Starting phenix.real_space_refine on Thu Aug 6 18:28:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9osu_70811/08_2026/9osu_70811.cif Found real_map, /net/cci-nas-00/data/ceres_data/9osu_70811/08_2026/9osu_70811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9osu_70811/08_2026/9osu_70811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9osu_70811/08_2026/9osu_70811.map" model { file = "/net/cci-nas-00/data/ceres_data/9osu_70811/08_2026/9osu_70811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9osu_70811/08_2026/9osu_70811.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 76 5.16 5 C 10272 2.51 5 N 2855 2.21 5 O 3089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16292 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2414 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 300} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 17} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1313 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 1, 'TRANS': 169} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2456 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 300} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1335 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 169} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2431 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 20, 'TRANS': 300} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "F" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1366 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 169} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 891 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 915 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 753 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 748 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "M" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 920 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 750 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 3.39, per 1000 atoms: 0.21 Number of scatterers: 16292 At special positions: 0 Unit cell: (122.199, 128.018, 150.236, 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 76 16.00 O 3089 8.00 N 2855 7.00 C 10272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.06 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 626.8 milliseconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3958 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 57 sheets defined 20.2% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 4.062A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.534A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 172 removed outlier: 4.256A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.665A pdb=" N GLU C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.597A pdb=" N LEU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 98 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 3.598A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 74 through 127 removed outlier: 3.517A pdb=" N LEU F 80 " --> pdb=" O ARG F 76 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 96 " --> pdb=" O TRP F 92 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU F 99 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 171 removed outlier: 3.691A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.799A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.974A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.969A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.846A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.820A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 14 removed outlier: 8.628A pdb=" N TRP B 14 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR A 17 " --> pdb=" O TRP B 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 removed outlier: 8.628A pdb=" N TRP B 14 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR A 17 " --> pdb=" O TRP B 14 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 134 " --> pdb=" O CYS B 137 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU B 139 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLU B 132 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.159A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 5.933A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.424A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.179A pdb=" N SER A 261 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 118 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA A 259 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG A 120 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA A 257 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.533A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 3.838A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AB5, first strand: chain 'C' and resid 12 through 17 removed outlier: 3.588A pdb=" N THR C 12 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB9, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.993A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.307A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.358A pdb=" N SER C 261 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE C 118 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 259 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG C 120 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 257 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.425A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC7, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.987A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AC9, first strand: chain 'E' and resid 12 through 17 Processing sheet with id=AD1, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.146A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD3, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'E' and resid 51 through 53 removed outlier: 5.846A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.338A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.179A pdb=" N SER E 261 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE E 118 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD8, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.623A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AE1, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE2, first strand: chain 'E' and resid 281 through 282 Processing sheet with id=AE3, first strand: