Starting phenix.real_space_refine on Fri Aug 7 11:20:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ost_70810/08_2026/9ost_70810.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ost_70810/08_2026/9ost_70810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ost_70810/08_2026/9ost_70810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ost_70810/08_2026/9ost_70810.map" model { file = "/net/cci-nas-00/data/ceres_data/9ost_70810/08_2026/9ost_70810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ost_70810/08_2026/9ost_70810.cif" } resolution = 2.64 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= 0.021 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 100 5.16 5 C 13109 2.51 5 N 3593 2.21 5 O 4013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 20815 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2425 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 168} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2429 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 20, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1351 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 168} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2413 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1352 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 168} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 958 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 693 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 962 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 699 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 698 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "O" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 873 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "P" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 641 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 876 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 637 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "X" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 872 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Y" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 630 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 3.63, per 1000 atoms: 0.17 Number of scatterers: 20815 At special positions: 0 Unit cell: (131.721, 131.192, 161.345, 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 100 16.00 O 4013 8.00 N 3593 7.00 C 13109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.04 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: 1.78 Conformation dependent library (CDL) restraints added in 919.7 milliseconds 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4990 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 67 sheets defined 15.2% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.909A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.553A pdb=" N LYS B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.768A pdb=" N GLU B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'D' and resid 37 through 58 removed outlier: 3.611A pdb=" N LYS D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.630A pdb=" N GLU D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.678A pdb=" N LYS F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 127 removed outlier: 3.529A pdb=" N GLU F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 171 removed outlier: 3.731A pdb=" N GLU F 171 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.928A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.529A pdb=" N ASP I 82 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 79 through 83' Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.652A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.637A pdb=" N ASP K 82 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 79 through 83' Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.945A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.615A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.813A pdb=" N THR O 87 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 87 removed outlier: 3.903A pdb=" N THR R 87 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.891A pdb=" N THR X 87 " --> pdb=" O ALA X 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.059A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.810A 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: 6.428A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.662A 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 117 through 122 removed outlier: 3.604A pdb=" N SER A 117 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 117 through 122 removed outlier: 3.604A pdb=" N SER A 117 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 140 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: 3.615A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.148A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.596A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.751A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.751A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (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 140 removed outlier: 4.693A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.522A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 31 through 36 Processing sheet with id=AC8, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 54 removed outlier: 7.766A pdb=" N LEU E 51 " --> pdb=" O CYS E 277 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA E 279 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU E 53 " --> pdb=" O ALA E 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.529A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 117 through 122 removed outlier: 3.604A pdb=" N SER E 117 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER E 261 