Starting phenix.real_space_refine on Thu Jun 12 14:29:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k36_36845/06_2025/8k36_36845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k36_36845/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k36_36845/06_2025/8k36_36845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k36_36845/06_2025/8k36_36845.map" model { file = "/net/cci-nas-00/data/ceres_data/8k36_36845/06_2025/8k36_36845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k36_36845/06_2025/8k36_36845.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.02, per 1000 atoms: 0.57 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: 3.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.16 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: 4.36 Time building geometry restraints manager: 3.77 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: 0.01 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: 0.540 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.150 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP I 18 PHE 0.017 0.002 PHE B 120 TYR 0.012 0.002 TYR K 20 ARG 0.004 0.001 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.20235 ( 462) hydrogen bonds : angle 9.68250 ( 1416) covalent geometry : bond 0.00830 (14520) covalent geometry : angle 0.81227 (19800) *********************** 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 : 1.619 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: 0.7590 (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: 0.7669 (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: 0.8104 (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: 0.3315 time to fit residues: 169.1657 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 : 1.598 ------------------------------------------------------------------------------- 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 151 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.2880 r_free = 0.2880 target = 0.088569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.074013 restraints weight = 20483.942| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 1.60 r_work: 0.2537 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2300 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= 0.190 Angle : 0.576 5.142 19800 Z= 0.307 Chirality : 0.047 0.151 2148 Planarity : 0.004 0.029 2580 Dihedral : 5.163 56.417 1986 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.00 % Allowed : 9.40 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 1824 helix: 1.46 (0.44), residues: 144 sheet: -0.48 (0.15), residues: 936 loop : -0.92 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 36 PHE 0.015 0.002 PHE E 120 TYR 0.014 0.002 TYR C 108 ARG 0.005 0.001 ARG I 148 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 462) hydrogen bonds : angle 6.44709 ( 1416) covalent geometry : bond 0.00461 (14520) covalent geometry : angle 0.57556 (19800) *********************** 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 276 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 1.532 Fit side-chains REVERT: A 134 LYS cc_start: 0.9313 (mtpt) cc_final: 0.9057 (mtmt) REVERT: B 61 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: B 63 GLU cc_start: 0.8325 (pm20) cc_final: 0.8085 (tp30) REVERT: C 11 LYS cc_start: 0.9471 (mttp) cc_final: 0.9264 (mttt) REVERT: C 43 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8233 (mtpp) REVERT: C 44 ASP cc_start: 0.8182 (m-30) cc_final: 0.7519 (m-30) REVERT: C 61 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: C 87 MET cc_start: 0.9316 (mtp) cc_final: 0.9093 (mtp) REVERT: C 114 ASN cc_start: 0.8945 (t0) cc_final: 0.8727 (t0) REVERT: D 58 SER cc_start: 0.8465 (m) cc_final: 0.8150 (p) REVERT: F 5 ASN cc_start: 0.8620 (t0) cc_final: 0.8325 (t0) REVERT: F 61 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: F 87 MET cc_start: 0.9283 (mtp) cc_final: 0.9067 (mtp) REVERT: G 53 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8159 (mp0) REVERT: G 101 ASN cc_start: 0.8861 (m110) cc_final: 0.8649 (m-40) REVERT: G 102 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7259 (tm-30) REVERT: G 118 ASP cc_start: 0.7809 (t0) cc_final: 0.7572 (t0) REVERT: H 135 GLU cc_start: 0.8664 (mp0) cc_final: 0.8408 (mp0) REVERT: I 20 TYR cc_start: 0.9086 (t80) cc_final: 0.8764 (t80) REVERT: I 32 SER cc_start: 0.8968 (t) cc_final: 0.8646 (m) REVERT: I 38 ARG cc_start: 0.9147 (ttt180) cc_final: 0.8910 (ttt180) REVERT: I 43 LYS cc_start: 0.9223 (mtpt) cc_final: 0.7755 (mptt) REVERT: I 97 LEU cc_start: 0.8969 (mt) cc_final: 0.8690 (mt) REVERT: J 135 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8467 (mp0) REVERT: K 5 ASN cc_start: 0.9000 (t0) cc_final: 0.8689 (t0) REVERT: K 38 ARG cc_start: 0.9158 (ttt180) cc_final: 0.8875 (ttt90) REVERT: L 29 ASN cc_start: 0.9371 (t0) cc_final: 0.9148 (t0) REVERT: L 101 ASN cc_start: 0.8947 (m-40) cc_final: 0.8415 (m-40) outliers start: 30 outliers final: 23 residues processed: 270 average time/residue: 0.3268 time to fit residues: 124.7339 Evaluate side-chains 213 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 54 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 F residue 83 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 3 VAL 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 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 5 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 33 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 = 0.2818 r_free = 0.2818 target = 0.085099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.070452 restraints weight = 20971.392| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 1.62 r_work: 0.2479 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2349 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14520 Z= 0.241 Angle : 0.591 5.474 19800 Z= 0.315 Chirality : 0.048 0.160 2148 Planarity : 0.004 0.037 2580 Dihedral : 5.299 56.144 1984 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.00 % Allowed : 10.80 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 1824 helix: 1.48 (0.43), residues: 144 sheet: -0.51 (0.15), residues: 936 loop : -0.96 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 36 PHE 0.015 0.002 PHE C 120 TYR 0.011 0.002 TYR C 108 ARG 0.003 0.001 ARG I 148 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 462) hydrogen bonds : angle 6.08838 ( 1416) covalent geometry : bond 0.00593 (14520) covalent geometry : angle 0.59104 (19800) *********************** 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 253 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 1.559 Fit side-chains REVERT: A 134 LYS cc_start: 0.9328 (mtpt) cc_final: 0.9110 (mtmt) REVERT: B 61 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: C 11 LYS cc_start: 0.9490 (mttp) cc_final: 0.9278 (mttt) REVERT: C 43 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8346 (mtpp) REVERT: C 44 ASP cc_start: 0.8286 (m-30) cc_final: 0.7618 (m-30) REVERT: C 87 MET cc_start: 0.9566 (mtp) cc_final: 0.9362 (mtp) REVERT: C 114 ASN cc_start: 0.8944 (t0) cc_final: 0.8733 (t0) REVERT: F 8 MET cc_start: 0.9081 (mmm) cc_final: 0.8421 (mtm) REVERT: G 5 ASN cc_start: 0.9049 (t0) cc_final: 0.8811 (t0) REVERT: G 53 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8245 (mp0) REVERT: G 118 ASP cc_start: 0.7797 (t0) cc_final: 0.7531 (t0) REVERT: H 29 ASN cc_start: 0.9253 (t0) cc_final: 0.9046 (t0) REVERT: I 20 TYR cc_start: 0.9051 (t80) cc_final: 0.8712 (t80) REVERT: I 32 SER cc_start: 0.9005 (t) cc_final: 0.8658 (m) REVERT: I 43 LYS cc_start: 0.9120 (mtpt) cc_final: 0.7570 (mptt) REVERT: I 97 LEU cc_start: 0.8931 (mt) cc_final: 0.8597 (mt) REVERT: J 101 ASN cc_start: 0.8813 (m-40) cc_final: 0.8592 (m110) REVERT: K 5 ASN cc_start: 0.8811 (t0) cc_final: 0.8534 (t0) REVERT: K 118 ASP cc_start: 0.8235 (t0) cc_final: 0.7837 (t0) REVERT: L 29 ASN cc_start: 0.9240 (t0) cc_final: 0.8989 (t0) REVERT: L 101 ASN cc_start: 0.8909 (m-40) cc_final: 0.8398 (m-40) outliers start: 60 outliers final: 52 residues processed: 250 average time/residue: 0.2878 time to fit residues: 101.3889 Evaluate side-chains 239 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 32 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 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU 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 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP 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 H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 81 SER 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 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 126 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 113 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.2897 r_free = 0.2897 target = 0.090205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.075683 restraints weight = 20391.020| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.61 r_work: 0.2574 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14520 Z= 0.089 Angle : 0.468 4.918 19800 Z= 0.245 Chirality : 0.043 0.148 2148 Planarity : 0.003 0.028 2580 Dihedral : 4.279 53.266 1982 