chain 'F' and resid 130 through 132 Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AE5, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.552A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.552A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AE8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.969A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.881A pdb=" N ILE I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 98 through 100 Processing sheet with id=AF3, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AF4, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.474A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 6 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.446A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'M' and resid 58 through 59 removed outlier: 3.522A pdb=" N GLU M 46 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET M 34 " --> pdb=" O PHE M 50 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE M 102 " --> pdb=" O LYS M 94 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 58 through 59 removed outlier: 3.522A pdb=" N GLU M 46 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET M 34 " --> pdb=" O PHE M 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 98 through 100 Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 7 removed outlier: 5.791A pdb=" N THR N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N GLN N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N SER N 67 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N ILE N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 11.515A pdb=" N SER N 65 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.498A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5347 1.34 - 1.47: 4038 1.47 - 1.60: 7186 1.60 - 1.73: 0 1.73 - 1.86: 104 Bond restraints: 16675 Sorted by residual: bond pdb=" CA SER E 85 " pdb=" CB SER E 85 " ideal model delta sigma weight residual 1.536 1.466 0.070 1.46e-02 4.69e+03 2.33e+01 bond pdb=" C MET M 34 " pdb=" N ASN M 35 " ideal model delta sigma weight residual 1.331 1.394 -0.063 1.41e-02 5.03e+03 2.02e+01 bond pdb=" CA SER A 261 " pdb=" CB SER A 261 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.38e-02 5.25e+03 1.68e+01 bond pdb=" CA SER E 83A" pdb=" CB SER E 83A" ideal model delta sigma weight residual 1.535 1.474 0.061 1.58e-02 4.01e+03 1.48e+01 bond pdb=" CA SER E 146 " pdb=" CB SER E 146 " ideal model delta sigma weight residual 1.534 1.483 0.051 1.34e-02 5.57e+03 1.44e+01 ... (remaining 16670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 21568 2.22 - 4.44: 923 4.44 - 6.66: 145 6.66 - 8.87: 33 8.87 - 11.09: 2 Bond angle restraints: 22671 Sorted by residual: angle pdb=" CA PHE B 9 " pdb=" CB PHE B 9 " pdb=" CG PHE B 9 " ideal model delta sigma weight residual 113.80 119.26 -5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA PHE F 9 " pdb=" CB PHE F 9 " pdb=" CG PHE F 9 " ideal model delta sigma weight residual 113.80 119.24 -5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" CA GLY F 134 " pdb=" C GLY F 134 " pdb=" O GLY F 134 " ideal model delta sigma weight residual 122.29 118.12 4.17 8.10e-01 1.52e+00 2.66e+01 angle pdb=" CA PHE D 3 " pdb=" CB PHE D 3 " pdb=" CG PHE D 3 " ideal model delta sigma weight residual 113.80 108.80 5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" C PHE D 3 " pdb=" CA PHE D 3 " pdb=" CB PHE D 3 " ideal model delta sigma weight residual 110.64 119.19 -8.55 1.72e+00 3.38e-01 2.47e+01 ... (remaining 22666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8498 17.68 - 35.35: 940 35.35 - 53.03: 291 53.03 - 70.71: 70 70.71 - 88.39: 19 Dihedral angle restraints: 9818 sinusoidal: 3612 harmonic: 6206 Sorted by residual: dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 76 " pdb=" CB CYS E 76 " ideal model delta sinusoidal sigma weight residual 93.00 157.24 -64.24 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CD ARG L 18 " pdb=" NE ARG L 18 " pdb=" CZ ARG L 18 " pdb=" NH1 ARG L 18 " ideal model delta sinusoidal sigma weight residual 0.00 53.57 -53.57 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CD ARG E 224 " pdb=" NE ARG E 224 " pdb=" CZ ARG E 224 " pdb=" NH1 ARG E 224 " ideal model delta sinusoidal sigma weight residual 0.00 48.51 -48.51 1 1.00e+01 1.00e-02 3.24e+01 ... (remaining 9815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2058 0.069 - 0.137: 344 0.137 - 0.206: 73 0.206 - 0.275: 18 0.275 - 0.344: 5 Chirality restraints: 2498 Sorted by residual: chirality pdb=" CA CYS A 97 " pdb=" N CYS A 97 " pdb=" C CYS A 97 " pdb=" CB CYS A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA CYS L 23 " pdb=" N CYS L 23 " pdb=" C CYS L 23 " pdb=" CB CYS L 23 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA LYS B 131 " pdb=" N LYS B 131 " pdb=" C LYS B 131 " pdb=" CB LYS B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2495 not shown) Planarity restraints: 2947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 18 " 0.878 9.50e-02 1.11e+02 3.94e-01 9.41e+01 pdb=" NE ARG L 18 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG L 18 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG L 18 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG L 18 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 224 " 0.824 9.50e-02 1.11e+02 3.69e-01 8.29e+01 pdb=" NE ARG E 224 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG E 224 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 224 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 224 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 61 " -0.732 9.50e-02 1.11e+02 3.28e-01 6.56e+01 pdb=" NE ARG N 61 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG N 61 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG N 61 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG N 61 " -0.024 2.00e-02 2.50e+03 ... (remaining 2944 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 255 2.64 - 3.21: 13806 3.21 - 3.77: 24802 3.77 - 4.34: 35862 4.34 - 4.90: 59567 Nonbonded interactions: 134292 Sorted by model distance: nonbonded pdb=" O ASN A 142 " pdb=" OD1 ASN A 142 " model vdw 2.075 3.040 nonbonded pdb=" OG SER E 114 " pdb=" OG SER E 265 " model vdw 2.221 3.040 nonbonded pdb=" O SER N 77 " pdb=" OG SER N 77 " model vdw 2.233 3.040 nonbonded pdb=" O PHE M 32 " pdb=" NH2 ARG M 71 " model vdw 2.251 3.120 nonbonded pdb=" O SER M 82B" pdb=" OG SER M 82B" model vdw 2.261 3.040 ... (remaining 