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.777A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.682A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.755A pdb=" N ASP H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.469A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.564A pdb=" N VAL I 97 " --> pdb=" O SER I 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.151A pdb=" N ASP J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.461A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 9 through 13 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AF2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'M' and resid 11 through 12 removed outlier: 5.590A pdb=" N TYR M 90 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN M 39 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N CYS M 92 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL M 37 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG M 94 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER M 35 " --> pdb=" O ARG M 94 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG M 96 " --> pdb=" O ASP M 33 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.472A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 9 through 13 Processing sheet with id=AF6, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AF7, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.580A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY O 33 " --> pdb=" O MET O 95 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE O 102 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.580A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY O 33 " --> pdb=" O MET O 95 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'P' and resid 53 through 54 removed outlier: 6.366A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'R' and resid 11 through 12 removed outlier: 6.946A pdb=" N MET R 34 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 11 through 12 removed outlier: 6.898A pdb=" N CYS R 92 " --> pdb=" O TRP R 103 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TRP R 103 " --> pdb=" O CYS R 92 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG R 94 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 4 through 6 Processing sheet with id=AG7, first strand: chain 'S' and resid 53 through 54 removed outlier: 6.372A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR S 49 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL S 33 " --> pdb=" O TYR S 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.651A pdb=" N SER X 21 " --> pdb=" O SER X 7 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 57 through 59 removed outlier: 6.552A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET X 34 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE X 102 " --> pdb=" O ARG X 94 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'X' and resid 57 through 59 removed outlier: 6.552A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET X 34 " --> pdb=" O PHE X 50 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 4 through 6 Processing sheet with id=AH3, first strand: chain 'Y' and resid 53 through 54 removed outlier: 3.504A pdb=" N THR Y 53 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN Y 37 " --> pdb=" O LEU Y 46 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR Y 97 " --> pdb=" O GLN Y 90 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 53 through 54 removed outlier: 3.504A pdb=" N THR Y 53 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN Y 37 " --> pdb=" O LEU Y 46 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2337 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: 3.16 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6783 1.34 - 1.46: 5145 1.46 - 1.58: 9227 1.58 - 1.70: 0 1.70 - 1.81: 137 Bond restraints: 21292 Sorted by residual: bond pdb=" C GLY E 319 " pdb=" N LEU E 320 " ideal model delta sigma weight residual 1.328 1.412 -0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" CA SER I 52 " pdb=" CB SER I 52 " ideal model delta sigma weight residual 1.533 1.472 0.061 1.60e-02 3.91e+03 1.44e+01 bond pdb=" CA SER E 210 " pdb=" CB SER E 210 " ideal model delta sigma weight residual 1.532 1.478 0.054 1.58e-02 4.01e+03 1.15e+01 bond pdb=" N ILE A 244 " pdb=" CA ILE A 244 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" CA PHE E 245 " pdb=" C PHE E 245 " ideal model delta sigma weight residual 1.522 1.484 0.038 1.19e-02 7.06e+03 1.04e+01 ... (remaining 21287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 28236 1.81 - 3.62: 570 3.62 - 5.43: 103 5.43 - 7.24: 15 7.24 - 9.06: 6 Bond angle restraints: 28930 Sorted by residual: angle pdb=" N ALA E 253 " pdb=" CA ALA E 253 " pdb=" C ALA E 253 " ideal model delta sigma weight residual 110.07 116.47 -6.40 1.46e+00 4.69e-01 1.92e+01 angle pdb=" C LYS D 68 " pdb=" CA LYS D 68 " pdb=" CB LYS D 68 " ideal model delta sigma weight residual 109.37 117.58 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" CA GLY A 249 " pdb=" C GLY A 249 " pdb=" O GLY A 249 " ideal model delta sigma weight residual 122.05 117.90 4.15 1.00e+00 1.00e+00 1.72e+01 angle pdb=" N LEU A 320 " pdb=" CA LEU A 320 " pdb=" CB LEU A 320 " ideal model delta sigma weight residual 110.60 104.33 6.27 1.52e+00 4.33e-01 1.70e+01 angle pdb=" CA GLY E 249 " pdb=" C GLY E 249 " pdb=" O GLY E 249 " ideal model delta sigma weight residual 122.05 117.93 4.12 1.00e+00 1.00e+00 1.70e+01 ... (remaining 28925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10805 17.93 - 35.86: 1289 35.86 - 53.80: 318 53.80 - 71.73: 61 71.73 - 89.66: 14 Dihedral angle restraints: 12487 sinusoidal: 4645 harmonic: 7842 Sorted by residual: dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " pdb=" CB CYS J 92 " ideal model delta sinusoidal sigma weight residual -86.00 -19.42 -66.58 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CA PRO S 95 " pdb=" C PRO S 95 " pdb=" N PRO