: 0.2529 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14520 Z= 0.120 Angle : 0.503 6.216 19800 Z= 0.263 Chirality : 0.044 0.160 2148 Planarity : 0.003 0.032 2580 Dihedral : 4.260 17.450 1980 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.00 % Allowed : 13.40 % Favored : 82.60 % 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 aren not related in a simple way. whole: -0.61 (0.17), residues: 1824 helix: 1.79 (0.42), residues: 144 sheet: -0.34 (0.16), residues: 936 loop : -0.77 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 121 TYR 0.008 0.001 TYR B 108 PHE 0.009 0.001 PHE E 120 TRP 0.010 0.001 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00291 (14520) covalent geometry : angle 0.50335 (19800) hydrogen bonds : bond 0.02917 ( 462) hydrogen bonds : angle 5.05484 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 0.594 Fit side-chains REVERT: A 10 VAL cc_start: 0.9235 (p) cc_final: 0.8872 (m) REVERT: A 134 LYS cc_start: 0.9267 (mtpt) cc_final: 0.8979 (mtmt) REVERT: B 61 ASP cc_start: 0.8477 (m-30) cc_final: 0.8129 (m-30) REVERT: C 11 LYS cc_start: 0.9447 (mttp) cc_final: 0.9210 (mttt) REVERT: D 58 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.7800 (p) REVERT: D 59 TYR cc_start: 0.8867 (m-80) cc_final: 0.8632 (m-10) REVERT: F 8 MET cc_start: 0.8978 (mmm) cc_final: 0.8296 (mtm) REVERT: F 10 VAL cc_start: 0.9296 (p) cc_final: 0.8955 (m) REVERT: G 102 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8031 (tm-30) REVERT: G 118 ASP cc_start: 0.8018 (m-30) cc_final: 0.7752 (m-30) REVERT: H 135 GLU cc_start: 0.8628 (mp0) cc_final: 0.8236 (mp0) REVERT: I 32 SER cc_start: 0.8994 (t) cc_final: 0.8562 (m) REVERT: I 43 LYS cc_start: 0.9064 (mtpt) cc_final: 0.7738 (mptt) REVERT: J 101 ASN cc_start: 0.8860 (m-40) cc_final: 0.8559 (m110) REVERT: K 5 ASN cc_start: 0.8649 (t0) cc_final: 0.8079 (t0) REVERT: K 42 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8676 (p) REVERT: L 29 ASN cc_start: 0.9286 (t0) cc_final: 0.8860 (t0) REVERT: L 41 LYS cc_start: 0.8990 (mttm) cc_final: 0.6942 (tptp) REVERT: L 101 ASN cc_start: 0.8956 (m-40) cc_final: 0.8571 (m-40) outliers start: 60 outliers final: 55 residues processed: 238 average time/residue: 0.1362 time to fit residues: 46.6538 Evaluate side-chains 242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.086275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.071550 restraints weight = 20917.474| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 1.63 r_work: 0.2499 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2367 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14520 Z= 0.181 Angle : 0.546 6.528 19800 Z= 0.287 Chirality : 0.045 0.161 2148 Planarity : 0.004 0.033 2580 Dihedral : 4.480 17.623 1980 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.47 % Allowed : 13.40 % Favored : 82.13 % 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 aren not related in a simple way. whole: -0.68 (0.17), residues: 1824 helix: 1.70 (0.42), residues: 144 sheet: -0.37 (0.16), residues: 936 loop : -0.84 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 121 TYR 0.015 0.002 TYR L 59 PHE 0.013 0.002 PHE E 120 TRP 0.011 0.001 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00448 (14520) covalent geometry : angle 0.54554 (19800) hydrogen bonds : bond 0.03223 ( 462) hydrogen bonds : angle 5.19254 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.573 Fit side-chains REVERT: A 134 LYS cc_start: 0.9271 (mtpt) cc_final: 0.9021 (mtmt) REVERT: B 61 ASP cc_start: 0.8484 (m-30) cc_final: 0.8124 (m-30) REVERT: C 11 LYS cc_start: 0.9454 (mttp) cc_final: 0.9241 (mttt) REVERT: C 63 GLU cc_start: 0.8208 (pm20) cc_final: 0.7978 (pm20) REVERT: D 58 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.7799 (p) REVERT: D 59 TYR cc_start: 0.8867 (m-80) cc_final: 0.8636 (m-10) REVERT: F 8 MET cc_start: 0.8979 (mmm) cc_final: 0.8330 (mtm) REVERT: F 10 VAL cc_start: 0.9318 (p) cc_final: 0.8972 (m) REVERT: G 5 ASN cc_start: 0.8981 (t0) cc_final: 0.8714 (t0) REVERT: G 102 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8024 (tm-30) REVERT: G 118 ASP cc_start: 0.8072 (m-30) cc_final: 0.7795 (m-30) REVERT: I 32 SER cc_start: 0.9021 (t) cc_final: 0.8570 (m) REVERT: I 43 LYS cc_start: 0.9090 (mtpt) cc_final: 0.7762 (mptt) REVERT: J 101 ASN cc_start: 0.8906 (m-40) cc_final: 0.8579 (m110) REVERT: K 5 ASN cc_start: 0.8741 (t0) cc_final: 0.8165 (t0) REVERT: K 42 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8534 (p) REVERT: L 29 ASN cc_start: 