134287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 49 or (resid 50 and (name N or nam \ e CA or name C or name O or name CB )) or resid 51 through 79 or (resid 80 and ( \ name N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 thr \ ough 83 and (name N or name CA or name C or name O or name CB )) or resid 83A or \ (resid 84 and (name N or name CA or name C or name O or name CB )) or resid 85 \ or (resid 86 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 7 through 91 or (resid 92 and (name N or name CA or name C or name O or name CB \ )) or resid 92A through 117 or (resid 118 through 119 and (name N or name CA or \ name C or name O or name CB )) or resid 120 through 143 or (resid 144 and (name \ N or name CA or name C or name O or name CB )) or resid 145 through 159 or (resi \ d 160 and (name N or name CA or name C or name O or name CB )) or resid 161 thro \ ugh 215 or (resid 216 and (name N or name CA or name C or name O or name CB )) o \ r resid 217 through 218 or (resid 219 and (name N or name CA or name C or name O \ or name CB )) or resid 220 through 275 or (resid 276 and (name N or name CA or \ name C or name O or name CB )) or resid 277 through 324)) selection = (chain 'C' and (resid 11 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB )) or resid 46 through 49 or (resid 50 and (name N or nam \ e CA or name C or name O or name CB )) or resid 51 through 53 or (resid 54 throu \ gh 55 and (name N or name CA or name C or name O or name CB )) or resid 55A thro \ ugh 74 or (resid 75 and (name N or name CA or name C or name O or name CB )) or \ resid 76 through 81 or (resid 82 through 83 and (name N or name CA or name C or \ name O or name CB )) or resid 83A or (resid 84 and (name N or name CA or name C \ or name O or name CB )) or resid 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 89 or (resid 90 and (name N or nam \ e CA or name C or name O or name CB )) or resid 91 or (resid 92 and (name N or n \ ame CA or name C or name O or name CB )) or resid 92A or (resid 93 and (name N o \ r name CA or name C or name O or name CB )) or resid 94 through 105 or (resid 10 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 107 through \ 117 or (resid 118 through 119 and (name N or name CA or name C or name O or name \ CB )) or resid 120 through 174 or (resid 175 and (name N or name CA or name C o \ r name O or name CB )) or resid 176 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 or (resid 190 and (name N or \ name CA or name C or name O or name CB )) or resid 191 through 215 or (resid 21 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 217 through \ 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) or re \ sid 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) o \ r resid 228 through 245 or (resid 246 through 247 and (name N or name CA or name \ C or name O or name CB )) or resid 248 through 274 or (resid 275 through 276 an \ d (name N or name CA or name C or name O or name CB )) or resid 277 through 279 \ or (resid 280 and (name N or name CA or name C or name O or name CB )) or resid \ 281 through 299 or (resid 300 and (name N or name CA or name C or name O or name \ CB )) or resid 301 through 303 or (resid 304 and (name N or name CA or name C o \ r name O or name CB )) or resid 305 through 324)) selection = (chain 'E' and (resid 11 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 43 or (resid 44 through 45 and (na \ me N or name CA or name C or name O or name CB )) or resid 46 through 53 or (res \ id 54 through 55 and (name N or name CA or name C or name O or name CB )) or res \ id 55A through 76 or (resid 77 through 78 and (name N or name CA or name C or na \ me O or name CB )) or resid 79 or (resid 80 and (name N or name CA or name C or \ name O or name CB )) or resid 81 through 89 or (resid 90 and (name N or name CA \ or name C or name O or name CB )) or resid 91 through 105 or (resid 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 159 or (resid 160 and (name N or name CA or name C or name O or name CB )) \ or resid 161 through 174 or (resid 175 and (name N or name CA or name C or name \ O or name CB )) or resid 176 through 187 or (resid 188 and (name N or name CA o \ r name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name \ CA or name C or name O or name CB )) or resid 191 through 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB )) or resid 199 through 218 or \ (resid 219 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 0 through 224 or (resid 225 and (name N or name CA or name C or name O or name C \ B )) or resid 226 or (resid 227 and (name N or name CA or name C or name O or na \ me CB )) or resid 228 through 237 or (resid 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 245 or (resid 246 through 247 and \ (name N or name CA or name C or name O or name CB )) or resid 248 through 279 or \ (resid 280 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 1 through 299 or (resid 300 and (name N or name CA or name C or name O or name C \ B )) or resid 301 through 303 or (resid 304 and (name N or name CA or name C or \ name O or name CB )) or resid 305 through 324)) } ncs_group { reference = (chain 'B' and (resid 2 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 170 or (resid 171 and (name N or \ name CA or name C or name O or name CB )) or resid 172)) selection = (chain 'D' and (resid 2 through 37 or (resid 38 through 39 and (name N or name C \ A or name C or name O or name CB )) or resid 40 through 56 or (resid 57 and (nam \ e N or name CA or name C or name O or name CB )) or resid 58 through 61 or (resi \ d 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throug \ h 72 or (resid 73 through 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 84 or (resid 85 and (name N or name CA or name C or na \ me O or name CB )) or resid 86 through 102 or (resid 103 and (name N or name CA \ or name C or name O or name CB )) or resid 104 through 138 or (resid 139 and (na \ me N or name CA or name C or name O or name CB )) or resid 140 through 172)) selection = (chain 'F' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 37 or (resid 38 through 39 and (nam \ e N or name CA or name C or name O or name CB )) or resid 40 through 56 or (resi \ d 57 and (name N or name CA or name C or name O or name CB )) or resid 58 throug \ h 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or re \ sid 61 or (resid 62 and (name N or