S 95A" pdb=" CA PRO S 95A" ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA PRO Y 95 " pdb=" C PRO Y 95 " pdb=" N PRO Y 95A" pdb=" CA PRO Y 95A" ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 12484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2480 0.047 - 0.093: 519 0.093 - 0.139: 169 0.139 - 0.186: 11 0.186 - 0.232: 5 Chirality restraints: 3184 Sorted by residual: chirality pdb=" CA ILE E 252 " pdb=" N ILE E 252 " pdb=" C ILE E 252 " pdb=" CB ILE E 252 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TRP S 94 " pdb=" N TRP S 94 " pdb=" C TRP S 94 " pdb=" CB TRP S 94 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TRP Y 94 " pdb=" N TRP Y 94 " pdb=" C TRP Y 94 " pdb=" CB TRP Y 94 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3181 not shown) Planarity restraints: 3734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 76 " -0.677 9.50e-02 1.11e+02 3.04e-01 5.64e+01 pdb=" NE ARG F 76 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 76 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 76 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 76 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 229 " 0.645 9.50e-02 1.11e+02 2.89e-01 5.10e+01 pdb=" NE ARG E 229 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG E 229 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 229 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 229 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 321 " 0.583 9.50e-02 1.11e+02 2.62e-01 4.18e+01 pdb=" NE ARG E 321 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG E 321 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 321 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 321 " 0.019 2.00e-02 2.50e+03 ... (remaining 3731 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2931 2.76 - 3.29: 17916 3.29 - 3.83: 34310 3.83 - 4.36: 40699 4.36 - 4.90: 73130 Nonbonded interactions: 168986 Sorted by model distance: nonbonded pdb=" OH TYR B 119 " pdb=" OE1 GLU B 132 " model vdw 2.220 3.040 nonbonded pdb=" OG SER X 7 " pdb=" OG SER X 21 " model vdw 2.238 3.040 nonbonded pdb=" O PRO Y 8 " pdb=" OG1 THR Y 102 " model vdw 2.266 3.040 nonbonded pdb=" CD1 LEU X 20 " pdb=" CE MET X 82 " model vdw 2.266 3.880 nonbonded pdb=" OE1 GLU B 105 " pdb=" NH2 ARG D 106 " model vdw 2.270 3.120 ... (remaining 168981 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 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 118 or (resid 119 and (name N or n \ ame CA or name C or name O or name CB )) or resid 120 through 125A or (resid 125 \ B and (name N or name CA or name C or name O or name CB )) or resid 125C through \ 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or r \ esid 167 through 325)) selection = (chain 'C' and (resid 11 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 118 or (resid 119 and (name N or n \ ame CA or name C or name O or name CB )) or resid 120 through 125A or (resid 125 \ B and (name N or name CA or name C or name O or name CB )) or resid 125C through \ 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or r \ esid 167 through 303 or (resid 304 and (name N or name CA or name C or name O or \ name CB )) or resid 305 through 325)) selection = (chain 'E' and (resid 11 through 303 or (resid 304 and (name N or name CA or nam \ e C or name O or name CB )) or resid 305 through 325)) } ncs_group { reference = (chain 'B' and (resid 2 through 63 or (resid 64 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 171)) selection = (chain 'D' 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 63 or (resid 64 through 65 and (nam \ e N or name CA or name C or name O or name CB )) or resid 66 through 171)) 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 76 or (resid 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 171)) } ncs_group { reference = (chain 'H' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 113)) selection = (chain 'J' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 113)) selection = (chain 'M' 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 113)) } ncs_group { reference = (chain 'I' and (resid 4 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 106A)) selection = (chain 'K' and (resid 4 through 25 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 80 or (resid 81 and (name N or name \ CA or name C or name O or name CB )) or resid 82 through 93 or (resid 94 throug \ h 95 and (name N or name CA or name C or name O or name CB )) or resid 95A throu \ gh 106A)) selection = (chain 'N' and (resid 4 through 25 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 93 or (resid 94 throug \ h 95 and (name N or name CA or name C or name O or name CB )) or resid 95A throu \ gh 106A)) } ncs_group { reference = (chain 'O' and (resid 3 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 113)) selection = (chain 'R' and (resid 3 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 84 or (resid 85 and (name N or name \ CA or name C or name O or name CB )) or resid 86 through 113)) selection = (chain 'X' and (resid 3 through 84 or (resid 85 and (name N or name CA or name C \ or name O or name CB )) or resid 86 through 113)) } ncs_group { reference = (chain 'P' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 26 or (resid 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 through 73 or resid 83 through \ 104)) selection = (chain 'S' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 73 or resid 83 through 104)) selection = (chain 'Y' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 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: 34.530 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: 0.660 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.410 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 : 0.004 0.083 21315 Z= 0.221 Angle : 0.634 9.055 28976 Z= 0.370 Chirality : 0.043 0.232 3184 Planarity : 