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.07 % Allowed : 12.40 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 1824 helix: 1.81 (0.41), residues: 144 sheet: -0.36 (0.16), residues: 936 loop : -0.72 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 36 PHE 0.008 0.001 PHE B 120 TYR 0.008 0.001 TYR B 108 ARG 0.004 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 462) hydrogen bonds : angle 5.20368 ( 1416) covalent geometry : bond 0.00206 (14520) covalent geometry : angle 0.46800 (19800) *********************** 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 265 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 1.509 Fit side-chains REVERT: A 10 VAL cc_start: 0.9204 (p) cc_final: 0.8844 (m) REVERT: A 134 LYS cc_start: 0.9290 (mtpt) cc_final: 0.8992 (mtmt) REVERT: B 61 ASP cc_start: 0.8654 (m-30) cc_final: 0.8228 (m-30) REVERT: C 10 VAL cc_start: 0.9353 (p) cc_final: 0.9054 (m) REVERT: C 11 LYS cc_start: 0.9410 (mttp) cc_final: 0.9173 (mttt) REVERT: C 43 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8464 (mtpp) REVERT: C 87 MET cc_start: 0.9294 (mtp) cc_final: 0.9092 (mtp) REVERT: E 84 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8663 (pp) REVERT: F 10 VAL cc_start: 0.9250 (p) cc_final: 0.8878 (m) REVERT: H 29 ASN cc_start: 0.9277 (t0) cc_final: 0.8991 (t0) REVERT: H 135 GLU cc_start: 0.8543 (mp0) cc_final: 0.8254 (mp0) REVERT: I 20 TYR cc_start: 0.9044 (t80) cc_final: 0.8405 (t80) REVERT: I 32 SER cc_start: 0.8982 (t) cc_final: 0.8639 (m) REVERT: I 43 LYS cc_start: 0.9005 (mtpt) cc_final: 0.7573 (mptt) REVERT: J 87 MET cc_start: 0.8689 (mtm) cc_final: 0.8475 (mtm) REVERT: J 101 ASN cc_start: 0.8803 (m-40) cc_final: 0.8551 (m110) REVERT: K 5 ASN cc_start: 0.8587 (t0) cc_final: 0.8246 (t0) REVERT: K 38 ARG cc_start: 0.9233 (ttt180) cc_final: 0.8910 (ttt90) REVERT: K 74 GLN cc_start: 0.9079 (tt0) cc_final: 0.8704 (tt0) REVERT: K 102 GLU cc_start: 0.8030 (tt0) cc_final: 0.7806 (tm-30) REVERT: K 118 ASP cc_start: 0.8114 (t0) cc_final: 0.7711 (t0) REVERT: K 135 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8106 (mp0) REVERT: L 29 ASN cc_start: 0.9275 (t0) cc_final: 0.8959 (t0) REVERT: L 101 ASN cc_start: 0.8771 (m-40) cc_final: 0.8301 (m-40) outliers start: 46 outliers final: 39 residues processed: 260 average time/residue: 0.2843 time to fit residues: 105.2272 Evaluate side-chains 231 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 117 VAL 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 124 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 37 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 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 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 124 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 81 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 111 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 overall best weight: 2.6982 ------------------------------------------------------------------------------- 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 = 0.2838 r_free = 0.2838 target = 0.086510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.071795 restraints weight = 20802.575| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 1.63 r_work: 0.2504 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2373 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14520 Z= 0.175 Angle : 0.537 6.502 19800 Z= 0.283 Chirality : 0.045 0.158 2148 Planarity : 0.003 0.032 2580 Dihedral : 4.435 15.918 1980 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.33 % Allowed : 12.13 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 1824 helix: 1.71 (0.41), residues: 144 sheet: -0.40 (0.16), residues: 936 loop : -0.76 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 PHE 0.014 0.002 PHE E 120 TYR 0.011 0.002 TYR C 108 ARG 0.004 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 462) hydrogen bonds : angle 5.27384 ( 1416) covalent geometry : bond 0.00431 (14520) covalent geometry : angle 0.53684 (19800) *********************** 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 270 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 190 time to evaluate : 1.650 Fit side-chains REVERT: A 61 ASP cc_start: 0.8748 (t0) cc_final: 0.8524 (t0) REVERT: A 134 LYS cc_start: 0.9271 (mtpt) cc_final: 0.8988 (mtmt) REVERT: B 61 ASP cc_start: 0.8579 (m-30) cc_final: 0.8115 (m-30) REVERT: C 11 LYS cc_start: 0.9442 (mttp) cc_final: 0.9226 (mttt) REVERT: E 84 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8719 (pp) REVERT: F 8 