name CA or name C or name O or name CB )) or \ resid 63 through 71 or (resid 72 through 74 and (name N or name CA or name C or \ name O or name CB )) or resid 75 through 84 or (resid 85 and (name N or name CA \ or name C or name O or name CB )) or resid 86 through 102 or (resid 103 and (nam \ e N or name CA or name C or name O or name CB )) or resid 104 or (resid 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 138 or \ (resid 139 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 0 through 142 or (resid 143 and (name N or name CA or name C or name O or name C \ B )) or resid 144 through 149 or (resid 150 and (name N or name CA or name C or \ name O or name CB )) or resid 151 through 170 or (resid 171 and (name N or name \ CA or name C or name O or name CB )) or resid 172)) } ncs_group { reference = (chain 'H' and (resid 2 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113)) selection = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 60 or (resid 61 and (name N or name CA \ or name C or name O or name CB )) or resid 62 through 71 or (resid 72 and (name \ N or name CA or name C or name O or name CB )) or resid 73 through 97 or (resid \ 98 through 99 and (name N or name CA or name C or name O or name CB )) or resid \ 100 through 106 or (resid 107 through 108 and (name N or name CA or name C or n \ ame O or name CB )) or resid 109 through 113)) selection = (chain 'M' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 or (resid 5 through 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 60 or (resid 61 and (name N or name CA \ or name C or name O or name CB )) or resid 62 through 71 or (resid 72 and (name \ N or name CA or name C or name O or name CB )) or resid 73 through 74 or (resid \ 75 and (name N or name CA or name C or name O or name CB )) or resid 76 through \ 97 or (resid 98 through 99 and (name N or name CA or name C or name O or name C \ B )) or resid 100 through 106 or (resid 107 through 108 and (name N or name CA o \ r name C or name O or name CB )) or resid 109 through 111 or (resid 112 and (nam \ e N or name CA or name C or name O or name CB )) or resid 113)) } ncs_group { reference = (chain 'K' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 through 104)) selection = (chain 'L' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 26 or (resid 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 through 44 or (resid 45 and (n \ ame N or name CA or name C or name O or name CB )) or resid 46 through 69 or (re \ sid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 thro \ ugh 104)) selection = (chain 'N' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 through 16 or (resid 17 and (name N or name CA \ or name C or name O or name CB )) or resid 18 through 26 or (resid 27 and (name \ N or name CA or name C or name O or name CB )) or resid 28 through 44 or (resid \ 45 and (name N or name CA or name C or name O or name CB )) or resid 46 through \ 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) or res \ id 71 through 104)) } 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: 31.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.620 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.007 0.070 16694 Z= 0.441 Angle : 0.982 11.092 22709 Z= 0.635 Chirality : 0.060 0.344 2498 Planarity : 0.015 0.394 2947 Dihedral : 17.006 88.386 5803 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 3.83 % Allowed : 23.53 % Favored : 72.64 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2144 helix: -0.74 (0.26), residues: 381 sheet: -0.36 (0.23), residues: 554 loop : -1.77 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 192 TYR 0.027 0.002 TYR E 148 PHE 0.024 0.002 PHE D 3 TRP 0.018 0.002 TRP H 36 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.44 (16675) covalent geometry : angle 0.97678 / 0.63 (22671) SS BOND : bond 0.00761 / 0.40 ( 19) SS BOND : angle 2.62431 / 1.47 ( 38) hydrogen bonds : bond 0.17235 / 11.82 ( 647) hydrogen bonds : angle 8.28552 / 5.73 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 366 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 THR cc_start: 0.8424 (p) cc_final: 0.8199 (m) REVERT: A 277 CYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4864 (p) REVERT: A 316 MET cc_start: 0.8441 (mtp) cc_final: 0.8236 (ttm) REVERT: B 123 LYS cc_start: 0.8719 (ttpp) cc_final: 0.8498 (ttmm) REVERT: B 132 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6943 (mt-10) REVERT: B 154 ASN cc_start: 0.7260 (t0) cc_final: 0.7019 (t0) REVERT: C 94 ASN cc_start: 0.7084 (m-40) cc_final: 0.6588 (m110) REVERT: C 216 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6861 (mt-10) REVERT: C 315 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8608 (mtt-85) REVERT: D 22 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: D 58 LYS cc_start: 0.8576 (mptt) cc_final: 0.8069 (mptt) REVERT: D 132 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7279 (mt-10) REVERT: D 135 ASN cc_start: 0.7424 (p0) cc_final: 0.6935 (p0) REVERT: E 106 GLU cc_start: 0.7953 (mp0) cc_final: 0.7684 (mp0) REVERT: E 160 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7519 (pp) REVERT: F 74 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7231 (mt-10) REVERT: I 39 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: K 4 MET cc_start: 0.7312 (mtp) cc_final: 0.7039 (mmm) REVERT: K 92 TYR cc_start: 0.8301 (t80) cc_final: 0.7391 (t80) outliers start: 65 outliers final: 20 residues processed: 412 average time/residue: 0.5447 time to fit residues: 249.5998 Evaluate side-chains 359 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 335 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 62 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 0.0870 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN B 43 ASN B 125 GLN B 169 ASN C 271 ASN D 154 ASN E 63 ASN E 73 ASN E 150 ASN E 170 ASN E 187 ASN E 282 GLN F 129 ASN I 39 GLN K 37 GLN K 38 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099958 restraints weight = 22843.872| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.72 r_work: 0.3291 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16694 Z= 0.161 Angle : 0.558 7.811 22709 Z= 0.293 Chirality : 0.043 0.140 2498 Planarity : 0.005 0.069 2947 Dihedral : 5.538 85.628 2361 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.42 % Allowed : 23.00 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2144 helix: 0.92 (0.27), residues: 