0.013 0.304 3734 Dihedral : 16.404 89.660 7428 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 2.87 % Allowed : 25.07 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2693 helix: 2.12 (0.27), residues: 351 sheet: 0.50 (0.19), residues: 713 loop : -1.09 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 262 TYR 0.011 0.001 TYR A 168 PHE 0.014 0.001 PHE D 9 TRP 0.025 0.001 TRP S 94 HIS 0.003 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.22 (21292) covalent geometry : angle 0.62965 / 0.37 (28930) SS BOND : bond 0.00535 / 0.33 ( 23) SS BOND : angle 1.97559 / 1.45 ( 46) hydrogen bonds : bond 0.12232 / 7.92 ( 816) hydrogen bonds : angle 6.29039 / 4.44 ( 2337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 453 time to evaluate : 0.729 Fit side-chains REVERT: A 175 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 238 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7463 (mm-30) REVERT: B 126 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 150 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7218 (mp0) REVERT: C 50 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8235 (mtpp) REVERT: C 94 ASN cc_start: 0.8157 (m-40) cc_final: 0.7852 (OUTLIER) REVERT: C 119 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7068 (tm-30) REVERT: C 131 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.8038 (t) REVERT: C 222 LYS cc_start: 0.8136 (mtpm) cc_final: 0.7935 (mtpm) REVERT: C 255 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7852 (ttt90) REVERT: D 58 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8621 (mptp) REVERT: E 94 ASN cc_start: 0.7578 (m-40) cc_final: 0.7339 (m110) REVERT: E 120 ARG cc_start: 0.8871 (ttt-90) cc_final: 0.8666 (ttt180) REVERT: E 255 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7940 (ttt90) REVERT: F 58 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8385 (mttm) REVERT: J 21 SER cc_start: 0.8630 (m) cc_final: 0.8328 (p) REVERT: M 4 LEU cc_start: 0.8875 (mp) cc_final: 0.8636 (mt) REVERT: R 107 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7831 (p) REVERT: X 83 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7654 (mtm180) outliers start: 63 outliers final: 36 residues processed: 482 average time/residue: 0.5618 time to fit residues: 307.6765 Evaluate side-chains 479 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 437 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN A 250 ASN A 322 ASN B 95 ASN C 130 HIS D 60 ASN D 95 ASN E 250 ASN E 269 ASN F 95 ASN K 17 GLN M 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114443 restraints weight = 27571.672| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.91 r_work: 0.3342 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21315 Z= 0.272 Angle : 0.591 11.714 28976 Z= 0.308 Chirality : 0.044 0.300 3184 Planarity : 0.005 0.050 3734 Dihedral : 6.379 59.376 3039 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.60 % Allowed : 23.25 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2693 helix: 1.64 (0.27), residues: 375 sheet: 0.64 (0.20), residues: 699 loop : -1.08 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 262 TYR 0.017 0.002 TYR Y 91 PHE 0.020 0.002 PHE D 9 TRP 0.022 0.002 TRP S 94 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.27 (21292) covalent geometry : angle 0.58677 / 0.31 (28930) SS BOND : bond 0.00713 / 0.47 ( 23) SS BOND : angle 1.80173 / 1.18 ( 46) hydrogen bonds : bond 0.04913 / 3.28 ( 816) hydrogen bonds : angle 4.99495 / 3.52 ( 2337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 443 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 238 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7459 (mm-30) REVERT: B 150 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7269 (mp0) REVERT: C 50 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8260 (mtpp) REVERT: C 119 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6873 (tm-30) REVERT: D 57 GLU cc_start: 0.7864 (tt0) cc_final: 0.7652 (tt0) REVERT: J 21 SER cc_start: 0.8688 (m) cc_final: 0.8356 (p) REVERT: P 22 SER cc_start: 0.7417 (OUTLIER) cc_final: 0.7092 (p) REVERT: R 107 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7874 (p) REVERT: X 94 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7263 (ttp-170) REVERT: X 95 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.6909 (mpt) outliers start: 101 outliers final: 52 residues processed: 503 average time/residue: 0.5176 time to fit residues: 297.0284 Evaluate side-chains 500 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 444 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 104 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 94 ARG Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain Y residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 257 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 117 optimal weight: 0.0970 chunk 136 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 79 optimal weight: 0.0050 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 269 ASN F 125 GLN M 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114067 restraints weight = 27893.578| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.92 r_work: 0.3366 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21315 Z= 0.130 Angle : 0.518 9.319 28976 Z= 0.270 Chirality : 0.041 0.256 3184 Planarity : 0.004 0.049 3734 Dihedral : 4.641 52.972 2972 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.87 % Allowed : 23.52 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2693 helix: 2.07 (0.27), residues: 375 sheet: 0.60 (0.20), residues: 725 loop : -1.03 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 262 TYR 0.018 0.001 TYR Y 91 PHE 0.014 0.001 PHE D 9 TRP 0.020 0.001 TRP S 94 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21292) covalent geometry : angle 0.51340 / 0.27 (28930) SS BOND : bond 0.00430 / 0.29 ( 23) SS BOND : angle 