MET cc_start: 0.9044 (mmm) cc_final: 0.8539 (mtm) REVERT: F 10 VAL cc_start: 0.9325 (p) cc_final: 0.8972 (m) REVERT: H 29 ASN cc_start: 0.9239 (t0) cc_final: 0.8878 (t0) REVERT: H 42 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8786 (t) REVERT: H 135 GLU cc_start: 0.8659 (mp0) cc_final: 0.8310 (mp0) REVERT: I 32 SER cc_start: 0.9042 (t) cc_final: 0.8686 (m) REVERT: I 43 LYS cc_start: 0.9095 (mtpt) cc_final: 0.7657 (mptt) REVERT: I 97 LEU cc_start: 0.8857 (mt) cc_final: 0.8558 (mt) REVERT: J 87 MET cc_start: 0.8833 (mtm) cc_final: 0.8587 (mtm) REVERT: J 101 ASN cc_start: 0.8843 (m-40) cc_final: 0.8582 (m110) REVERT: K 5 ASN cc_start: 0.8737 (t0) cc_final: 0.8332 (t0) REVERT: K 102 GLU cc_start: 0.8132 (tt0) cc_final: 0.7392 (mt-10) REVERT: L 29 ASN cc_start: 0.9279 (t0) cc_final: 0.8948 (t0) REVERT: L 101 ASN cc_start: 0.8923 (m-40) cc_final: 0.8435 (m-40) outliers start: 80 outliers final: 63 residues processed: 262 average time/residue: 0.2871 time to fit residues: 106.7994 Evaluate side-chains 249 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 97 LEU 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 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU 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 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 54 SER Chi-restraints excluded: chain E residue 84 LEU 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 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 G residue 124 VAL 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 I residue 81 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.084884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.070108 restraints weight = 21172.823| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 1.63 r_work: 0.2474 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2342 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14520 Z= 0.223 Angle : 0.574 6.743 19800 Z= 0.303 Chirality : 0.047 0.162 2148 Planarity : 0.004 0.035 2580 Dihedral : 4.755 17.515 1980 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.27 % Allowed : 13.33 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 1824 helix: 1.58 (0.43), residues: 144 sheet: -0.48 (0.16), residues: 936 loop : -0.87 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 36 PHE 0.016 0.002 PHE C 120 TYR 0.011 0.002 TYR C 108 ARG 0.005 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 462) hydrogen bonds : angle 5.41832 ( 1416) covalent geometry : bond 0.00550 (14520) covalent geometry : angle 0.57379 (19800) *********************** 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 265 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 186 time to evaluate : 1.510 Fit side-chains REVERT: A 61 ASP cc_start: 0.8745 (t0) cc_final: 0.8537 (t0) REVERT: A 134 LYS cc_start: 0.9307 (mtpt) cc_final: 0.9085 (mtmt) REVERT: F 8 MET cc_start: 0.8961 (mmm) cc_final: 0.8365 (mtm) REVERT: F 10 VAL cc_start: 0.9353 (p) cc_final: 0.8994 (m) REVERT: F 114 ASN cc_start: 0.8974 (t0) cc_final: 0.8701 (t0) REVERT: H 29 ASN cc_start: 0.9271 (t0) cc_final: 0.8845 (t0) REVERT: H 42 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8779 (t) REVERT: I 8 MET cc_start: 0.8695 (mmm) cc_final: 0.8471 (mmm) REVERT: I 20 TYR cc_start: 0.9046 (t80) cc_final: 0.8609 (t80) REVERT: I 32 SER cc_start: 0.9032 (t) cc_final: 0.8684 (m) REVERT: I 43 LYS cc_start: 0.9117 (mtpt) cc_final: 0.7691 (mptt) REVERT: J 101 ASN cc_start: 0.8877 (m-40) cc_final: 0.8565 (m110) REVERT: K 5 ASN cc_start: 0.8750 (t0) cc_final: 0.8300 (t0) REVERT: L 29 ASN cc_start: 0.9291 (t0) cc_final: 0.8938 (t0) REVERT: L 101 ASN cc_start: 0.8908 (m-40) cc_final: 0.8357 (m-40) outliers start: 79 outliers final: 67 residues processed: 255 average time/residue: 0.2805 time to fit residues: 101.7481 Evaluate side-chains 250 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 182 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 51 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 81 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER 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 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 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 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 H residue 31 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 J residue 37 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR 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 118 ASP Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 122 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.2876 