390 sheet: -0.06 (0.22), residues: 574 loop : -1.48 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 71 TYR 0.019 0.001 TYR F 141 PHE 0.025 0.002 PHE F 9 TRP 0.012 0.001 TRP C 84 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (16675) covalent geometry : angle 0.55665 / 0.29 (22671) SS BOND : bond 0.00299 / 0.19 ( 19) SS BOND : angle 1.03926 / 0.64 ( 38) hydrogen bonds : bond 0.04589 / 3.21 ( 647) hydrogen bonds : angle 5.22994 / 3.66 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 321 time to evaluate : 0.857 Fit side-chains REVERT: A 107 GLU cc_start: 0.8030 (tp30) cc_final: 0.7739 (tp30) REVERT: A 212 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8573 (mmmm) REVERT: B 123 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8596 (ttmm) REVERT: B 127 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8278 (mtmm) REVERT: B 132 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7336 (mt-10) REVERT: C 94 ASN cc_start: 0.7165 (m-40) cc_final: 0.6629 (m110) REVERT: C 315 ARG cc_start: 0.8832 (mtp85) cc_final: 0.8624 (mtt-85) REVERT: D 131 LYS cc_start: 0.8383 (ttpp) cc_final: 0.7984 (ttpp) REVERT: D 135 ASN cc_start: 0.7854 (p0) cc_final: 0.7501 (p0) REVERT: D 139 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: E 106 GLU cc_start: 0.8054 (mp0) cc_final: 0.7760 (mp0) REVERT: E 160 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7280 (pp) REVERT: E 192 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.7933 (mtm-85) REVERT: E 222 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8082 (mtpp) REVERT: E 227 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7745 (mt-10) REVERT: F 74 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7429 (mt-10) REVERT: I 39 GLN cc_start: 0.8554 (tt0) cc_final: 0.8345 (tt0) REVERT: K 4 MET cc_start: 0.7329 (mtp) cc_final: 0.6966 (mmm) REVERT: K 92 TYR cc_start: 0.8554 (t80) cc_final: 0.7710 (t80) REVERT: M 82 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7992 (mtp) outliers start: 75 outliers final: 32 residues processed: 359 average time/residue: 0.6971 time to fit residues: 274.4089 Evaluate side-chains 345 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 95 optimal weight: 1.9990 chunk 105 optimal weight: 0.0020 chunk 28 optimal weight: 0.0020 chunk 170 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN C 170 ASN D 95 ASN D 154 ASN E 170 ASN E 282 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099334 restraints weight = 23122.675| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.73 r_work: 0.3281 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16694 Z= 0.145 Angle : 0.524 9.092 22709 Z= 0.275 Chirality : 0.042 0.142 2498 Planarity : 0.004 0.063 2947 Dihedral : 4.788 56.997 2335 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.95 % Allowed : 23.17 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2144 helix: 1.40 (0.27), residues: 396 sheet: 0.15 (0.23), residues: 554 loop : -1.31 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.016 0.001 TYR F 141 PHE 0.021 0.002 PHE B 9 TRP 0.008 0.001 TRP C 84 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (16675) covalent geometry : angle 0.52321 / 0.27 (22671) SS BOND : bond 0.00437 / 0.26 ( 19) SS BOND : angle 0.94416 / 0.58 ( 38) hydrogen bonds : bond 0.04320 / 3.03 ( 647) hydrogen bonds : angle 4.86918 / 3.42 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 308 time to evaluate : 0.650 Fit side-chains REVERT: A 107 GLU cc_start: 0.8030 (tp30) cc_final: 0.7746 (tp30) REVERT: A 194 LEU cc_start: 0.8674 (mt) cc_final: 0.8469 (mp) REVERT: B 123 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8601 (ttmm) REVERT: B 132 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7293 (mt-10) REVERT: C 75 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7520 (mm-30) REVERT: C 94 ASN cc_start: 0.7191 (m-40) cc_final: 0.6665 (m110) REVERT: D 131 LYS cc_start: 0.8388 (ttpp) cc_final: 0.7980 (ttpp) REVERT: D 135 ASN cc_start: 0.7845 (p0) cc_final: 0.7539 (p0) REVERT: D 139 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: E 106 GLU cc_start: 0.8062 (mp0) cc_final: 0.7789 (mp0) REVERT: E 175 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 192 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: E 222 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8067 (mtpp) REVERT: E 227 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7736 (mt-10) REVERT: E 310 ARG cc_start: 0.8359 (ttm110) cc_final: 0.8154 (mtm110) REVERT: F 154 ASN cc_start: 0.6896 (t0) cc_final: 0.6689 (t0) REVERT: K 4 MET cc_start: 0.7386 (mtp) cc_final: 0.6890 (mmm) REVERT: M 82 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7949 (mtp) REVERT: N 67 SER cc_start: 0.7834 (OUTLIER) cc_final: 0.7601 (t) outliers start: 67 outliers final: 40 residues processed: 349 average time/residue: 0.6671 time to fit residues: 255.4878 Evaluate side-chains 356 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 chunk 93 optimal weight: 0.0060 chunk 118 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN B 169 ASN C 170 ASN D 95 ASN D 154 ASN E 170 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098459 restraints weight = 22983.598| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.71 r_work: 0.3259 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16694 Z= 0.185 Angle : 0.543 8.777 22709 Z= 0.284 Chirality : 0.043 0.139 2498 Planarity : 0.004 0.060 2947 Dihedral : 4.808 55.908 2333 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.54 % Allowed : 22.35 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2144 helix: 2.00 (0.28), residues: 372 sheet: 0.21 (0.23), residues: 554 loop : -1.28 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 71 TYR 0.016 0.001 TYR F 141 PHE 0.021 0.002 PHE B 9 TRP 0.010 0.001 TRP I 47 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (16675) covalent geometry : angle 0.54218 / 0.28 (22671) SS BOND : bond 0.00372 / 0.24 ( 19) SS BOND : angle 0.99782 / 0.62 ( 38) hydrogen bonds : bond 0.04507 / 3.17 ( 647) hydrogen bonds : angle 4.86459 / 3.41 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 318 time to evaluate : 0.650 Fit side-chains REVERT: A 107 GLU cc_start: 0.8031 (tp30) cc_final: 0.7686 (tp30) REVERT: A 194 LEU cc_start: 0.8696 (mt) cc_final: 0.8476 (mp) REVERT: B 123 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8560 (ttmm) REVERT: B 132 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7316 (mt-10) REVERT: C 75 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 222 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8147 (mtpp) REVERT: D 135 ASN cc_start: 0.7883 (p0) cc_final: 0.7590 (p0) REVERT: D 139 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: E 106 GLU cc_start: 0.8032 (mp0) cc_final: 0.7745 (mp0) REVERT: E 175 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7620 (mt-10) REVERT: E 192 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.7947 (mtm-85) REVERT: E 219 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7791 (tttt) REVERT: E 222 LYS cc_start: 0.8369 (mtpp) cc_final: 0.8076 (mtpp) REVERT: E 227 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7649 (mt-10) REVERT: F 38 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: F 71 ASN cc_start: 0.8293 (p0) cc_final: 0.7834 (p0) REVERT: F 154 ASN cc_start: 0.6922 (t0) cc_final: 0.6694 (t0) REVERT: K 4 MET cc_start: 0.7449 (mtp) cc_final: 0.6898 (mmm) REVERT: M 82 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8012 (mtp) outliers start: 77 outliers final: 48 residues processed: 360 average time/residue: 0.5663 time to fit residues: 223.8966 Evaluate side-chains 367 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 47 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN C 170 ASN D 28 ASN D 95 ASN D 154 ASN E 170 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098174 restraints weight = 22799.208| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.70 r_work: 0.3259 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16694 Z= 0.217 Angle : 0.564 9.318 22709 Z= 0.294 Chirality : 0.043 0.184 2498 Planarity : 0.004 0.059 2947 Dihedral : 4.888 54.601 2331 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.30 % Allowed : 22.35 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2144 helix: 1.55 (0.27), residues: 396 sheet: 0.25 (0.23), residues: 554 loop : -1.25 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 71 TYR 0.014 0.002 TYR F 141 PHE 0.019 0.002 PHE B 9 TRP 0.011 0.001 TRP I 47 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (16675) covalent geometry : angle 0.56285 / 0.29 (22671) SS BOND : bond 0.00357 / 0.24 ( 19) SS BOND : angle 1.07474 / 0.67 ( 38) hydrogen bonds : bond 0.04644 / 3.26 ( 647) hydrogen bonds : angle 4.88973 / 3.43 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 311 time to evaluate : 0.503 Fit side-chains REVERT: A 107 GLU cc_start: 0.8046 (tp30) cc_final: 0.7718 (tp30) REVERT: A 149 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8288 (mtmm) REVERT: A 194 LEU cc_start: 0.8704 (mt) cc_final: 0.8485 (mp) REVERT: A 220 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7406 (mtm180) REVERT: B 132 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7405 (mt-10) REVERT: C 75 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7530 (mm-30) REVERT: C 222 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8140 (mtpp) REVERT: D 135 ASN cc_start: 0.7927 (p0) cc_final: 0.7680 (p0) REVERT: D 139 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: E 106 GLU cc_start: 0.8019 (mp0) cc_final: 0.7738 (mp0) REVERT: E 175 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7632 (mt-10) REVERT: E 192 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7982 (mtm-85) REVERT: E 219 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7848 (tttt) REVERT: E 222 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8073 (mtpp) REVERT: E 227 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7656 (mt-10) REVERT: F 38 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: F 71 ASN cc_start: 0.8312 (p0) cc_final: 0.7922 (p0) REVERT: F 74 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7351 (mt-10) REVERT: F 154 ASN cc_start: 0.6928 (t0) cc_final: 0.6718 (t0) REVERT: K 4 MET cc_start: 0.7480 (mtp) cc_final: 0.6906 (mmm) REVERT: M 82 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8010 (mtp) outliers start: 73 outliers final: 47 residues processed: 349 average time/residue: 0.6029 time to fit residues: 229.9693 Evaluate side-chains 362 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 103 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 196 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 0.0270 chunk 99 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 125 GLN C 170 ASN D 95 ASN E 170 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098171 restraints weight = 22937.468| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.72 r_work: 0.3265 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16694 Z= 0.167 Angle : 0.534 9.676 22709 Z= 0.279 Chirality : 0.042 0.192 2498 Planarity : 0.004 0.058 2947 Dihedral : 4.659 53.840 2329 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.42 % Allowed : 22.35 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.18), residues: 2144 helix: 1.81 (0.27), residues: 390 sheet: 0.42 (0.23), residues: 524 loop : -1.22 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 192 TYR 0.013 0.001 TYR E 201 PHE 0.018 0.002 PHE B 9 TRP 0.010 0.001 TRP I 47 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (16675) covalent geometry : angle 0.53315 / 0.28 (22671) SS BOND : bond 0.00307 / 0.21 ( 19) SS BOND : angle 0.89066 / 0.56 ( 38) hydrogen bonds : bond 0.04351 / 3.05 ( 647) hydrogen bonds : angle 4.76066 / 3.35 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 312 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8044 (tp30) cc_final: 0.7730 (tp30) REVERT: A 194 LEU cc_start: 0.8679 (mt) cc_final: 0.8466 (mp) REVERT: C 23 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8470 (m) REVERT: C 75 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7515 (mm-30) REVERT: C 132 THR cc_start: 0.8822 (p) cc_final: 0.8434 (p) REVERT: C 222 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8152 (mtpp) REVERT: D 131 LYS cc_start: 0.8465 (ttpp) cc_final: 0.7953 (ttpp) REVERT: D 135 ASN cc_start: 0.7890 (p0) cc_final: 0.7645 (p0) REVERT: D 139 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: E 106 GLU cc_start: 0.8037 (mp0) cc_final: 0.7738 (mp0) REVERT: E 175 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7594 (tt0) REVERT: E 192 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7958 (mtm-85) REVERT: E 219 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7838 (tttt) REVERT: E 222 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8074 (mtpp) REVERT: E 227 