1.75807 / 1.16 ( 46) hydrogen bonds : bond 0.04065 / 2.71 ( 816) hydrogen bonds : angle 4.59143 / 3.25 ( 2337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 443 time to evaluate : 0.517 Fit side-chains REVERT: A 175 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 238 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7532 (mm-30) REVERT: B 126 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8372 (mp) REVERT: B 150 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7289 (mp0) REVERT: C 50 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8204 (mtpp) REVERT: C 82 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7658 (mmm160) REVERT: C 83 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: C 119 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6822 (tm-30) REVERT: C 211 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7802 (ttp80) REVERT: C 222 LYS cc_start: 0.8130 (mtpm) cc_final: 0.7914 (mtpm) REVERT: D 57 GLU cc_start: 0.7887 (tt0) cc_final: 0.7676 (tt0) REVERT: D 68 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8126 (mtmt) REVERT: E 118 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7554 (t80) REVERT: E 220 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7651 (mtm-85) REVERT: F 59 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8348 (ttp) REVERT: J 21 SER cc_start: 0.8647 (m) cc_final: 0.8382 (p) REVERT: K 72 SER cc_start: 0.8264 (m) cc_final: 0.7958 (p) REVERT: P 22 SER cc_start: 0.7374 (OUTLIER) cc_final: 0.7068 (p) REVERT: X 83 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7611 (mtm180) REVERT: X 95 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.6779 (mpt) outliers start: 107 outliers final: 58 residues processed: 498 average time/residue: 0.5054 time to fit residues: 285.0938 Evaluate side-chains 496 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 430 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain S residue 104 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 128 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN A 285 GLN D 60 ASN E 269 ASN F 125 GLN M 76 ASN Y 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113576 restraints weight = 27816.852| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.90 r_work: 0.3350 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21315 Z= 0.197 Angle : 0.549 9.785 28976 Z= 0.283 Chirality : 0.042 0.274 3184 Planarity : 0.005 0.050 3734 Dihedral : 4.676 54.651 2969 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 5.19 % Allowed : 23.29 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2693 helix: 2.02 (0.27), residues: 375 sheet: 0.59 (0.20), residues: 728 loop : -1.02 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 262 TYR 0.021 0.001 TYR Y 91 PHE 0.017 0.002 PHE D 9 TRP 0.019 0.001 TRP Y 94 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (21292) covalent geometry : angle 0.54563 / 0.28 (28930) SS BOND : bond 0.00556 / 0.39 ( 23) SS BOND : angle 1.59432 / 0.99 ( 46) hydrogen bonds : bond 0.04383 / 2.92 ( 816) hydrogen bonds : angle 4.59045 / 3.25 ( 2337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 431 time to evaluate : 0.850 Fit side-chains REVERT: A 175 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7392 (mt-10) REVERT: A 238 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 126 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 150 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7296 (mp0) REVERT: C 50 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8256 (mtpp) REVERT: C 83 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 211 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7741 (ttp80) REVERT: C 222 LYS cc_start: 0.8193 (mtpm) cc_final: 0.7935 (mtpm) REVERT: E 118 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7737 (t80) REVERT: E 126 SER cc_start: 0.7316 (t) cc_final: 0.6769 (m) REVERT: E 220 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: E 255 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8163 (ttt90) REVERT: E 290 SER cc_start: 0.8720 (p) cc_final: 0.8374 (t) REVERT: F 59 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8444 (ttp) REVERT: J 21 SER cc_start: 0.8692 (m) cc_final: 0.8394 (p) REVERT: O 82 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: P 22 SER cc_start: 0.7254 (OUTLIER) cc_final: 0.6952 (p) REVERT: R 95 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7027 (mpt) REVERT: X 83 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7687 (mtm180) REVERT: X 95 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.6858 (mpt) outliers start: 114 outliers final: 64 residues processed: 495 average time/residue: 0.6357 time to fit residues: 357.8155 Evaluate side-chains 506 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 431 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 104 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 33 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 128 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 142 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 260 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN D 60 ASN E 269 ASN F 125 GLN K 17 GLN M 76 ASN S 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112483 restraints weight = 27682.167| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.92 r_work: 0.3344 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21315 Z= 0.213 Angle : 0.556 9.903 28976 Z= 0.287 Chirality : 0.043 0.289 3184 Planarity : 0.005 0.051 3734 Dihedral : 4.669 56.169 2964 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.78 % Allowed : 22.79 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2693 helix: 1.96 (0.27), residues: 375 sheet: 0.56 (0.19), residues: 728 loop : -1.05 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.021 0.001 TYR Y 91 PHE 0.018 0.002 PHE D 9 TRP 0.019 0.001 TRP S 94 