r_free = 0.2876 target = 0.088908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.074133 restraints weight = 20725.273| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 1.63 r_work: 0.2542 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14520 Z= 0.103 Angle : 0.486 6.553 19800 Z= 0.252 Chirality : 0.043 0.153 2148 Planarity : 0.003 0.031 2580 Dihedral : 4.110 15.743 1980 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.47 % Allowed : 14.27 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 1824 helix: 1.81 (0.41), residues: 144 sheet: -0.36 (0.16), residues: 936 loop : -0.71 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 PHE 0.009 0.001 PHE G 120 TYR 0.009 0.001 TYR G 108 ARG 0.005 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 462) hydrogen bonds : angle 4.91409 ( 1416) covalent geometry : bond 0.00246 (14520) covalent geometry : angle 0.48588 (19800) *********************** 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 262 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 195 time to evaluate : 1.865 Fit side-chains REVERT: A 10 VAL cc_start: 0.9231 (p) cc_final: 0.8873 (m) REVERT: A 134 LYS cc_start: 0.9256 (mtpt) cc_final: 0.8990 (mtmt) REVERT: B 61 ASP cc_start: 0.8494 (m-30) cc_final: 0.8054 (m-30) REVERT: F 8 MET cc_start: 0.8944 (mmm) cc_final: 0.8473 (mtm) REVERT: F 10 VAL cc_start: 0.9270 (p) cc_final: 0.8967 (m) REVERT: H 42 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8743 (t) REVERT: H 135 GLU cc_start: 0.8560 (mp0) cc_final: 0.8180 (mp0) REVERT: I 8 MET cc_start: 0.8644 (mmm) cc_final: 0.8388 (mmm) REVERT: I 20 TYR cc_start: 0.9021 (t80) cc_final: 0.8487 (t80) REVERT: I 32 SER cc_start: 0.8985 (t) cc_final: 0.8630 (m) REVERT: I 43 LYS cc_start: 0.9027 (mtpt) cc_final: 0.7664 (mptt) REVERT: J 101 ASN cc_start: 0.8876 (m-40) cc_final: 0.8605 (m110) REVERT: K 5 ASN cc_start: 0.8585 (t0) cc_final: 0.8075 (t0) REVERT: K 118 ASP cc_start: 0.8094 (t0) cc_final: 0.7757 (t0) REVERT: K 132 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8770 (t) REVERT: K 135 GLU cc_start: 0.8431 (mp0) cc_final: 0.8084 (mp0) REVERT: L 29 ASN cc_start: 0.9284 (t0) cc_final: 0.8859 (t0) REVERT: L 101 ASN cc_start: 0.8759 (m-40) cc_final: 0.8318 (m-40) outliers start: 67 outliers final: 58 residues processed: 251 average time/residue: 0.3504 time to fit residues: 127.7725 Evaluate side-chains 242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL 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 81 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 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 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 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 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 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 I residue 81 SER Chi-restraints excluded: chain I residue 84 LEU 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 J residue 124 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 37 SER 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 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 47 optimal weight: 0.3980 chunk 122 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.088693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.074071 restraints weight = 20661.603| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 1.61 r_work: 0.2543 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14520 Z= 0.109 Angle : 0.488 5.762 19800 Z= 0.254 Chirality : 0.043 0.154 2148 Planarity : 0.003 0.030 2580 Dihedral : 4.055 15.720 1980 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.67 % Allowed : 14.53 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 1824 helix: 1.99 (0.41), residues: 144 sheet: -0.30 (0.16), residues: 936 loop : -0.68 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 36 PHE 0.009 0.001 PHE E 120 TYR 0.009 0.001 TYR B 108 ARG 0.006 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 462) hydrogen bonds : angle 4.79641 ( 1416) covalent geometry : bond 0.00263 (14520) covalent geometry : angle 0.48754 (19800) *********************** 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 259 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 189 time to evaluate : 2.348 Fit side-chains REVERT: A 10 VAL cc_start: 0.9217 (p) cc_final: 0.8870 (m) REVERT: A 134 LYS cc_start: 0.9226 (mtpt) cc_final: 0.8979 (mtmt) REVERT: B 61 ASP cc_start: 0.8452 (m-30) cc_final: 0.7859 (m-30) REVERT: F 8 MET cc_start: 0.8957 (mmm) cc_final: 0.8294 (mtm) REVERT: F 10 VAL cc_start: 0.9318 (p) cc_final: 0.8963 (m) REVERT: H 42 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8721 (t) REVERT: H 135 GLU cc_start: 0.8501 (mp0) cc_final: 0.8106 (mp0) REVERT: I 20 TYR cc_start: 0.9027 (t80) cc_final: 0.8506 (t80) REVERT: I 32 SER cc_start: 0.8990 (t) cc_final: 0.8570 (m) REVERT: I 43 LYS cc_start: 0.9026 (mtpt) cc_final: 0.7692 (mptt) REVERT: J 101 ASN cc_start: 0.8898 (m-40) cc_final: 0.8615 (m110) REVERT: K 5 ASN cc_start: 0.8663 (t0) cc_final: 0.8101 (t0) REVERT: K 42 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8586 (p) REVERT: K 118 ASP cc_start: 0.8047 (t0) cc_final: 0.7721 (t0) REVERT: L 29 ASN cc_start: 0.9298 (t0) cc_final: 0.9086 (t0) REVERT: L 101 ASN cc_start: 0.8780 (m-40) cc_final: 0.8334 (m-40) outliers start: 70 outliers final: 62 residues processed: 246 average time/residue: 0.2997 time to fit residues: 106.8569 Evaluate side-chains 249 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL 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 81 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER 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 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 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 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 31 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 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 51 THR 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 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.2815 r_free = 0.2815 target = 0.085017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.070355 restraints weight = 20883.099| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 1.62 r_work: 0.2479 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14520 Z= 0.226 Angle : 0.586 7.890 19800 Z= 0.306 Chirality : 0.047 0.163 2148 Planarity : 0.004 0.037 2580 Dihedral : 4.661 17.179 1980 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.93 % Allowed : 14.60 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 1824 helix: 1.24 (0.41), residues: 156 sheet: -0.43 (0.16), residues: 936 loop : -0.77 (0.17), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 18 PHE 0.015 0.002 PHE C 120 TYR 0.011 0.002 TYR C 108 ARG 0.006 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 462) hydrogen bonds : angle 5.26156 ( 1416) covalent geometry : bond 0.00558 (14520) covalent geometry : angle 0.58553 (19800) *********************** 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 257 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 183 time to evaluate : 1.626 Fit side-chains REVERT: A 134 LYS cc_start: 0.9303 (mtpt) cc_final: 0.9101 (mtmt) REVERT: B 61 ASP cc_start: 0.8491 (m-30) cc_final: 0.8136 (m-30) REVERT: C 63 GLU cc_start: 0.8248 (pm20) cc_final: 0.8029 (pm20) REVERT: F 8 MET cc_start: 0.8984 (mmm) cc_final: 0.8382 (mtm) REVERT: F 10 VAL cc_start: 0.9332 (p) cc_final: 0.8980 (m) REVERT: F 21 LYS cc_start: 0.8885 (pttt) cc_final: 0.8645 (ptpp) REVERT: I 20 TYR cc_start: 0.8955 (t80) cc_final: 0.8551 (t80) REVERT: I 32 SER cc_start: 0.9084 (t) cc_final: 0.8604 (m) REVERT: I 43 LYS cc_start: 0.9101 (mtpt) cc_final: 0.7756 (mptt) REVERT: J 44 ASP cc_start: 0.8112 (t0) cc_final: 0.7906 (t70) REVERT: J 101 ASN cc_start: 0.8903 (m-40) cc_final: 0.8573 (m110) REVERT: K 5 ASN cc_start: 0.8772 (t0) cc_final: 0.8239 (t0) REVERT: K 42 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8551 (p) REVERT: K 135 GLU cc_start: 0.8446 (mp0) cc_final: 0.8112 (mp0) REVERT: L 29 ASN cc_start: 0.9304 (t0) cc_final: 0.8893 (t0) REVERT: L 101 ASN cc_start: 0.8989 (m-40) cc_final: 0.8569 (m-40) outliers start: 74 outliers final: 65 residues processed: 249 average time/residue: 0.2752 time to fit residues: 98.1792 Evaluate side-chains 247 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 181 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 117 VAL 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 81 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 51 THR 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 54 SER 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 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 H residue 31 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 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 51 THR 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 122 optimal weight: 0.0070 chunk 76 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 overall best weight: 1.4802 ------------------------------------------------------------------------------- 