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7652 (mt-10) REVERT: E 310 ARG cc_start: 0.8383 (ttm110) cc_final: 0.8171 (mtm110) REVERT: F 38 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: F 74 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7588 (mt-10) REVERT: F 150 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: F 154 ASN cc_start: 0.6917 (t0) cc_final: 0.6704 (t0) REVERT: K 4 MET cc_start: 0.7478 (mtp) cc_final: 0.6883 (mmm) REVERT: M 82 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7981 (mtp) outliers start: 75 outliers final: 47 residues processed: 350 average time/residue: 0.5467 time to fit residues: 209.9755 Evaluate side-chains 363 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 166 optimal weight: 0.5980 chunk 149 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 109 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 96 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 125 GLN B 145 ASN C 111 GLN C 170 ASN D 95 ASN E 170 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.100499 restraints weight = 22849.265| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.73 r_work: 0.3281 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16694 Z= 0.106 Angle : 0.493 10.382 22709 Z= 0.256 Chirality : 0.041 0.171 2498 Planarity : 0.004 0.057 2947 Dihedral : 4.335 52.376 2329 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.48 % Allowed : 23.17 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2144 helix: 2.10 (0.28), residues: 390 sheet: 0.38 (0.24), residues: 497 loop : -0.98 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 315 TYR 0.013 0.001 TYR E 201 PHE 0.017 0.001 PHE B 9 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (16675) covalent geometry : angle 0.49274 / 0.26 (22671) SS BOND : bond 0.00246 / 0.17 ( 19) SS BOND : angle 0.66719 / 0.43 ( 38) hydrogen bonds : bond 0.03773 / 2.65 ( 647) hydrogen bonds : angle 4.49543 / 3.18 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 319 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8010 (tp30) cc_final: 0.7717 (tp30) REVERT: A 220 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7252 (mtm180) REVERT: B 123 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8360 (tttp) REVERT: B 132 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7096 (mt-10) REVERT: C 75 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7535 (mm-30) REVERT: C 132 THR cc_start: 0.8801 (p) cc_final: 0.8436 (p) REVERT: D 131 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8079 (ttpp) REVERT: D 135 ASN cc_start: 0.7834 (p0) cc_final: 0.7521 (p0) REVERT: D 139 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: E 106 GLU cc_start: 0.7994 (mp0) cc_final: 0.7714 (mp0) REVERT: E 175 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7633 (tt0) REVERT: E 192 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8014 (mtm-85) REVERT: E 219 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7772 (tttt) REVERT: E 222 LYS cc_start: 0.8372 (mtpp) cc_final: 0.8129 (mtpp) REVERT: E 310 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8034 (mtm110) REVERT: F 71 ASN cc_start: 0.8250 (p0) cc_final: 0.7850 (p0) REVERT: F 74 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7282 (mt-10) REVERT: F 150 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: K 4 MET cc_start: 0.7423 (mtp) cc_final: 0.6821 (mmm) REVERT: L 4 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7359 (mmm) outliers start: 59 outliers final: 37 residues processed: 351 average time/residue: 0.5838 time to fit residues: 224.4617 Evaluate side-chains 360 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 317 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 169 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 119 optimal weight: 0.0010 chunk 162 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 183 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN C 170 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099857 restraints weight = 22850.279| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.73 r_work: 0.3273 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16694 Z= 0.127 Angle : 0.516 9.795 22709 Z= 0.267 Chirality : 0.042 0.208 2498 Planarity : 0.004 0.056 2947 Dihedral : 4.349 50.975 2329 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.54 % Allowed : 23.64 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2144 helix: 2.12 (0.27), residues: 390 sheet: 0.52 (0.24), residues: 527 loop : -1.05 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 315 TYR 0.015 0.001 TYR E 201 PHE 0.015 0.001 PHE B 9 TRP 0.008 0.001 TRP I 47 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16675) covalent geometry : angle 0.51505 / 0.27 (22671) SS BOND : bond 0.00257 / 0.18 ( 19) SS BOND : angle 0.86840 / 0.52 ( 38) hydrogen bonds : bond 0.03955 / 2.79 ( 647) hydrogen bonds : angle 4.55832 / 3.22 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8003 (tp30) cc_final: 0.7711 (tp30) REVERT: A 220 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7320 (mtm180) REVERT: B 123 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8428 (tttm) REVERT: C 75 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7549 (mm-30) REVERT: C 132 THR cc_start: 0.8802 (p) cc_final: 0.8436 (p) REVERT: C 194 LEU cc_start: 0.8462 (mt) cc_final: 0.8255 (mp) REVERT: D 131 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8087 (ttpp) REVERT: D 139 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: E 106 GLU cc_start: 0.7997 (mp0) cc_final: 0.7721 (mp0) REVERT: E 175 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7626 (tt0) REVERT: E 192 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: E 219 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7656 (tttt) REVERT: E 222 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8127 (mtpp) REVERT: E 310 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8036 (mtm110) REVERT: F 38 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: F 150 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: K 4 MET cc_start: 0.7438 (mtp) cc_final: 0.6832 (mmm) outliers start: 60 outliers final: 42 residues processed: 351 average time/residue: 0.6143 time to fit residues: 235.9303 Evaluate side-chains 361 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 173 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 208 optimal weight: 0.2980 chunk 154 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 