0.9284 (t0) cc_final: 0.8854 (t0) REVERT: L 41 LYS cc_start: 0.9027 (mttm) cc_final: 0.6953 (tptp) REVERT: L 101 ASN cc_start: 0.8985 (m-40) cc_final: 0.8564 (m-40) outliers start: 67 outliers final: 61 residues processed: 244 average time/residue: 0.1382 time to fit residues: 48.0317 Evaluate side-chains 248 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.089345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.074767 restraints weight = 20580.775| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 1.61 r_work: 0.2559 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14520 Z= 0.100 Angle : 0.483 5.787 19800 Z= 0.252 Chirality : 0.043 0.157 2148 Planarity : 0.003 0.034 2580 Dihedral : 4.011 15.914 1980 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.80 % Allowed : 13.87 % Favored : 82.33 % 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 aren not related in a simple way. whole: -0.51 (0.17), residues: 1824 helix: 1.94 (0.41), residues: 144 sheet: -0.28 (0.16), residues: 936 loop : -0.72 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 121 TYR 0.009 0.001 TYR L 59 PHE 0.008 0.001 PHE J 120 TRP 0.010 0.001 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00242 (14520) covalent geometry : angle 0.48310 (19800) hydrogen bonds : bond 0.02713 ( 462) hydrogen bonds : angle 4.83232 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.571 Fit side-chains REVERT: A 10 VAL cc_start: 0.9217 (p) cc_final: 0.8861 (m) REVERT: A 134 LYS cc_start: 0.9237 (mtpt) cc_final: 0.8968 (mtmt) REVERT: B 61 ASP cc_start: 0.8422 (m-30) cc_final: 0.7997 (m-30) REVERT: B 87 MET cc_start: 0.9335 (mtm) cc_final: 0.9099 (mtp) REVERT: C 10 VAL cc_start: 0.9388 (p) cc_final: 0.9105 (m) REVERT: C 11 LYS cc_start: 0.9412 (mttp) cc_final: 0.9176 (mttt) REVERT: C 63 GLU cc_start: 0.8203 (pm20) cc_final: 0.7930 (pm20) REVERT: D 58 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.7917 (p) REVERT: D 59 TYR cc_start: 0.8795 (m-80) cc_final: 0.8546 (m-10) REVERT: F 8 MET cc_start: 0.8971 (mmm) cc_final: 0.8431 (mtm) REVERT: F 10 VAL cc_start: 0.9263 (p) cc_final: 0.8941 (m) REVERT: G 5 ASN cc_start: 0.8956 (t0) cc_final: 0.8732 (t0) REVERT: G 102 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7939 (tm-30) REVERT: H 57 ASP cc_start: 0.8503 (t0) cc_final: 0.8198 (t0) REVERT: H 135 GLU cc_start: 0.8501 (mp0) cc_final: 0.8103 (mp0) REVERT: I 32 SER cc_start: 0.9050 (t) cc_final: 0.8573 (m) REVERT: I 43 LYS cc_start: 0.9013 (mtpt) cc_final: 0.7680 (mptt) REVERT: J 101 ASN cc_start: 0.8875 (m-40) cc_final: 0.8548 (m110) REVERT: J 135 GLU cc_start: 0.8413 (mp0) cc_final: 0.8186 (mp0) REVERT: K 5 ASN cc_start: 0.8647 (t0) cc_final: 0.8082 (t0) REVERT: K 42 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8508 (p) REVERT: K 118 ASP cc_start: 0.8078 (t0) cc_final: 0.7709 (t0) REVERT: K 135 GLU cc_start: 0.8249 (mp0) cc_final: 0.7709 (pm20) REVERT: L 29 ASN cc_start: 0.9297 (t0) cc_final: 0.9061 (t0) REVERT: L 41 LYS cc_start: 0.9014 (mttm) cc_final: 0.7127 (tptp) REVERT: L 101 ASN cc_start: 0.8856 (m-40) cc_final: 0.8206 (m-40) outliers start: 57 outliers final: 54 residues processed: 248 average time/residue: 0.1329 time to fit residues: 47.4429 Evaluate side-chains 254 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 198 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 178 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.089290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.074669 restraints weight = 20578.904| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 1.62 r_work: 0.2560 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14520 Z= 0.107 Angle : 0.487 5.868 19800 Z= 0.253 Chirality : 0.043 0.153 2148 Planarity : 0.003 0.033 2580 Dihedral : 3.994 15.863 1980 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.87 % Allowed : 14.00 % Favored : 82.13 % 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 aren not related in a simple way. whole: -0.45 (0.17), residues: 1824 helix: 2.06 (0.41), residues: 144 sheet: -0.24 (0.16), residues: 936 loop : -0.72 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 121 TYR 0.009 0.001 TYR B 108 PHE 0.009 0.001 PHE B 120 TRP 0.010 0.001 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00260 (14520) covalent geometry : angle 0.48713 (19800) hydrogen bonds : bond 0.02747 ( 462) hydrogen bonds : angle 4.80595 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.85 seconds wall clock time: 53 minutes 28.23 seconds (3208.23 seconds total)