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 = 0.2861 r_free = 0.2861 target = 0.087995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.073321 restraints weight = 20727.041| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 1.62 r_work: 0.2534 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14520 Z= 0.114 Angle : 0.501 6.251 19800 Z= 0.260 Chirality : 0.044 0.154 2148 Planarity : 0.003 0.033 2580 Dihedral : 4.164 16.435 1980 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.33 % Allowed : 15.07 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 1824 helix: 1.85 (0.42), residues: 144 sheet: -0.34 (0.16), residues: 936 loop : -0.74 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 36 PHE 0.010 0.001 PHE F 120 TYR 0.009 0.001 TYR L 108 ARG 0.006 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.02834 ( 462) hydrogen bonds : angle 4.86531 ( 1416) covalent geometry : bond 0.00275 (14520) covalent geometry : angle 0.50096 (19800) ********************** 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 256 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 2.012 Fit side-chains REVERT: A 10 VAL cc_start: 0.9229 (p) cc_final: 0.8870 (m) REVERT: A 134 LYS cc_start: 0.9256 (mtpt) cc_final: 0.8995 (mtmt) REVERT: B 61 ASP cc_start: 0.8426 (m-30) cc_final: 0.7979 (m-30) REVERT: C 63 GLU cc_start: 0.8209 (pm20) cc_final: 0.7943 (pm20) REVERT: D 59 TYR cc_start: 0.8801 (m-80) cc_final: 0.8540 (m-10) REVERT: F 8 MET cc_start: 0.8955 (mmm) cc_final: 0.8285 (mtm) REVERT: F 10 VAL cc_start: 0.9280 (p) cc_final: 0.8955 (m) REVERT: F 21 LYS cc_start: 0.8883 (pttt) cc_final: 0.8618 (ptpp) REVERT: G 5 ASN cc_start: 0.9009 (t0) cc_final: 0.8745 (t0) REVERT: H 57 ASP cc_start: 0.8532 (t0) cc_final: 0.8264 (t0) REVERT: H 135 GLU cc_start: 0.8583 (mp0) cc_final: 0.8175 (mp0) REVERT: I 20 TYR cc_start: 0.9023 (t80) cc_final: 0.8518 (t80) REVERT: I 32 SER cc_start: 0.9062 (t) cc_final: 0.8588 (m) REVERT: I 43 LYS cc_start: 0.9010 (mtpt) cc_final: 0.7694 (mptt) REVERT: J 101 ASN cc_start: 0.8908 (m-40) cc_final: 0.8617 (m110) REVERT: K 5 ASN cc_start: 0.8695 (t0) cc_final: 0.8142 (t0) REVERT: K 42 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8521 (p) REVERT: K 118 ASP cc_start: 0.8021 (t0) cc_final: 0.7688 (t0) REVERT: K 135 GLU cc_start: 0.8242 (mp0) cc_final: 0.7881 (mp0) REVERT: L 29 ASN cc_start: 0.9306 (t0) cc_final: 0.9079 (t0) REVERT: L 101 ASN cc_start: 0.8805 (m-40) cc_final: 0.8379 (m-40) REVERT: L 151 MET cc_start: 0.9183 (mmp) cc_final: 0.8420 (mmp) outliers start: 65 outliers final: 63 residues processed: 244 average time/residue: 0.3280 time to fit residues: 115.2508 Evaluate side-chains 252 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 188 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER 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 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 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 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 H residue 31 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 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 51 THR 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 K residue 132 THR Chi-restraints excluded: chain L residue 31 LEU 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 129 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 0.0040 chunk 71 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- 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 = 0.088030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.073333 restraints weight = 20769.561| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 1.61 r_work: 0.2531 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14520 Z= 0.119 Angle : 0.508 7.144 19800 Z= 0.263 Chirality : 0.044 0.154 2148 Planarity : 0.003 0.034 2580 Dihedral : 4.103 16.256 1980 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.47 % Allowed : 15.00 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 1824 helix: 1.98 (0.41), residues: 144 sheet: -0.31 (0.16), residues: 936 loop : -0.72 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 PHE 0.010 0.001 PHE E 120 TYR 0.009 0.001 TYR B 108 ARG 0.006 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.02834 ( 462) hydrogen bonds : angle 4.81772 ( 1416) covalent geometry : bond 0.00290 (14520) covalent geometry : angle 0.50751 (19800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6655.94 seconds wall clock time: 117 minutes 32.82 seconds (7052.82 seconds total)