143 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN F 28 ASN F 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098824 restraints weight = 22859.686| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.72 r_work: 0.3267 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16694 Z= 0.174 Angle : 0.566 10.441 22709 Z= 0.290 Chirality : 0.043 0.284 2498 Planarity : 0.004 0.056 2947 Dihedral : 4.522 49.873 2327 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.42 % Allowed : 23.94 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2144 helix: 1.97 (0.27), residues: 390 sheet: 0.56 (0.24), residues: 524 loop : -1.09 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 315 TYR 0.018 0.001 TYR E 201 PHE 0.014 0.002 PHE B 9 TRP 0.009 0.001 TRP I 47 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (16675) covalent geometry : angle 0.56267 / 0.29 (22671) SS BOND : bond 0.00467 / 0.25 ( 19) SS BOND : angle 1.56285 / 0.89 ( 38) hydrogen bonds : bond 0.04312 / 3.03 ( 647) hydrogen bonds : angle 4.73364 / 3.34 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 314 time to evaluate : 0.505 Fit side-chains REVERT: A 107 GLU cc_start: 0.8008 (tp30) cc_final: 0.7707 (tp30) REVERT: B 123 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8397 (tttp) REVERT: C 75 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7526 (mm-30) REVERT: C 132 THR cc_start: 0.8800 (p) cc_final: 0.8438 (p) REVERT: C 194 LEU cc_start: 0.8472 (mt) cc_final: 0.8069 (mp) REVERT: C 291 SER cc_start: 0.8233 (t) cc_final: 0.7975 (p) REVERT: D 131 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8173 (ttpp) REVERT: D 139 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: E 106 GLU cc_start: 0.7951 (mp0) cc_final: 0.7673 (mp0) REVERT: E 116 SER cc_start: 0.8483 (m) cc_final: 0.8150 (p) REVERT: E 175 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7612 (tt0) REVERT: E 192 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: E 219 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7708 (tttm) REVERT: E 222 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8091 (mtpp) REVERT: E 227 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7745 (mt-10) REVERT: F 38 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: F 71 ASN cc_start: 0.8362 (p0) cc_final: 0.8072 (p0) REVERT: F 74 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7508 (mt-10) REVERT: F 150 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: K 4 MET cc_start: 0.7425 (mtp) cc_final: 0.6801 (mmm) outliers start: 58 outliers final: 38 residues processed: 347 average time/residue: 0.6462 time to fit residues: 245.3953 Evaluate side-chains 356 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 108 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 125 GLN B 142 HIS ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.111095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098949 restraints weight = 22685.887| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.72 r_work: 0.3238 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 16694 Z= 0.250 Angle : 0.615 12.805 22709 Z= 0.317 Chirality : 0.045 0.283 2498 Planarity : 0.004 0.056 2947 Dihedral : 4.818 49.487 2327 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.89 % Allowed : 24.23 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2144 helix: 1.76 (0.27), residues: 390 sheet: 0.51 (0.24), residues: 527 loop : -1.21 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 315 TYR 0.019 0.002 TYR E 201 PHE 0.017 0.002 PHE D 9 TRP 0.010 0.001 TRP I 47 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (16675) covalent geometry : angle 0.61226 / 0.32 (22671) SS BOND : bond 0.00551 / 0.29 ( 19) SS BOND : angle 1.58279 / 0.94 ( 38) hydrogen bonds : bond 0.04806 / 3.38 ( 647) hydrogen bonds : angle 4.92806 / 3.47 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 315 time to evaluate : 0.712 Fit side-chains REVERT: A 107 GLU cc_start: 0.8032 (tp30) cc_final: 0.7696 (tp30) REVERT: B 123 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8357 (tttm) REVERT: C 75 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 132 THR cc_start: 0.8855 (p) cc_final: 0.8486 (p) REVERT: C 194 LEU cc_start: 0.8472 (mt) cc_final: 0.8055 (mp) REVERT: C 291 SER cc_start: 0.8301 (t) cc_final: 0.8047 (p) REVERT: D 131 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8213 (ttpp) REVERT: E 106 GLU cc_start: 0.7998 (mp0) cc_final: 0.7706 (mp0) REVERT: E 116 SER cc_start: 0.8479 (m) cc_final: 0.8111 (p) REVERT: E 192 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.7981 (mtm-85) REVERT: F 38 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: F 71 ASN cc_start: 0.8337 (p0) cc_final: 0.8031 (p0) REVERT: F 74 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7482 (mt-10) REVERT: F 150 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: K 4 MET cc_start: 0.7478 (mtp) cc_final: 0.6833 (mmm) outliers start: 49 outliers final: 43 residues processed: 345 average time/residue: 0.6857 time to fit residues: 258.3158 Evaluate side-chains 354 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 152 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 157 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 176 optimal weight: 0.2980 chunk 131 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 125 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098081 restraints weight = 22892.514| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.72 r_work: 0.3271 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16694 Z= 0.143 Angle : 0.546 11.376 22709 Z= 0.282 Chirality : 0.042 0.214 2498 Planarity : 0.004 0.055 2947 Dihedral : 4.558 49.447 2327 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.83 % Allowed : 24.17 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2144 helix: 2.00 (0.27), residues: 390 sheet: 0.51 (0.24), residues: 527 loop : -1.12 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 315 TYR 0.017 0.001 TYR E 201 PHE 0.014 0.001 PHE B 9 TRP 0.008 0.001 TRP I 47 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16675) covalent geometry : angle 0.54491 / 0.28 (22671) SS BOND : bond 0.00459 / 0.24 ( 19) SS BOND : angle 1.13575 / 0.69 ( 38) hydrogen bonds : bond 0.04132 / 2.91 ( 647) hydrogen bonds : angle 4.70608 / 3.32 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6907.53 seconds wall clock time: 118 minutes 23.22 seconds (7103.22 seconds total)