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (21292) covalent geometry : angle 0.55163 / 0.29 (28930) SS BOND : bond 0.00611 / 0.40 ( 23) SS BOND : angle 1.84490 / 1.27 ( 46) hydrogen bonds : bond 0.04439 / 2.96 ( 816) hydrogen bonds : angle 4.57894 / 3.24 ( 2337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 424 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 238 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 126 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 132 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7299 (mm-30) REVERT: B 150 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7281 (mp0) REVERT: C 50 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8228 (mtpp) REVERT: C 83 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: C 211 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7745 (ttp80) REVERT: C 238 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 290 SER cc_start: 0.8679 (p) cc_final: 0.8468 (m) REVERT: D 58 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8429 (mptp) REVERT: E 118 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7780 (t80) REVERT: E 220 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7598 (mtm-85) REVERT: E 255 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8145 (ttt90) REVERT: E 290 SER cc_start: 0.8683 (p) cc_final: 0.8373 (t) REVERT: F 59 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8423 (ttp) REVERT: J 21 SER cc_start: 0.8662 (m) cc_final: 0.8377 (p) REVERT: K 72 SER cc_start: 0.8275 (m) cc_final: 0.7965 (p) REVERT: M 71 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.6305 (mtp85) REVERT: P 22 SER cc_start: 0.7275 (OUTLIER) cc_final: 0.6993 (p) REVERT: R 95 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7069 (mpt) REVERT: X 83 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7651 (mtm180) REVERT: X 95 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.6856 (mpt) outliers start: 127 outliers final: 78 residues processed: 497 average time/residue: 0.5832 time to fit residues: 329.8454 Evaluate side-chains 513 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 423 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 104 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 33 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 12 optimal weight: 0.0170 chunk 184 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 191 optimal weight: 0.0970 chunk 248 optimal weight: 0.9980 chunk 68 optimal weight: 0.0020 chunk 207 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 overall best weight: 0.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 269 ASN F 125 GLN M 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.133881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114873 restraints weight = 27772.189| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.88 r_work: 0.3370 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21315 Z= 0.115 Angle : 0.504 9.296 28976 Z= 0.260 Chirality : 0.041 0.244 3184 Planarity : 0.004 0.048 3734 Dihedral : 4.394 57.314 2964 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.73 % Allowed : 24.07 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2693 helix: 2.28 (0.27), residues: 375 sheet: 0.63 (0.19), residues: 728 loop : -0.97 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 262 TYR 0.020 0.001 TYR Y 91 PHE 0.013 0.001 PHE D 9 TRP 0.020 0.001 TRP S 94 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (21292) covalent geometry : angle 0.50156 / 0.26 (28930) SS BOND : bond 0.00406 / 0.25 ( 23) SS BOND : angle 1.38638 / 0.92 ( 46) hydrogen bonds : bond 0.03814 / 2.54 ( 816) hydrogen bonds : angle 4.34506 / 3.09 ( 2337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 432 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 238 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7533 (mm-30) REVERT: B 126 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 132 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 150 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7237 (mp0) REVERT: C 50 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8219 (mtpp) REVERT: C 83 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: C 238 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 68 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8104 (mtmt) REVERT: E 220 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7682 (mtm-85) REVERT: E 255 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7949 (ttt90) REVERT: E 290 SER cc_start: 0.8666 (p) cc_final: 0.8333 (t) REVERT: F 58 LYS cc_start: 0.8504 (mttm) cc_final: 0.8285 (mptm) REVERT: J 21 SER cc_start: 0.8654 (m) cc_final: 0.8389 (p) REVERT: R 95 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.6965 (mpt) REVERT: X 83 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7551 (mtm180) REVERT: X 95 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.6738 (mpt) outliers start: 104 outliers final: 62 residues processed: 489 average time/residue: 0.5538 time to fit residues: 308.9725 Evaluate side-chains 490 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 422 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain Y residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 113 optimal weight: 0.0570 chunk 14 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 259 optimal weight: 0.0020 chunk 58 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 269 ASN F 125 GLN M 76 ASN P 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114844 restraints weight = 27904.059| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.89 r_work: 0.3366 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21315 Z= 0.139 Angle : 0.519 9.229 28976 Z= 0.268 Chirality : 0.041 0.247 3184 Planarity : 0.004 0.048 3734 Dihedral : 4.419 58.826 2964 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.37 % Allowed : 24.16 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.02 (0.16), residues: 2693 helix: 2.28 (0.27), residues: 375 sheet: 0.70 (0.19), residues: 758 loop : -0.95 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 262 TYR 0.023 0.001 TYR Y 91 PHE 0.015 0.001 PHE D 9 TRP 0.020 0.001 TRP Y 94 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (21292) covalent geometry : angle 0.51398 / 0.27 (28930) SS BOND : bond 0.00618 / 0.45 ( 23) SS BOND : angle 1.80838 / 1.18 ( 46) hydrogen bonds : bond 0.03962 / 2.64 ( 816) hydrogen bonds : angle 4.34575 / 3.08 ( 2337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 414 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 238 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7545 (mm-30) REVERT: B 126 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8360 (mp) REVERT: B 132 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 150 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7278 (mp0) REVERT: C 50 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8235 (mtpp) REVERT: C 83 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: C 238 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 58 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8320 (mptp) REVERT: E 126 SER cc_start: 0.7215 (t) cc_final: 0.6743 (m) REVERT: E 220 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7675 (mtm-85) REVERT: E 290 SER cc_start: 0.8658 (p) cc_final: 0.8293 (t) REVERT: F 58 LYS cc_start: 0.8524 (mttm) cc_final: 0.8314 (mptm) REVERT: K 72 SER cc_start: 0.8229 (m) cc_final: 0.7909 (p) REVERT: M 71 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.6399 (mtp85) REVERT: R 95 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.6918 (mpt) REVERT: X 83 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7585 (mtm180) REVERT: X 95 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.6700 (mpt) outliers start: 96 outliers final: 62 residues processed: 468 average time/residue: 0.6197 time to fit residues: 328.9483 Evaluate side-chains 486 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 417 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 253 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS A 269 ASN D 27 GLN D 60 ASN E 269 ASN F 125 GLN M 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112250 restraints weight = 27680.461| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.93 r_work: 0.3347 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21315 Z= 0.216 Angle : 0.560 9.883 28976 Z= 0.289 Chirality : 0.043 0.284 3184 Planarity : 0.005 0.050 3734 Dihedral : 4.656 59.239 2964 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.46 % Allowed : 24.25 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2693 helix: 2.08 (0.27), residues: 375 sheet: 0.64 (0.20), residues: 728 loop : -1.00 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.024 0.001 TYR Y 91 PHE 0.018 0.002 PHE D 9 TRP 0.019 0.001 TRP Y 94 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (21292) covalent geometry : angle 0.55458 / 0.29 (28930) SS BOND : bond 0.00779 / 0.55 ( 23) SS BOND : angle 1.95899 / 1.21 ( 46) hydrogen bonds : bond 0.04432 / 2.96 ( 816) hydrogen bonds : angle 4.49909 / 3.19 ( 2337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 418 time to evaluate : 0.609 Fit side-chains REVERT: A 175 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 238 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 126 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 132 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7222 (mm-30) REVERT: B 150 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7307 (mp0) REVERT: C 50 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8252 (mtpp) REVERT: C 83 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: C 238 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7685 (mm-30) REVERT: E 126 SER cc_start: 0.7269 (t) cc_final: 0.6760 (m) REVERT: E 220 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7643 (mtm-85) REVERT: E 290 SER cc_start: 0.8663 (p) cc_final: 0.8315 (t) REVERT: M 71 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.6242 (mtp85) REVERT: O 18 LEU cc_start: 0.8177 (tp) cc_final: 0.7929 (tt) REVERT: R 95 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.6958 (mpt) REVERT: X 83 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7657 (mtm180) REVERT: X 95 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.6827 (mpt) outliers start: 98 outliers final: 68 residues processed: 474 average time/residue: 0.5479 time to fit residues: 294.6021 Evaluate side-chains 490 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 416 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 72 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 127 optimal weight: 0.4980 chunk 204 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN C 170 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 60 ASN E 269 ASN E 282 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN P 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114074 restraints weight = 27528.029| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.91 r_work: 0.3356 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21315 Z= 0.162 Angle : 0.539 9.468 28976 Z= 0.277 Chirality : 0.042 0.265 3184 Planarity : 0.004 0.049 3734 Dihedral : 4.554 58.996 2964 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.14 % Allowed : 24.89 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2693 helix: 2.14 (0.27), residues: 375 sheet: 0.65 (0.19), residues: 728 loop : -0.99 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.022 0.001 TYR Y 91 PHE 0.016 0.002 PHE D 9 TRP 0.020 0.001 TRP Y 94 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (21292) covalent geometry : angle 0.53588 / 0.28 (28930) SS BOND : bond 0.00612 / 0.43 ( 23) SS BOND : angle 1.62869 / 1.00 ( 46) hydrogen bonds : bond 0.04142 / 2.77 ( 816) hydrogen bonds : angle 4.42091 / 3.13 ( 2337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 416 time to evaluate : 0.747 Fit side-chains REVERT: A 175 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 238 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7563 (mm-30) REVERT: B 126 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 132 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 150 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7242 (mp0) REVERT: C 50 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8242 (mtpp) REVERT: C 83 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: C 238 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7652 (mm-30) REVERT: C 290 SER cc_start: 0.8649 (p) cc_final: 0.8438 (m) REVERT: E 220 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7687 (mtm-85) REVERT: E 290 SER cc_start: 0.8636 (p) cc_final: 0.8271 (t) REVERT: F 58 LYS cc_start: 0.8595 (mttp) cc_final: 0.8387 (mptm) REVERT: M 71 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.6357 (mtp85) REVERT: O 18 LEU cc_start: 0.8123 (tp) cc_final: 0.7885 (tt) REVERT: R 95 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.6861 (mpt) REVERT: X 83 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7667 (mtm180) REVERT: X 95 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.6619 (mpt) outliers start: 91 outliers final: 72 residues processed: 470 average time/residue: 0.6079 time to fit residues: 323.7359 Evaluate side-chains 492 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 414 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 30 ASN Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 166 optimal weight: 0.0050 chunk 117 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 217 optimal weight: 0.9990 chunk 158 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 258 optimal weight: 0.0770 chunk 46 optimal weight: 0.9990 overall best weight: 0.3110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 269 ASN E 282 GLN F 125 GLN M 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116243 restraints weight = 27562.825| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.92 r_work: 0.3376 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21315 Z= 0.112 Angle : 0.512 9.020 28976 Z= 0.262 Chirality : 0.041 0.234 3184 Planarity : 0.004 0.048 3734 Dihedral : 4.318 57.617 2964 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.64 % Allowed : 25.16 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.11 (0.16), residues: 2693 helix: 2.30 (0.27), residues: 375 sheet: 0.86 (0.19), residues: 744 loop : -0.92 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.023 0.001 TYR Y 91 PHE 0.013 0.001 PHE D 9 TRP 0.021 0.001 TRP S 94 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (21292) covalent geometry : angle 0.50949 / 0.26 (28930) SS BOND : bond 0.00543 / 0.38 ( 23) SS BOND : angle 1.32432 / 0.81 ( 46) hydrogen bonds : bond 0.03734 / 2.51 ( 816) hydrogen bonds : angle 4.27285 / 3.03 ( 2337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 428 time to evaluate : 0.793 Fit side-chains REVERT: A 175 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 238 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 126 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8306 (mp) REVERT: B 132 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7170 (mm-30) REVERT: B 150 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7244 (mp0) REVERT: C 50 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8200 (mtpp) REVERT: C 83 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: C 238 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7621 (mm-30) REVERT: E 126 SER cc_start: 0.7173 (t) cc_final: 0.6715 (m) REVERT: E 220 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7958 (mtm-85) REVERT: E 290 SER cc_start: 0.8609 (p) cc_final: 0.8347 (m) REVERT: F 58 LYS cc_start: 0.8568 (mttp) cc_final: 0.8358 (mptm) REVERT: R 95 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.6817 (mpt) REVERT: X 83 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7665 (mtm180) REVERT: X 95 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.6535 (mpt) outliers start: 80 outliers final: 62 residues processed: 473 average time/residue: 0.6040 time to fit residues: 324.4763 Evaluate side-chains 480 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 413 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 95 MET Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 135 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 120 optimal weight: 0.0970 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 187 optimal weight: 0.1980 chunk 79 optimal weight: 0.2980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN E 269 ASN E 282 GLN F 125 GLN M 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115667 restraints weight = 27749.357| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.94 r_work: 0.3383 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21315 Z= 0.104 Angle : 0.505 8.832 28976 Z= 0.258 Chirality : 0.041 0.224 3184 Planarity : 0.004 0.047 3734 Dihedral : 4.222 57.149 2964 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.46 % Allowed : 25.02 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2693 helix: 2.42 (0.27), residues: 375 sheet: 0.80 (0.19), residues: 774 loop : -0.88 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 262 TYR 0.025 0.001 TYR Y 91 PHE 0.012 0.001 PHE D 9 TRP 0.020 0.001 TRP Y 94 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (21292) covalent geometry : angle 0.50260 / 0.26 (28930) SS BOND : bond 0.00453 / 0.30 ( 23) SS BOND : angle 1.34921 / 0.82 ( 46) hydrogen bonds : bond 0.03610 / 2.42 ( 816) hydrogen bonds : angle 4.18495 / 2.97 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9377.83 seconds wall clock time: 160 minutes 11.58 seconds (9611.58 seconds total)